Starting phenix.real_space_refine on Thu Feb 15 09:10:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tfy_8405/02_2024/5tfy_8405.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tfy_8405/02_2024/5tfy_8405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tfy_8405/02_2024/5tfy_8405.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tfy_8405/02_2024/5tfy_8405.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tfy_8405/02_2024/5tfy_8405.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tfy_8405/02_2024/5tfy_8405.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 78 5.16 5 C 20852 2.51 5 N 5096 2.21 5 O 6110 1.98 5 H 33046 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I GLU 5": "OE1" <-> "OE2" Residue "I TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 78": "OE1" <-> "OE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 5": "OE1" <-> "OE2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 5": "OE1" <-> "OE2" Residue "B TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 5": "OE1" <-> "OE2" Residue "C TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 5": "OE1" <-> "OE2" Residue "D TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 5": "OE1" <-> "OE2" Residue "E TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "F TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 78": "OE1" <-> "OE2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 5": "OE1" <-> "OE2" Residue "G TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 78": "OE1" <-> "OE2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 5": "OE1" <-> "OE2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 78": "OE1" <-> "OE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 5": "OE1" <-> "OE2" Residue "J TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 78": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 5": "OE1" <-> "OE2" Residue "K TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 78": "OE1" <-> "OE2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 5": "OE1" <-> "OE2" Residue "L TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 78": "OE1" <-> "OE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 5": "OE1" <-> "OE2" Residue "M TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M GLU 81": "OE1" <-> "OE2" Residue "M TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 5": "OE1" <-> "OE2" Residue "N TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 78": "OE1" <-> "OE2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 5": "OE1" <-> "OE2" Residue "O TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 78": "OE1" <-> "OE2" Residue "O GLU 81": "OE1" <-> "OE2" Residue "O TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 5": "OE1" <-> "OE2" Residue "P TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 78": "OE1" <-> "OE2" Residue "P GLU 81": "OE1" <-> "OE2" Residue "P TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 5": "OE1" <-> "OE2" Residue "Q TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 78": "OE1" <-> "OE2" Residue "Q GLU 81": "OE1" <-> "OE2" Residue "Q TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 5": "OE1" <-> "OE2" Residue "R TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "R GLU 81": "OE1" <-> "OE2" Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 5": "OE1" <-> "OE2" Residue "S TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 78": "OE1" <-> "OE2" Residue "S GLU 81": "OE1" <-> "OE2" Residue "S TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T GLU 5": "OE1" <-> "OE2" Residue "T TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "T GLU 81": "OE1" <-> "OE2" Residue "T TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U GLU 5": "OE1" <-> "OE2" Residue "U TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U GLU 78": "OE1" <-> "OE2" Residue "U GLU 81": "OE1" <-> "OE2" Residue "U TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V GLU 5": "OE1" <-> "OE2" Residue "V TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V GLU 81": "OE1" <-> "OE2" Residue "V TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 5": "OE1" <-> "OE2" Residue "W TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 78": "OE1" <-> "OE2" Residue "W GLU 81": "OE1" <-> "OE2" Residue "W TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X GLU 5": "OE1" <-> "OE2" Residue "X TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X GLU 78": "OE1" <-> "OE2" Residue "X GLU 81": "OE1" <-> "OE2" Residue "X TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y GLU 5": "OE1" <-> "OE2" Residue "Y TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y GLU 78": "OE1" <-> "OE2" Residue "Y GLU 81": "OE1" <-> "OE2" Residue "Y TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z GLU 5": "OE1" <-> "OE2" Residue "Z TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z GLU 78": "OE1" <-> "OE2" Residue "Z GLU 81": "OE1" <-> "OE2" Residue "Z TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 65182 Number of models: 1 Model: "" Number of chains: 26 Chain: "I" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "A" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "B" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "C" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "D" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "E" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "F" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "G" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "H" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "J" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "K" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "L" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "M" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "N" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "O" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "P" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "Q" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "R" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "S" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "T" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "U" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "V" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "W" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "X" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "Y" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "Z" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2507 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Time building chain proxies: 21.13, per 1000 atoms: 0.32 Number of scatterers: 65182 At special positions: 0 Unit cell: (102.7, 105.3, 245.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 O 6110 8.00 N 5096 7.00 C 20852 6.00 H 33046 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 43.42 Conformation dependent library (CDL) restraints added in 5.6 seconds 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7592 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 78 sheets defined 30.4% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.85 Creating SS restraints... Processing helix chain 'I' and resid 2 through 48 removed outlier: 3.937A pdb=" N ALA I 6 " --> pdb=" O SER I 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA I 12 " --> pdb=" O ILE I 8 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR I 39 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 88 No H-bonds generated for 'chain 'I' and resid 86 through 88' Processing helix chain 'A' and resid 2 through 48 removed outlier: 3.939A pdb=" N ALA A 6 " --> pdb=" O SER A 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 12 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'B' and resid 2 through 48 removed outlier: 3.941A pdb=" N ALA B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 12 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'C' and resid 2 through 48 removed outlier: 3.940A pdb=" N ALA C 6 " --> pdb=" O SER C 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 12 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'D' and resid 2 through 48 removed outlier: 3.937A pdb=" N ALA D 6 " --> pdb=" O SER D 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 12 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'E' and resid 2 through 48 removed outlier: 3.934A pdb=" N ALA E 6 " --> pdb=" O SER E 2 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA E 12 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'F' and resid 2 through 48 removed outlier: 3.941A pdb=" N ALA F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA F 12 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR F 39 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 48 removed outlier: 3.942A pdb=" N ALA G 6 " --> pdb=" O SER G 2 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA G 12 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR G 39 " --> pdb=" O SER G 35 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 88 No H-bonds generated for 'chain 'G' and resid 86 through 88' Processing helix chain 'H' and resid 2 through 48 removed outlier: 3.931A pdb=" N ALA H 6 " --> pdb=" O SER H 2 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA H 12 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA H 46 " --> pdb=" O GLY H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 88 No H-bonds generated for 'chain 'H' and resid 86 through 88' Processing helix chain 'J' and resid 2 through 48 removed outlier: 3.936A pdb=" N ALA J 6 " --> pdb=" O SER J 2 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA J 12 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR J 39 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA J 46 " --> pdb=" O GLY J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 88 No H-bonds generated for 'chain 'J' and resid 86 through 88' Processing helix chain 'K' and resid 2 through 48 removed outlier: 3.938A pdb=" N ALA K 6 " --> pdb=" O SER K 2 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA K 12 " --> pdb=" O ILE K 8 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR K 39 " --> pdb=" O SER K 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 88 No H-bonds generated for 'chain 'K' and resid 86 through 88' Processing helix chain 'L' and resid 2 through 48 removed outlier: 3.942A pdb=" N ALA L 6 " --> pdb=" O SER L 2 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR L 39 " --> pdb=" O SER L 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA L 46 " --> pdb=" O GLY L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 88 No H-bonds generated for 'chain 'L' and resid 86 through 88' Processing helix chain 'M' and resid 2 through 48 removed outlier: 3.941A pdb=" N ALA M 6 " --> pdb=" O SER M 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA M 12 " --> pdb=" O ILE M 8 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA M 46 " --> pdb=" O GLY M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 88 No H-bonds generated for 'chain 'M' and resid 86 through 88' Processing helix chain 'N' and resid 2 through 48 removed outlier: 3.942A pdb=" N ALA N 6 " --> pdb=" O SER N 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA N 12 " --> pdb=" O ILE N 8 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR N 39 " --> pdb=" O SER N 35 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA N 46 " --> pdb=" O GLY N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 88 No H-bonds generated for 'chain 'N' and resid 86 through 88' Processing helix chain 'O' and resid 2 through 48 removed outlier: 3.942A pdb=" N ALA O 6 " --> pdb=" O SER O 2 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA O 12 " --> pdb=" O ILE O 8 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR O 39 " --> pdb=" O SER O 35 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA O 46 " --> pdb=" O GLY O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 88 No H-bonds generated for 'chain 'O' and resid 86 through 88' Processing helix chain 'P' and resid 2 through 48 removed outlier: 3.935A pdb=" N ALA P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA P 12 " --> pdb=" O ILE P 8 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR P 39 " --> pdb=" O SER P 35 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA P 46 " --> pdb=" O GLY P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 88 No H-bonds generated for 'chain 'P' and resid 86 through 88' Processing helix chain 'Q' and resid 2 through 48 removed outlier: 3.943A pdb=" N ALA Q 6 " --> pdb=" O SER Q 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR Q 39 " --> pdb=" O SER Q 35 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA Q 46 " --> pdb=" O GLY Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 88 No H-bonds generated for 'chain 'Q' and resid 86 through 88' Processing helix chain 'R' and resid 2 through 48 removed outlier: 3.943A pdb=" N ALA R 6 " --> pdb=" O SER R 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA R 12 " --> pdb=" O ILE R 8 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR R 39 " --> pdb=" O SER R 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA R 46 " --> pdb=" O GLY R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'S' and resid 2 through 48 removed outlier: 3.942A pdb=" N ALA S 6 " --> pdb=" O SER S 2 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA S 12 " --> pdb=" O ILE S 8 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR S 39 " --> pdb=" O SER S 35 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA S 46 " --> pdb=" O GLY S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 86 through 88 No H-bonds generated for 'chain 'S' and resid 86 through 88' Processing helix chain 'T' and resid 2 through 48 removed outlier: 3.932A pdb=" N ALA T 6 " --> pdb=" O SER T 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA T 12 " --> pdb=" O ILE T 8 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR T 39 " --> pdb=" O SER T 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA T 46 " --> pdb=" O GLY T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 86 through 88 No H-bonds generated for 'chain 'T' and resid 86 through 88' Processing helix chain 'U' and resid 2 through 48 removed outlier: 3.932A pdb=" N ALA U 6 " --> pdb=" O SER U 2 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA U 12 " --> pdb=" O ILE U 8 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR U 39 " --> pdb=" O SER U 35 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA U 46 " --> pdb=" O GLY U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 88 No H-bonds generated for 'chain 'U' and resid 86 through 88' Processing helix chain 'V' and resid 2 through 48 removed outlier: 3.942A pdb=" N ALA V 6 " --> pdb=" O SER V 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA V 12 " --> pdb=" O ILE V 8 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR V 39 " --> pdb=" O SER V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 88 No H-bonds generated for 'chain 'V' and resid 86 through 88' Processing helix chain 'W' and resid 2 through 48 removed outlier: 3.942A pdb=" N ALA W 6 " --> pdb=" O SER W 2 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA W 12 " --> pdb=" O ILE W 8 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR W 39 " --> pdb=" O SER W 35 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA W 46 " --> pdb=" O GLY W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 86 through 88 No H-bonds generated for 'chain 'W' and resid 86 through 88' Processing helix chain 'X' and resid 2 through 48 removed outlier: 3.946A pdb=" N ALA X 6 " --> pdb=" O SER X 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA X 12 " --> pdb=" O ILE X 8 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR X 39 " --> pdb=" O SER X 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA X 46 " --> pdb=" O GLY X 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 88 No H-bonds generated for 'chain 'X' and resid 86 through 88' Processing helix chain 'Y' and resid 2 through 48 removed outlier: 3.936A pdb=" N ALA Y 6 " --> pdb=" O SER Y 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA Y 12 " --> pdb=" O ILE Y 8 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR Y 39 " --> pdb=" O SER Y 35 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA Y 46 " --> pdb=" O GLY Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 88 No H-bonds generated for 'chain 'Y' and resid 86 through 88' Processing helix chain 'Z' and resid 2 through 48 removed outlier: 3.934A pdb=" N ALA Z 6 " --> pdb=" O SER Z 2 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA Z 12 " --> pdb=" O ILE Z 8 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR Z 39 " --> pdb=" O SER Z 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA Z 46 " --> pdb=" O GLY Z 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 86 through 88 No H-bonds generated for 'chain 'Z' and resid 86 through 88' Processing sheet with id=AA1, first strand: chain 'I' and resid 104 through 105 removed outlier: 4.800A pdb=" N SER I 104 " --> pdb=" O THR I 123 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN I 69 " --> pdb=" O SER I 59 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR I 73 " --> pdb=" O MET I 55 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET I 55 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS I 75 " --> pdb=" O ASP I 53 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP I 53 " --> pdb=" O LYS I 75 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE I 56 " --> pdb=" O ILE I 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 83 through 84 Processing sheet with id=AA3, first strand: chain 'I' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 removed outlier: 4.801A pdb=" N SER A 104 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 69 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR A 73 " --> pdb=" O MET A 55 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET A 55 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS A 75 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP A 53 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE A 56 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 84 Processing sheet with id=AA6, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=AA7, first strand: chain 'B' and resid 104 through 105 removed outlier: 4.800A pdb=" N SER B 104 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN B 69 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR B 73 " --> pdb=" O MET B 55 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N MET B 55 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS B 75 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP B 53 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE B 56 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AB1, first strand: chain 'C' and resid 104 through 105 removed outlier: 4.790A pdb=" N SER C 104 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN C 69 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR C 73 " --> pdb=" O MET C 55 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N MET C 55 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS C 75 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP C 53 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE C 56 " --> pdb=" O ILE C 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 83 through 84 Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AB4, first strand: chain 'D' and resid 104 through 105 removed outlier: 4.801A pdb=" N SER D 104 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN D 69 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR D 73 " --> pdb=" O MET D 55 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET D 55 " --> pdb=" O TYR D 73 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS D 75 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP D 53 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE D 56 " --> pdb=" O ILE D 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 83 through 84 Processing sheet with id=AB6, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=AB7, first strand: chain 'E' and resid 104 through 105 removed outlier: 4.799A pdb=" N SER E 104 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN E 69 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR E 73 " --> pdb=" O MET E 55 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET E 55 " --> pdb=" O TYR E 73 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS E 75 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP E 53 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE E 56 " --> pdb=" O ILE E 163 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 83 through 84 Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 101 Processing sheet with id=AC1, first strand: chain 'F' and resid 104 through 105 removed outlier: 4.796A pdb=" N SER F 104 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN F 69 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR F 73 " --> pdb=" O MET F 55 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET F 55 " --> pdb=" O TYR F 73 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS F 75 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP F 53 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE F 56 " --> pdb=" O ILE F 163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 83 through 84 Processing sheet with id=AC3, first strand: chain 'F' and resid 100 through 101 Processing sheet with id=AC4, first strand: chain 'G' and resid 104 through 105 removed outlier: 4.799A pdb=" N SER G 104 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN G 69 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR G 73 " --> pdb=" O MET G 55 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET G 55 " --> pdb=" O TYR G 73 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS G 75 " --> pdb=" O ASP G 53 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP G 53 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE G 56 " --> pdb=" O ILE G 163 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 83 through 84 Processing sheet with id=AC6, first strand: chain 'G' and resid 100 through 101 Processing sheet with id=AC7, first strand: chain 'H' and resid 104 through 105 removed outlier: 4.798A pdb=" N SER H 104 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN H 69 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR H 73 " --> pdb=" O MET H 55 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET H 55 " --> pdb=" O TYR H 73 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS H 75 " --> pdb=" O ASP H 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP H 53 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE H 56 " --> pdb=" O ILE H 163 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 83 through 84 Processing sheet with id=AC9, first strand: chain 'H' and resid 100 through 101 Processing sheet with id=AD1, first strand: chain 'J' and resid 104 through 105 removed outlier: 4.797A pdb=" N SER J 104 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR J 73 " --> pdb=" O MET J 55 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET J 55 " --> pdb=" O TYR J 73 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS J 75 " --> pdb=" O ASP J 53 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP J 53 " --> pdb=" O LYS J 75 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE J 56 " --> pdb=" O ILE J 163 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 83 through 84 Processing sheet with id=AD3, first strand: chain 'J' and resid 100 through 101 Processing sheet with id=AD4, first strand: chain 'K' and resid 104 through 105 removed outlier: 4.799A pdb=" N SER K 104 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN K 69 " --> pdb=" O SER K 59 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR K 73 " --> pdb=" O MET K 55 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET K 55 " --> pdb=" O TYR K 73 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS K 75 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP K 53 " --> pdb=" O LYS K 75 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE K 56 " --> pdb=" O ILE K 163 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 83 through 84 Processing sheet with id=AD6, first strand: chain 'K' and resid 100 through 101 Processing sheet with id=AD7, first strand: chain 'L' and resid 104 through 105 removed outlier: 4.793A pdb=" N SER L 104 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN L 69 " --> pdb=" O SER L 59 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR L 73 " --> pdb=" O MET L 55 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET L 55 " --> pdb=" O TYR L 73 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS L 75 " --> pdb=" O ASP L 53 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP L 53 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE L 56 " --> pdb=" O ILE L 163 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 83 through 84 Processing sheet with id=AD9, first strand: chain 'L' and resid 100 through 101 Processing sheet with id=AE1, first strand: chain 'M' and resid 104 through 105 removed outlier: 4.797A pdb=" N SER M 104 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN M 69 " --> pdb=" O SER M 59 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR M 73 " --> pdb=" O MET M 55 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N MET M 55 " --> pdb=" O TYR M 73 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS M 75 " --> pdb=" O ASP M 53 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP M 53 " --> pdb=" O LYS M 75 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE M 56 " --> pdb=" O ILE M 163 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 83 through 84 Processing sheet with id=AE3, first strand: chain 'M' and resid 100 through 101 Processing sheet with id=AE4, first strand: chain 'N' and resid 104 through 105 removed outlier: 4.798A pdb=" N SER N 104 " --> pdb=" O THR N 123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN N 69 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR N 73 " --> pdb=" O MET N 55 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N MET N 55 " --> pdb=" O TYR N 73 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS N 75 " --> pdb=" O ASP N 53 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP N 53 " --> pdb=" O LYS N 75 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE N 56 " --> pdb=" O ILE N 163 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 83 through 84 Processing sheet with id=AE6, first strand: chain 'N' and resid 100 through 101 Processing sheet with id=AE7, first strand: chain 'O' and resid 104 through 105 removed outlier: 4.793A pdb=" N SER O 104 " --> pdb=" O THR O 123 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN O 69 " --> pdb=" O SER O 59 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR O 73 " --> pdb=" O MET O 55 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET O 55 " --> pdb=" O TYR O 73 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS O 75 " --> pdb=" O ASP O 53 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP O 53 " --> pdb=" O LYS O 75 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE O 56 " --> pdb=" O ILE O 163 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 83 through 84 Processing sheet with id=AE9, first strand: chain 'O' and resid 100 through 101 Processing sheet with id=AF1, first strand: chain 'P' and resid 104 through 105 removed outlier: 4.800A pdb=" N SER P 104 " --> pdb=" O THR P 123 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN P 69 " --> pdb=" O SER P 59 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR P 73 " --> pdb=" O MET P 55 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N MET P 55 " --> pdb=" O TYR P 73 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS P 75 " --> pdb=" O ASP P 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP P 53 " --> pdb=" O LYS P 75 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE P 56 " --> pdb=" O ILE P 163 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 83 through 84 Processing sheet with id=AF3, first strand: chain 'P' and resid 100 through 101 Processing sheet with id=AF4, first strand: chain 'Q' and resid 104 through 105 removed outlier: 4.798A pdb=" N SER Q 104 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN Q 69 " --> pdb=" O SER Q 59 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR Q 73 " --> pdb=" O MET Q 55 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET Q 55 " --> pdb=" O TYR Q 73 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS Q 75 " --> pdb=" O ASP Q 53 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP Q 53 " --> pdb=" O LYS Q 75 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE Q 56 " --> pdb=" O ILE Q 163 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 83 through 84 Processing sheet with id=AF6, first strand: chain 'Q' and resid 100 through 101 Processing sheet with id=AF7, first strand: chain 'R' and resid 104 through 105 removed outlier: 4.798A pdb=" N SER R 104 " --> pdb=" O THR R 123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN R 69 " --> pdb=" O SER R 59 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR R 73 " --> pdb=" O MET R 55 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET R 55 " --> pdb=" O TYR R 73 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS R 75 " --> pdb=" O ASP R 53 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP R 53 " --> pdb=" O LYS R 75 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE R 56 " --> pdb=" O ILE R 163 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 83 through 84 Processing sheet with id=AF9, first strand: chain 'R' and resid 100 through 101 Processing sheet with id=AG1, first strand: chain 'S' and resid 104 through 105 removed outlier: 4.790A pdb=" N SER S 104 " --> pdb=" O THR S 123 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN S 69 " --> pdb=" O SER S 59 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR S 73 " --> pdb=" O MET S 55 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET S 55 " --> pdb=" O TYR S 73 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS S 75 " --> pdb=" O ASP S 53 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP S 53 " --> pdb=" O LYS S 75 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE S 56 " --> pdb=" O ILE S 163 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 83 through 84 Processing sheet with id=AG3, first strand: chain 'S' and resid 100 through 101 Processing sheet with id=AG4, first strand: chain 'T' and resid 104 through 105 removed outlier: 4.797A pdb=" N SER T 104 " --> pdb=" O THR T 123 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN T 69 " --> pdb=" O SER T 59 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR T 73 " --> pdb=" O MET T 55 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N MET T 55 " --> pdb=" O TYR T 73 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS T 75 " --> pdb=" O ASP T 53 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP T 53 " --> pdb=" O LYS T 75 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE T 56 " --> pdb=" O ILE T 163 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 83 through 84 Processing sheet with id=AG6, first strand: chain 'T' and resid 100 through 101 Processing sheet with id=AG7, first strand: chain 'U' and resid 104 through 105 removed outlier: 4.796A pdb=" N SER U 104 " --> pdb=" O THR U 123 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN U 69 " --> pdb=" O SER U 59 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR U 73 " --> pdb=" O MET U 55 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET U 55 " --> pdb=" O TYR U 73 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS U 75 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP U 53 " --> pdb=" O LYS U 75 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE U 56 " --> pdb=" O ILE U 163 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 83 through 84 Processing sheet with id=AG9, first strand: chain 'U' and resid 100 through 101 Processing sheet with id=AH1, first strand: chain 'V' and resid 104 through 105 removed outlier: 4.799A pdb=" N SER V 104 " --> pdb=" O THR V 123 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN V 69 " --> pdb=" O SER V 59 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR V 73 " --> pdb=" O MET V 55 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET V 55 " --> pdb=" O TYR V 73 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS V 75 " --> pdb=" O ASP V 53 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP V 53 " --> pdb=" O LYS V 75 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE V 56 " --> pdb=" O ILE V 163 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'V' and resid 83 through 84 Processing sheet with id=AH3, first strand: chain 'V' and resid 100 through 101 Processing sheet with id=AH4, first strand: chain 'W' and resid 104 through 105 removed outlier: 4.799A pdb=" N SER W 104 " --> pdb=" O THR W 123 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN W 69 " --> pdb=" O SER W 59 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR W 73 " --> pdb=" O MET W 55 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET W 55 " --> pdb=" O TYR W 73 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS W 75 " --> pdb=" O ASP W 53 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP W 53 " --> pdb=" O LYS W 75 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE W 56 " --> pdb=" O ILE W 163 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'W' and resid 83 through 84 Processing sheet with id=AH6, first strand: chain 'W' and resid 100 through 101 Processing sheet with id=AH7, first strand: chain 'X' and resid 104 through 105 removed outlier: 4.788A pdb=" N SER X 104 " --> pdb=" O THR X 123 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN X 69 " --> pdb=" O SER X 59 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR X 73 " --> pdb=" O MET X 55 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET X 55 " --> pdb=" O TYR X 73 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS X 75 " --> pdb=" O ASP X 53 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP X 53 " --> pdb=" O LYS X 75 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE X 56 " --> pdb=" O ILE X 163 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'X' and resid 83 through 84 Processing sheet with id=AH9, first strand: chain 'X' and resid 100 through 101 Processing sheet with id=AI1, first strand: chain 'Y' and resid 104 through 105 removed outlier: 4.794A pdb=" N SER Y 104 " --> pdb=" O THR Y 123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN Y 69 " --> pdb=" O SER Y 59 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR Y 73 " --> pdb=" O MET Y 55 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET Y 55 " --> pdb=" O TYR Y 73 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS Y 75 " --> pdb=" O ASP Y 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP Y 53 " --> pdb=" O LYS Y 75 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE Y 56 " --> pdb=" O ILE Y 163 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 83 through 84 Processing sheet with id=AI3, first strand: chain 'Y' and resid 100 through 101 Processing sheet with id=AI4, first strand: chain 'Z' and resid 104 through 105 removed outlier: 4.793A pdb=" N SER Z 104 " --> pdb=" O THR Z 123 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN Z 69 " --> pdb=" O SER Z 59 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR Z 73 " --> pdb=" O MET Z 55 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET Z 55 " --> pdb=" O TYR Z 73 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS Z 75 " --> pdb=" O ASP Z 53 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP Z 53 " --> pdb=" O LYS Z 75 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE Z 56 " --> pdb=" O ILE Z 163 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Z' and resid 83 through 84 Processing sheet with id=AI6, first strand: chain 'Z' and resid 100 through 101 1725 hydrogen bonds defined for protein. 4785 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: 24.45 Time building geometry restraints manager: 45.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 32968 1.02 - 1.22: 106 1.22 - 1.42: 13039 1.42 - 1.61: 19537 1.61 - 1.81: 156 Bond restraints: 65806 Sorted by residual: bond pdb=" N VAL I 99 " pdb=" H VAL I 99 " ideal model delta sigma weight residual 0.860 1.115 -0.255 2.00e-02 2.50e+03 1.62e+02 bond pdb=" N VAL Q 99 " pdb=" H VAL Q 99 " ideal model delta sigma weight residual 0.860 1.112 -0.252 2.00e-02 2.50e+03 1.59e+02 bond pdb=" N VAL U 99 " pdb=" H VAL U 99 " ideal model delta sigma weight residual 0.860 1.110 -0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" N VAL W 99 " pdb=" H VAL W 99 " ideal model delta sigma weight residual 0.860 1.110 -0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" N VAL O 99 " pdb=" H VAL O 99 " ideal model delta sigma weight residual 0.860 1.107 -0.247 2.00e-02 2.50e+03 1.53e+02 ... (remaining 65801 not shown) Histogram of bond angle deviations from ideal: 91.09 - 99.76: 257 99.76 - 108.43: 18261 108.43 - 117.10: 71501 117.10 - 125.77: 28864 125.77 - 134.45: 379 Bond angle restraints: 119262 Sorted by residual: angle pdb=" N THR Y 103 " pdb=" CA THR Y 103 " pdb=" C THR Y 103 " ideal model delta sigma weight residual 111.07 130.07 -19.00 1.07e+00 8.73e-01 3.15e+02 angle pdb=" N THR K 103 " pdb=" CA THR K 103 " pdb=" C THR K 103 " ideal model delta sigma weight residual 111.07 130.04 -18.97 1.07e+00 8.73e-01 3.14e+02 angle pdb=" N THR I 103 " pdb=" CA THR I 103 " pdb=" C THR I 103 " ideal model delta sigma weight residual 111.07 130.02 -18.95 1.07e+00 8.73e-01 3.13e+02 angle pdb=" N THR S 103 " pdb=" CA THR S 103 " pdb=" C THR S 103 " ideal model delta sigma weight residual 111.07 130.00 -18.93 1.07e+00 8.73e-01 3.13e+02 angle pdb=" N THR C 103 " pdb=" CA THR C 103 " pdb=" C THR C 103 " ideal model delta sigma weight residual 111.07 129.98 -18.91 1.07e+00 8.73e-01 3.12e+02 ... (remaining 119257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.31: 28283 15.31 - 30.61: 1420 30.61 - 45.92: 755 45.92 - 61.22: 508 61.22 - 76.53: 52 Dihedral angle restraints: 31018 sinusoidal: 16822 harmonic: 14196 Sorted by residual: dihedral pdb=" CA ASP G 156 " pdb=" C ASP G 156 " pdb=" N GLY G 157 " pdb=" CA GLY G 157 " ideal model delta harmonic sigma weight residual -180.00 -145.06 -34.94 0 5.00e+00 4.00e-02 4.88e+01 dihedral pdb=" CA ASP T 156 " pdb=" C ASP T 156 " pdb=" N GLY T 157 " pdb=" CA GLY T 157 " ideal model delta harmonic sigma weight residual 180.00 -145.08 -34.92 0 5.00e+00 4.00e-02 4.88e+01 dihedral pdb=" CA ASP J 156 " pdb=" C ASP J 156 " pdb=" N GLY J 157 " pdb=" CA GLY J 157 " ideal model delta harmonic sigma weight residual -180.00 -145.17 -34.83 0 5.00e+00 4.00e-02 4.85e+01 ... (remaining 31015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4387 0.083 - 0.167: 629 0.167 - 0.250: 118 0.250 - 0.333: 81 0.333 - 0.416: 89 Chirality restraints: 5304 Sorted by residual: chirality pdb=" CA THR U 103 " pdb=" N THR U 103 " pdb=" C THR U 103 " pdb=" CB THR U 103 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA THR E 103 " pdb=" N THR E 103 " pdb=" C THR E 103 " pdb=" CB THR E 103 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA GLN D 110 " pdb=" N GLN D 110 " pdb=" C GLN D 110 " pdb=" CB GLN D 110 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 5301 not shown) Planarity restraints: 9594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA H 98 " -0.132 2.00e-02 2.50e+03 2.17e-01 4.72e+02 pdb=" N VAL H 99 " 0.376 2.00e-02 2.50e+03 pdb=" CA VAL H 99 " -0.121 2.00e-02 2.50e+03 pdb=" H VAL H 99 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 98 " -0.132 2.00e-02 2.50e+03 2.17e-01 4.72e+02 pdb=" N VAL D 99 " 0.376 2.00e-02 2.50e+03 pdb=" CA VAL D 99 " -0.122 2.00e-02 2.50e+03 pdb=" H VAL D 99 " -0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA Y 98 " 0.132 2.00e-02 2.50e+03 2.17e-01 4.71e+02 pdb=" N VAL Y 99 " -0.376 2.00e-02 2.50e+03 pdb=" CA VAL Y 99 " 0.121 2.00e-02 2.50e+03 pdb=" H VAL Y 99 " 0.123 2.00e-02 2.50e+03 ... (remaining 9591 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.84: 306 1.84 - 2.53: 61893 2.53 - 3.22: 212773 3.22 - 3.91: 279988 3.91 - 4.60: 454291 Nonbonded interactions: 1009251 Sorted by model distance: nonbonded pdb=" OD1 ASP I 53 " pdb=" HH TYR B 22 " model vdw 1.154 1.850 nonbonded pdb=" OD1 ASP C 53 " pdb=" HH TYR O 22 " model vdw 1.154 1.850 nonbonded pdb=" HH TYR F 22 " pdb=" OD1 ASP V 53 " model vdw 1.155 1.850 nonbonded pdb=" OD1 ASP F 53 " pdb=" HH TYR R 22 " model vdw 1.155 1.850 nonbonded pdb=" HH TYR G 22 " pdb=" OD1 ASP W 53 " model vdw 1.155 1.850 ... (remaining 1009246 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.730 Extract box with map and model: 5.980 Check model and map are aligned: 0.710 Set scattering table: 0.470 Process input model: 168.700 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 182.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 : 0.007 0.045 32760 Z= 0.479 Angle : 1.915 19.693 44512 Z= 1.271 Chirality : 0.085 0.416 5304 Planarity : 0.005 0.049 5512 Dihedral : 13.178 76.527 11596 Min Nonbonded Distance : 1.377 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.79 % Allowed : 5.30 % Favored : 90.91 % Cbeta Deviations : 3.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % 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: -2.21 (0.11), residues: 4212 helix: -0.54 (0.14), residues: 1170 sheet: -2.03 (0.12), residues: 1170 loop : -1.54 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP A 92 PHE 0.024 0.004 PHE H 1 TYR 0.020 0.003 TYR Q 73 ARG 0.007 0.001 ARG O 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2436 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 2306 time to evaluate : 3.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 13 PHE cc_start: 0.8894 (m-10) cc_final: 0.8638 (m-10) REVERT: I 45 GLN cc_start: 0.8909 (tp-100) cc_final: 0.8531 (tp-100) REVERT: I 81 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9265 (mm-30) REVERT: I 112 LEU cc_start: 0.8985 (mp) cc_final: 0.8740 (mm) REVERT: I 143 LYS cc_start: 0.9143 (ttpp) cc_final: 0.8907 (tptt) REVERT: A 112 LEU cc_start: 0.9162 (mp) cc_final: 0.8844 (mm) REVERT: B 86 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.9178 (tppt) REVERT: B 112 LEU cc_start: 0.8991 (mp) cc_final: 0.8724 (mm) REVERT: B 139 GLU cc_start: 0.9527 (tt0) cc_final: 0.9287 (tt0) REVERT: C 34 LYS cc_start: 0.9507 (tptt) cc_final: 0.9223 (tppt) REVERT: D 25 LEU cc_start: 0.9616 (mt) cc_final: 0.9212 (mt) REVERT: D 30 PHE cc_start: 0.9382 (t80) cc_final: 0.8988 (t80) REVERT: D 36 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8766 (mm-40) REVERT: D 53 ASP cc_start: 0.9388 (t70) cc_final: 0.9105 (t0) REVERT: E 112 LEU cc_start: 0.8929 (mp) cc_final: 0.8706 (mm) REVERT: F 30 PHE cc_start: 0.9453 (t80) cc_final: 0.9250 (t80) REVERT: F 112 LEU cc_start: 0.9176 (mp) cc_final: 0.8882 (mm) REVERT: G 86 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.9131 (tppt) REVERT: G 112 LEU cc_start: 0.9118 (mp) cc_final: 0.8856 (mm) REVERT: H 86 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.9055 (tppt) REVERT: H 112 LEU cc_start: 0.9001 (mp) cc_final: 0.8788 (mm) REVERT: J 25 LEU cc_start: 0.9611 (mt) cc_final: 0.9116 (mt) REVERT: J 30 PHE cc_start: 0.9411 (t80) cc_final: 0.9015 (t80) REVERT: K 34 LYS cc_start: 0.9481 (tptt) cc_final: 0.9197 (tppt) REVERT: K 112 LEU cc_start: 0.8949 (mp) cc_final: 0.8685 (mm) REVERT: L 13 PHE cc_start: 0.8939 (m-10) cc_final: 0.8677 (m-10) REVERT: L 45 GLN cc_start: 0.9067 (tp-100) cc_final: 0.8715 (tp-100) REVERT: L 143 LYS cc_start: 0.9192 (ttpp) cc_final: 0.8876 (tptt) REVERT: N 25 LEU cc_start: 0.9561 (mt) cc_final: 0.9274 (mt) REVERT: N 86 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9165 (tppt) REVERT: N 112 LEU cc_start: 0.9077 (mp) cc_final: 0.8834 (mm) REVERT: O 34 LYS cc_start: 0.9535 (tptt) cc_final: 0.9279 (tppt) REVERT: O 45 GLN cc_start: 0.9077 (tp-100) cc_final: 0.8853 (tp40) REVERT: O 112 LEU cc_start: 0.8952 (mp) cc_final: 0.8727 (mm) REVERT: P 22 TYR cc_start: 0.9284 (t80) cc_final: 0.8833 (t80) REVERT: P 30 PHE cc_start: 0.9345 (t80) cc_final: 0.8949 (t80) REVERT: P 44 LYS cc_start: 0.9394 (ttmt) cc_final: 0.9146 (ttmt) REVERT: Q 30 PHE cc_start: 0.9383 (t80) cc_final: 0.9170 (t80) REVERT: Q 34 LYS cc_start: 0.9480 (tptt) cc_final: 0.9176 (tppt) REVERT: Q 86 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.9084 (tppt) REVERT: Q 112 LEU cc_start: 0.8940 (mp) cc_final: 0.8672 (mm) REVERT: R 25 LEU cc_start: 0.9330 (mt) cc_final: 0.9064 (mt) REVERT: R 86 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9096 (tppt) REVERT: S 86 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9097 (tppt) REVERT: T 13 PHE cc_start: 0.8881 (m-10) cc_final: 0.8619 (m-10) REVERT: T 36 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8747 (mm-40) REVERT: T 40 TYR cc_start: 0.8944 (m-10) cc_final: 0.8448 (m-80) REVERT: T 112 LEU cc_start: 0.9026 (mp) cc_final: 0.8793 (mm) REVERT: T 143 LYS cc_start: 0.9325 (ttpp) cc_final: 0.8840 (tptt) REVERT: U 30 PHE cc_start: 0.9461 (t80) cc_final: 0.9152 (t80) REVERT: U 36 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8682 (mm-40) REVERT: U 45 GLN cc_start: 0.9108 (tp-100) cc_final: 0.8885 (tp-100) REVERT: U 86 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.9082 (tppt) REVERT: U 112 LEU cc_start: 0.8902 (mp) cc_final: 0.8659 (mm) REVERT: V 30 PHE cc_start: 0.9544 (t80) cc_final: 0.9337 (t80) REVERT: V 112 LEU cc_start: 0.9076 (mp) cc_final: 0.8754 (mm) REVERT: V 147 SER cc_start: 0.9230 (m) cc_final: 0.8834 (p) REVERT: W 45 GLN cc_start: 0.9067 (tp-100) cc_final: 0.8797 (tp-100) REVERT: W 86 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.9183 (tppt) REVERT: W 112 LEU cc_start: 0.9022 (mp) cc_final: 0.8702 (mm) REVERT: W 136 PHE cc_start: 0.8661 (p90) cc_final: 0.8447 (p90) REVERT: X 44 LYS cc_start: 0.9262 (ttmt) cc_final: 0.9061 (ttmt) REVERT: X 45 GLN cc_start: 0.9086 (tp-100) cc_final: 0.8833 (tp-100) REVERT: X 112 LEU cc_start: 0.9143 (mp) cc_final: 0.8890 (mm) REVERT: Y 25 LEU cc_start: 0.9617 (mt) cc_final: 0.9223 (mt) REVERT: Y 30 PHE cc_start: 0.9476 (t80) cc_final: 0.9152 (t80) REVERT: Y 112 LEU cc_start: 0.8994 (mp) cc_final: 0.8748 (mm) REVERT: Y 147 SER cc_start: 0.9357 (m) cc_final: 0.8972 (p) REVERT: Z 36 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8818 (mm-40) REVERT: Z 86 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9098 (tppt) REVERT: Z 112 LEU cc_start: 0.8955 (mp) cc_final: 0.8682 (mm) outliers start: 130 outliers final: 57 residues processed: 2332 average time/residue: 0.8609 time to fit residues: 3187.1263 Evaluate side-chains 2162 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 2091 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 1 PHE Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain A residue 1 PHE Chi-restraints excluded: chain B residue 1 PHE Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain C residue 1 PHE Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 1 PHE Chi-restraints excluded: chain D residue 36 GLN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain F residue 1 PHE Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain G residue 1 PHE Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain H residue 1 PHE Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain J residue 1 PHE Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 1 PHE Chi-restraints excluded: chain L residue 1 PHE Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain O residue 1 PHE Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain P residue 1 PHE Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 86 LYS Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain R residue 1 PHE Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 86 LYS Chi-restraints excluded: chain S residue 1 PHE Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 86 LYS Chi-restraints excluded: chain T residue 1 PHE Chi-restraints excluded: chain T residue 36 GLN Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain U residue 1 PHE Chi-restraints excluded: chain U residue 36 GLN Chi-restraints excluded: chain U residue 86 LYS Chi-restraints excluded: chain V residue 1 PHE Chi-restraints excluded: chain V residue 36 GLN Chi-restraints excluded: chain W residue 1 PHE Chi-restraints excluded: chain W residue 36 GLN Chi-restraints excluded: chain W residue 86 LYS Chi-restraints excluded: chain X residue 1 PHE Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain Y residue 1 PHE Chi-restraints excluded: chain Y residue 36 GLN Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Z residue 1 PHE Chi-restraints excluded: chain Z residue 36 GLN Chi-restraints excluded: chain Z residue 86 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 351 optimal weight: 10.0000 chunk 315 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 326 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 242 optimal weight: 0.6980 chunk 377 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 109 ASN A 36 GLN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN H 109 ASN J 109 ASN J 113 ASN K 83 GLN ** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 83 GLN ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 ASN N 36 GLN ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 113 ASN ** Q 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 109 ASN S 109 ASN ** T 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 113 ASN U 33 GLN U 109 ASN W 33 GLN W 83 GLN ** W 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 GLN ** X 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 113 ASN ** Y 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32760 Z= 0.255 Angle : 0.685 6.811 44512 Z= 0.386 Chirality : 0.047 0.163 5304 Planarity : 0.004 0.040 5512 Dihedral : 8.907 59.813 4752 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.26 % Allowed : 22.61 % Favored : 74.13 % 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: -1.66 (0.11), residues: 4212 helix: 0.58 (0.13), residues: 1144 sheet: -1.61 (0.12), residues: 1248 loop : -1.75 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 92 PHE 0.020 0.002 PHE C 136 TYR 0.016 0.001 TYR N 73 ARG 0.003 0.001 ARG Z 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2280 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 2168 time to evaluate : 3.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 22 TYR cc_start: 0.9119 (t80) cc_final: 0.8522 (t80) REVERT: I 72 PHE cc_start: 0.8475 (p90) cc_final: 0.8218 (p90) REVERT: I 90 TYR cc_start: 0.8339 (m-80) cc_final: 0.8133 (m-80) REVERT: A 25 LEU cc_start: 0.9489 (mt) cc_final: 0.8867 (mt) REVERT: B 36 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8753 (tt0) REVERT: B 45 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8674 (tp-100) REVERT: C 45 GLN cc_start: 0.8999 (tp-100) cc_final: 0.8715 (tp-100) REVERT: D 22 TYR cc_start: 0.9102 (t80) cc_final: 0.8526 (t80) REVERT: F 25 LEU cc_start: 0.9456 (mt) cc_final: 0.9176 (mt) REVERT: G 45 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8717 (tp-100) REVERT: G 152 ARG cc_start: 0.8913 (mmt-90) cc_final: 0.8491 (mmt90) REVERT: H 45 GLN cc_start: 0.9024 (tp-100) cc_final: 0.8710 (tp-100) REVERT: J 83 GLN cc_start: 0.8920 (mm110) cc_final: 0.8522 (mm110) REVERT: J 147 SER cc_start: 0.9313 (m) cc_final: 0.8977 (p) REVERT: L 25 LEU cc_start: 0.9409 (mt) cc_final: 0.9105 (mt) REVERT: L 119 LYS cc_start: 0.9231 (ttpp) cc_final: 0.8981 (mtpp) REVERT: L 143 LYS cc_start: 0.9031 (ttpp) cc_final: 0.8702 (tptt) REVERT: M 119 LYS cc_start: 0.9110 (ttpp) cc_final: 0.8852 (tttp) REVERT: N 24 MET cc_start: 0.8268 (ttt) cc_final: 0.8013 (ttt) REVERT: N 83 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8729 (mm110) REVERT: O 83 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8664 (mm110) REVERT: O 91 LEU cc_start: 0.8922 (mt) cc_final: 0.8713 (mt) REVERT: P 73 TYR cc_start: 0.8487 (m-80) cc_final: 0.8184 (m-80) REVERT: P 83 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8539 (mm110) REVERT: P 147 SER cc_start: 0.9328 (m) cc_final: 0.9007 (p) REVERT: Q 83 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8667 (mm110) REVERT: Q 86 LYS cc_start: 0.9202 (ttmm) cc_final: 0.8991 (tppt) REVERT: R 25 LEU cc_start: 0.9190 (mt) cc_final: 0.8786 (mt) REVERT: R 29 PHE cc_start: 0.9021 (m-10) cc_final: 0.8797 (m-10) REVERT: R 81 GLU cc_start: 0.9242 (mm-30) cc_final: 0.9038 (mm-30) REVERT: R 83 GLN cc_start: 0.9039 (mm110) cc_final: 0.8648 (mm110) REVERT: R 86 LYS cc_start: 0.9378 (ttmm) cc_final: 0.9119 (tppt) REVERT: T 22 TYR cc_start: 0.9251 (t80) cc_final: 0.8833 (t80) REVERT: T 73 TYR cc_start: 0.8507 (m-80) cc_final: 0.8187 (m-80) REVERT: T 119 LYS cc_start: 0.9263 (ttpp) cc_final: 0.9028 (mtpp) REVERT: T 143 LYS cc_start: 0.9148 (ttpp) cc_final: 0.8776 (tptt) REVERT: U 45 GLN cc_start: 0.8897 (tp-100) cc_final: 0.8633 (tp-100) REVERT: U 91 LEU cc_start: 0.9086 (mt) cc_final: 0.8786 (mt) REVERT: V 22 TYR cc_start: 0.9137 (t80) cc_final: 0.8884 (t80) REVERT: V 48 SER cc_start: 0.9264 (m) cc_final: 0.9059 (t) REVERT: V 83 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8552 (tp40) REVERT: W 22 TYR cc_start: 0.9106 (t80) cc_final: 0.8557 (t80) REVERT: W 30 PHE cc_start: 0.9493 (t80) cc_final: 0.9188 (t80) REVERT: W 119 LYS cc_start: 0.9285 (ttpp) cc_final: 0.9043 (tttp) REVERT: W 136 PHE cc_start: 0.8686 (p90) cc_final: 0.8428 (p90) REVERT: W 152 ARG cc_start: 0.8795 (mmt-90) cc_final: 0.8410 (mmt-90) REVERT: X 22 TYR cc_start: 0.9098 (t80) cc_final: 0.8795 (t80) REVERT: X 44 LYS cc_start: 0.9127 (ttmt) cc_final: 0.8904 (ttmt) REVERT: X 45 GLN cc_start: 0.8992 (tp-100) cc_final: 0.8684 (tp-100) REVERT: Y 22 TYR cc_start: 0.9047 (t80) cc_final: 0.8791 (t80) REVERT: Z 36 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8808 (tt0) REVERT: Z 91 LEU cc_start: 0.9093 (mt) cc_final: 0.8812 (mt) REVERT: Z 119 LYS cc_start: 0.9144 (ttpp) cc_final: 0.8852 (mtpp) outliers start: 112 outliers final: 61 residues processed: 2187 average time/residue: 0.8708 time to fit residues: 3004.0254 Evaluate side-chains 2127 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 2064 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain M residue 83 GLN Chi-restraints excluded: chain M residue 105 ILE Chi-restraints excluded: chain N residue 36 GLN Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain Q residue 131 ILE Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 131 ILE Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain V residue 36 GLN Chi-restraints excluded: chain V residue 135 LYS Chi-restraints excluded: chain W residue 86 LYS Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 149 ILE Chi-restraints excluded: chain Y residue 36 GLN Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Z residue 36 GLN Chi-restraints excluded: chain Z residue 51 ILE Chi-restraints excluded: chain Z residue 113 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 209 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 314 optimal weight: 0.8980 chunk 257 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 378 optimal weight: 0.6980 chunk 408 optimal weight: 9.9990 chunk 337 optimal weight: 6.9990 chunk 375 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 303 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 109 ASN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 ASN J 109 ASN L 109 ASN O 109 ASN ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 ASN R 83 GLN R 109 ASN S 109 ASN T 96 ASN ** T 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 109 ASN ** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN ** Y 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32760 Z= 0.212 Angle : 0.611 5.115 44512 Z= 0.333 Chirality : 0.044 0.163 5304 Planarity : 0.004 0.037 5512 Dihedral : 6.355 57.985 4618 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.73 % Allowed : 28.99 % Favored : 67.28 % 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: -1.22 (0.12), residues: 4212 helix: 0.94 (0.13), residues: 1144 sheet: -1.22 (0.13), residues: 1118 loop : -1.60 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 92 PHE 0.016 0.002 PHE N 20 TYR 0.017 0.001 TYR L 73 ARG 0.005 0.000 ARG H 152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2222 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 2094 time to evaluate : 3.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 29 PHE cc_start: 0.8994 (m-10) cc_final: 0.8771 (m-80) REVERT: I 72 PHE cc_start: 0.8549 (p90) cc_final: 0.8198 (p90) REVERT: I 90 TYR cc_start: 0.8391 (m-80) cc_final: 0.8149 (m-80) REVERT: A 25 LEU cc_start: 0.9498 (mt) cc_final: 0.9155 (mt) REVERT: B 34 LYS cc_start: 0.9436 (tptt) cc_final: 0.9231 (mmmm) REVERT: B 36 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8779 (tt0) REVERT: B 86 LYS cc_start: 0.9249 (ttmm) cc_final: 0.8990 (tppt) REVERT: B 112 LEU cc_start: 0.8971 (mm) cc_final: 0.8765 (mm) REVERT: B 136 PHE cc_start: 0.8687 (p90) cc_final: 0.8313 (p90) REVERT: C 45 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8573 (tp-100) REVERT: C 83 GLN cc_start: 0.8827 (mm110) cc_final: 0.8593 (mm110) REVERT: D 83 GLN cc_start: 0.8765 (mm110) cc_final: 0.8436 (mm110) REVERT: D 147 SER cc_start: 0.9286 (m) cc_final: 0.9060 (p) REVERT: E 25 LEU cc_start: 0.9413 (mt) cc_final: 0.9157 (mt) REVERT: E 45 GLN cc_start: 0.8807 (tp-100) cc_final: 0.8532 (tp-100) REVERT: E 83 GLN cc_start: 0.7857 (mm110) cc_final: 0.7642 (mm110) REVERT: E 147 SER cc_start: 0.9257 (m) cc_final: 0.9006 (p) REVERT: F 25 LEU cc_start: 0.9476 (mt) cc_final: 0.8820 (mt) REVERT: G 45 GLN cc_start: 0.8878 (tp-100) cc_final: 0.8502 (tp-100) REVERT: G 111 GLN cc_start: 0.9109 (mp10) cc_final: 0.8639 (mp10) REVERT: H 45 GLN cc_start: 0.8898 (tp-100) cc_final: 0.8651 (tp-100) REVERT: H 119 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8838 (mtpp) REVERT: K 45 GLN cc_start: 0.8833 (tp-100) cc_final: 0.8574 (tp-100) REVERT: K 147 SER cc_start: 0.9273 (m) cc_final: 0.8992 (p) REVERT: L 119 LYS cc_start: 0.9303 (ttpp) cc_final: 0.8993 (mtpp) REVERT: L 143 LYS cc_start: 0.9064 (ttpp) cc_final: 0.8764 (tptt) REVERT: M 119 LYS cc_start: 0.9076 (ttpp) cc_final: 0.8763 (tttp) REVERT: N 25 LEU cc_start: 0.9359 (mt) cc_final: 0.9132 (mt) REVERT: O 83 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8291 (mm110) REVERT: O 119 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8780 (mtpp) REVERT: P 73 TYR cc_start: 0.8486 (m-80) cc_final: 0.8250 (m-80) REVERT: P 83 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8321 (mm110) REVERT: P 119 LYS cc_start: 0.9014 (ttpp) cc_final: 0.8750 (tttp) REVERT: Q 83 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8709 (mm110) REVERT: Q 86 LYS cc_start: 0.9172 (ttmm) cc_final: 0.8921 (tppt) REVERT: Q 147 SER cc_start: 0.9342 (m) cc_final: 0.9126 (p) REVERT: R 25 LEU cc_start: 0.9190 (mt) cc_final: 0.8752 (mt) REVERT: R 86 LYS cc_start: 0.9329 (ttmm) cc_final: 0.9103 (tppt) REVERT: T 22 TYR cc_start: 0.9220 (t80) cc_final: 0.8996 (t80) REVERT: T 36 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8790 (mm-40) REVERT: T 119 LYS cc_start: 0.9238 (ttpp) cc_final: 0.8939 (mtpp) REVERT: T 136 PHE cc_start: 0.8923 (p90) cc_final: 0.8673 (p90) REVERT: T 143 LYS cc_start: 0.9110 (ttpp) cc_final: 0.8778 (tptt) REVERT: U 20 PHE cc_start: 0.8774 (t80) cc_final: 0.8532 (t80) REVERT: U 45 GLN cc_start: 0.8747 (tp-100) cc_final: 0.8424 (tp-100) REVERT: V 48 SER cc_start: 0.9357 (m) cc_final: 0.9112 (t) REVERT: V 83 GLN cc_start: 0.8758 (tp-100) cc_final: 0.8546 (tp40) REVERT: W 22 TYR cc_start: 0.9032 (t80) cc_final: 0.8640 (t80) REVERT: W 119 LYS cc_start: 0.9289 (ttpp) cc_final: 0.8868 (mtpp) REVERT: X 22 TYR cc_start: 0.9075 (t80) cc_final: 0.8845 (t80) REVERT: X 24 MET cc_start: 0.8452 (ttt) cc_final: 0.8214 (ttt) REVERT: X 45 GLN cc_start: 0.8872 (tp-100) cc_final: 0.8544 (tp-100) REVERT: Y 22 TYR cc_start: 0.9022 (t80) cc_final: 0.8704 (t80) REVERT: Y 152 ARG cc_start: 0.9015 (mmt-90) cc_final: 0.8678 (mmt90) REVERT: Z 22 TYR cc_start: 0.8814 (t80) cc_final: 0.8460 (t80) REVERT: Z 36 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8843 (tt0) REVERT: Z 45 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8528 (tp-100) REVERT: Z 81 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8950 (mm-30) REVERT: Z 83 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8606 (mm110) outliers start: 128 outliers final: 86 residues processed: 2110 average time/residue: 0.9531 time to fit residues: 3195.3406 Evaluate side-chains 2134 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 2043 time to evaluate : 3.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 135 LYS Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain M residue 83 GLN Chi-restraints excluded: chain N residue 36 GLN Chi-restraints excluded: chain N residue 39 THR Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain O residue 113 ASN Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 149 ILE Chi-restraints excluded: chain T residue 36 GLN Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 105 ILE Chi-restraints excluded: chain T residue 113 ASN Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 113 ASN Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain V residue 36 GLN Chi-restraints excluded: chain V residue 135 LYS Chi-restraints excluded: chain V residue 148 THR Chi-restraints excluded: chain W residue 86 LYS Chi-restraints excluded: chain W residue 148 THR Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain X residue 113 ASN Chi-restraints excluded: chain X residue 149 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 147 SER Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Z residue 36 GLN Chi-restraints excluded: chain Z residue 113 ASN Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 149 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 373 optimal weight: 7.9990 chunk 284 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 254 optimal weight: 2.9990 chunk 379 optimal weight: 0.8980 chunk 402 optimal weight: 9.9990 chunk 198 optimal weight: 7.9990 chunk 359 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN D 109 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN F 33 GLN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 GLN ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 36 GLN ** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN ** Y 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 113 ASN ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.6356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 32760 Z= 0.320 Angle : 0.620 5.867 44512 Z= 0.346 Chirality : 0.044 0.158 5304 Planarity : 0.004 0.033 5512 Dihedral : 5.930 59.912 4608 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 22.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.81 % Allowed : 31.18 % Favored : 64.02 % 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: -1.14 (0.12), residues: 4212 helix: 1.41 (0.12), residues: 1144 sheet: -1.35 (0.12), residues: 1274 loop : -1.69 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 92 PHE 0.024 0.002 PHE W 136 TYR 0.023 0.002 TYR E 73 ARG 0.005 0.001 ARG J 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2204 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 2039 time to evaluate : 3.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 72 PHE cc_start: 0.8753 (p90) cc_final: 0.8457 (p90) REVERT: I 119 LYS cc_start: 0.9331 (ttpp) cc_final: 0.8853 (mtpp) REVERT: A 25 LEU cc_start: 0.9472 (mt) cc_final: 0.9109 (mt) REVERT: B 36 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8919 (tt0) REVERT: B 136 PHE cc_start: 0.8853 (p90) cc_final: 0.8355 (p90) REVERT: C 45 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8647 (tp-100) REVERT: D 83 GLN cc_start: 0.8815 (mm110) cc_final: 0.8493 (mm110) REVERT: E 25 LEU cc_start: 0.9482 (mt) cc_final: 0.9259 (mt) REVERT: E 45 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8639 (tp-100) REVERT: E 147 SER cc_start: 0.9304 (m) cc_final: 0.9062 (p) REVERT: H 45 GLN cc_start: 0.8969 (tp-100) cc_final: 0.8690 (tp-100) REVERT: J 36 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.8967 (tt0) REVERT: K 45 GLN cc_start: 0.8934 (tp-100) cc_final: 0.8643 (tp-100) REVERT: K 147 SER cc_start: 0.9285 (m) cc_final: 0.9030 (p) REVERT: L 143 LYS cc_start: 0.9133 (ttpp) cc_final: 0.8874 (tptt) REVERT: L 152 ARG cc_start: 0.8760 (mmt-90) cc_final: 0.8393 (mmt180) REVERT: N 147 SER cc_start: 0.9253 (m) cc_final: 0.8991 (p) REVERT: P 22 TYR cc_start: 0.9059 (t80) cc_final: 0.8822 (t80) REVERT: P 83 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8403 (mm110) REVERT: Q 29 PHE cc_start: 0.9117 (m-10) cc_final: 0.8916 (m-10) REVERT: Q 83 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8571 (mm110) REVERT: Q 86 LYS cc_start: 0.9249 (ttmm) cc_final: 0.9023 (tppt) REVERT: Q 147 SER cc_start: 0.9357 (m) cc_final: 0.9145 (p) REVERT: R 25 LEU cc_start: 0.9215 (mt) cc_final: 0.8802 (mt) REVERT: R 86 LYS cc_start: 0.9387 (ttmm) cc_final: 0.9150 (tppt) REVERT: S 147 SER cc_start: 0.9233 (m) cc_final: 0.8951 (p) REVERT: T 36 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8721 (mm-40) REVERT: T 40 TYR cc_start: 0.8786 (m-10) cc_final: 0.8524 (m-10) REVERT: T 73 TYR cc_start: 0.8476 (m-80) cc_final: 0.8123 (m-80) REVERT: T 119 LYS cc_start: 0.9271 (ttpp) cc_final: 0.9017 (mtpp) REVERT: T 136 PHE cc_start: 0.8938 (p90) cc_final: 0.8644 (p90) REVERT: T 143 LYS cc_start: 0.9197 (ttpp) cc_final: 0.8824 (tptt) REVERT: U 20 PHE cc_start: 0.8894 (t80) cc_final: 0.8611 (t80) REVERT: U 45 GLN cc_start: 0.8847 (tp-100) cc_final: 0.8544 (tp-100) REVERT: V 45 GLN cc_start: 0.8779 (tp-100) cc_final: 0.8494 (tp-100) REVERT: V 83 GLN cc_start: 0.8985 (tp-100) cc_final: 0.8688 (mm110) REVERT: W 22 TYR cc_start: 0.9067 (t80) cc_final: 0.8520 (t80) REVERT: W 83 GLN cc_start: 0.8755 (mm110) cc_final: 0.8546 (mm110) REVERT: W 86 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9139 (tppt) REVERT: X 45 GLN cc_start: 0.8932 (tp-100) cc_final: 0.8600 (tp-100) REVERT: Y 22 TYR cc_start: 0.9072 (t80) cc_final: 0.8609 (t80) REVERT: Z 20 PHE cc_start: 0.8679 (t80) cc_final: 0.8468 (t80) REVERT: Z 22 TYR cc_start: 0.8833 (t80) cc_final: 0.8475 (t80) REVERT: Z 36 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8960 (tt0) REVERT: Z 45 GLN cc_start: 0.8835 (tp-100) cc_final: 0.8492 (tp-100) outliers start: 165 outliers final: 116 residues processed: 2075 average time/residue: 0.8913 time to fit residues: 2926.2351 Evaluate side-chains 2118 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1997 time to evaluate : 3.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 83 GLN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain N residue 39 THR Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 109 ASN Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 49 ASN Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 49 ASN Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 149 ILE Chi-restraints excluded: chain Q residue 149 ILE Chi-restraints excluded: chain R residue 49 ASN Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 149 ILE Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 36 GLN Chi-restraints excluded: chain T residue 49 ASN Chi-restraints excluded: chain T residue 105 ILE Chi-restraints excluded: chain T residue 113 ASN Chi-restraints excluded: chain T residue 149 ILE Chi-restraints excluded: chain U residue 44 LYS Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain U residue 113 ASN Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain U residue 148 THR Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain V residue 36 GLN Chi-restraints excluded: chain V residue 135 LYS Chi-restraints excluded: chain V residue 148 THR Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain W residue 86 LYS Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 149 ILE Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 147 SER Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Z residue 36 GLN Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain Z residue 113 ASN Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 149 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 334 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 299 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 343 optimal weight: 7.9990 chunk 277 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 205 optimal weight: 7.9990 chunk 360 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 36 GLN ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 109 ASN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 GLN ** T 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 113 ASN Y 109 ASN ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 83 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.6789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 32760 Z= 0.340 Angle : 0.631 6.975 44512 Z= 0.352 Chirality : 0.044 0.166 5304 Planarity : 0.004 0.049 5512 Dihedral : 5.793 57.565 4602 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 25.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 5.51 % Allowed : 33.04 % Favored : 61.45 % 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: -1.22 (0.12), residues: 4212 helix: 1.59 (0.13), residues: 1144 sheet: -1.54 (0.12), residues: 1274 loop : -1.80 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 92 PHE 0.031 0.002 PHE A 29 TYR 0.023 0.002 TYR O 73 ARG 0.008 0.001 ARG U 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2209 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 2020 time to evaluate : 3.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 72 PHE cc_start: 0.8712 (p90) cc_final: 0.8463 (p90) REVERT: I 119 LYS cc_start: 0.9320 (ttpp) cc_final: 0.8877 (mtpp) REVERT: I 136 PHE cc_start: 0.8633 (p90) cc_final: 0.8340 (p90) REVERT: B 22 TYR cc_start: 0.9212 (t80) cc_final: 0.8988 (t80) REVERT: B 36 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8945 (tt0) REVERT: B 136 PHE cc_start: 0.8761 (p90) cc_final: 0.8413 (p90) REVERT: C 36 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8928 (tt0) REVERT: C 45 GLN cc_start: 0.9006 (tp-100) cc_final: 0.8708 (tp-100) REVERT: E 45 GLN cc_start: 0.8981 (tp-100) cc_final: 0.8700 (tp-100) REVERT: F 34 LYS cc_start: 0.9551 (mmmt) cc_final: 0.9310 (mmmm) REVERT: G 22 TYR cc_start: 0.9207 (t80) cc_final: 0.8996 (t80) REVERT: H 45 GLN cc_start: 0.8996 (tp-100) cc_final: 0.8736 (tp-100) REVERT: J 36 GLN cc_start: 0.9284 (OUTLIER) cc_final: 0.8991 (tt0) REVERT: J 75 LYS cc_start: 0.9222 (ptpt) cc_final: 0.8970 (ptmm) REVERT: K 20 PHE cc_start: 0.8949 (t80) cc_final: 0.8714 (t80) REVERT: K 45 GLN cc_start: 0.8978 (tp-100) cc_final: 0.8697 (tp-100) REVERT: L 119 LYS cc_start: 0.9324 (ttpp) cc_final: 0.8962 (mtpp) REVERT: L 143 LYS cc_start: 0.9163 (ttpp) cc_final: 0.8881 (tptt) REVERT: P 147 SER cc_start: 0.9416 (m) cc_final: 0.9194 (p) REVERT: Q 25 LEU cc_start: 0.9028 (mt) cc_final: 0.8666 (mt) REVERT: Q 29 PHE cc_start: 0.9131 (m-10) cc_final: 0.8929 (m-10) REVERT: Q 112 LEU cc_start: 0.8937 (mm) cc_final: 0.8588 (mm) REVERT: R 25 LEU cc_start: 0.9171 (mt) cc_final: 0.8760 (mt) REVERT: R 86 LYS cc_start: 0.9387 (OUTLIER) cc_final: 0.9152 (tppt) REVERT: S 34 LYS cc_start: 0.9538 (mmmt) cc_final: 0.9289 (mmmm) REVERT: S 147 SER cc_start: 0.9258 (m) cc_final: 0.8996 (p) REVERT: T 36 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8790 (mm-40) REVERT: T 119 LYS cc_start: 0.9275 (ttpp) cc_final: 0.8998 (mtpp) REVERT: T 143 LYS cc_start: 0.9225 (ttpp) cc_final: 0.8871 (tptt) REVERT: U 20 PHE cc_start: 0.8869 (t80) cc_final: 0.8571 (t80) REVERT: U 45 GLN cc_start: 0.8846 (tp-100) cc_final: 0.8561 (tp-100) REVERT: V 45 GLN cc_start: 0.8793 (tp-100) cc_final: 0.8543 (tp-100) REVERT: V 152 ARG cc_start: 0.8751 (mmt-90) cc_final: 0.8390 (mmt-90) REVERT: W 22 TYR cc_start: 0.9087 (t80) cc_final: 0.8749 (t80) REVERT: Y 22 TYR cc_start: 0.9058 (t80) cc_final: 0.8668 (t80) REVERT: Z 22 TYR cc_start: 0.8882 (t80) cc_final: 0.8530 (t80) REVERT: Z 33 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8932 (mm-40) REVERT: Z 45 GLN cc_start: 0.8895 (tp-100) cc_final: 0.8587 (tp-100) REVERT: Z 72 PHE cc_start: 0.8719 (p90) cc_final: 0.8503 (p90) outliers start: 189 outliers final: 152 residues processed: 2070 average time/residue: 0.8752 time to fit residues: 2867.6457 Evaluate side-chains 2137 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1980 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 33 GLN Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain J residue 5 GLU Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain M residue 43 MET Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 83 GLN Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain N residue 5 GLU Chi-restraints excluded: chain N residue 39 THR Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 109 ASN Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 49 ASN Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 49 ASN Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 149 ILE Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 149 ILE Chi-restraints excluded: chain R residue 48 SER Chi-restraints excluded: chain R residue 49 ASN Chi-restraints excluded: chain R residue 86 LYS Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain S residue 5 GLU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 49 ASN Chi-restraints excluded: chain S residue 149 ILE Chi-restraints excluded: chain T residue 15 VAL Chi-restraints excluded: chain T residue 36 GLN Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 148 THR Chi-restraints excluded: chain U residue 44 LYS Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain U residue 113 ASN Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 109 ASN Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 135 LYS Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 149 ILE Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 147 SER Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Z residue 36 GLN Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain Z residue 113 ASN Chi-restraints excluded: chain Z residue 123 THR Chi-restraints excluded: chain Z residue 149 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 135 optimal weight: 0.2980 chunk 362 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 236 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 402 optimal weight: 6.9990 chunk 334 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 ASN ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 GLN ** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 113 ASN ** Y 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.7185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 32760 Z= 0.238 Angle : 0.593 8.215 44512 Z= 0.324 Chirality : 0.044 0.181 5304 Planarity : 0.003 0.032 5512 Dihedral : 5.539 59.825 4593 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 25.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.28 % Allowed : 34.85 % Favored : 60.87 % 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: -1.10 (0.12), residues: 4212 helix: 1.60 (0.13), residues: 1170 sheet: -1.43 (0.13), residues: 1144 loop : -1.75 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 92 PHE 0.024 0.002 PHE C 136 TYR 0.017 0.002 TYR L 73 ARG 0.005 0.000 ARG U 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2177 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 2030 time to evaluate : 3.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 36 GLN cc_start: 0.9029 (tt0) cc_final: 0.8522 (tm-30) REVERT: I 72 PHE cc_start: 0.8730 (p90) cc_final: 0.8522 (p90) REVERT: I 119 LYS cc_start: 0.9310 (ttpp) cc_final: 0.8912 (mtpp) REVERT: I 136 PHE cc_start: 0.8730 (p90) cc_final: 0.8411 (p90) REVERT: B 36 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8878 (tt0) REVERT: B 40 TYR cc_start: 0.8582 (m-80) cc_final: 0.7920 (m-80) REVERT: B 136 PHE cc_start: 0.8687 (p90) cc_final: 0.8368 (p90) REVERT: C 36 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8932 (tt0) REVERT: C 45 GLN cc_start: 0.8920 (tp-100) cc_final: 0.8588 (tp-100) REVERT: E 45 GLN cc_start: 0.8859 (tp-100) cc_final: 0.8531 (tp-100) REVERT: H 45 GLN cc_start: 0.8883 (tp-100) cc_final: 0.8615 (tp-100) REVERT: J 36 GLN cc_start: 0.9258 (OUTLIER) cc_final: 0.8979 (tt0) REVERT: K 20 PHE cc_start: 0.8907 (t80) cc_final: 0.8691 (t80) REVERT: K 45 GLN cc_start: 0.8896 (tp-100) cc_final: 0.8575 (tp-100) REVERT: L 45 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8473 (tp-100) REVERT: L 119 LYS cc_start: 0.9301 (ttpp) cc_final: 0.9005 (mtpp) REVERT: L 143 LYS cc_start: 0.9173 (ttpp) cc_final: 0.8927 (tptt) REVERT: M 81 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8082 (mm-30) REVERT: M 83 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8253 (mp10) REVERT: P 147 SER cc_start: 0.9348 (m) cc_final: 0.9120 (p) REVERT: Q 25 LEU cc_start: 0.9045 (mt) cc_final: 0.8648 (mt) REVERT: Q 29 PHE cc_start: 0.9125 (m-10) cc_final: 0.8847 (m-10) REVERT: Q 112 LEU cc_start: 0.8842 (mm) cc_final: 0.8531 (mm) REVERT: R 25 LEU cc_start: 0.9121 (mt) cc_final: 0.8749 (mt) REVERT: R 86 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.9069 (tppt) REVERT: S 34 LYS cc_start: 0.9509 (mmmt) cc_final: 0.9259 (mmmm) REVERT: S 75 LYS cc_start: 0.8845 (ptmt) cc_final: 0.8528 (ptmm) REVERT: S 87 TYR cc_start: 0.8829 (m-80) cc_final: 0.8622 (m-10) REVERT: T 36 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8750 (mm-40) REVERT: T 119 LYS cc_start: 0.9271 (ttpp) cc_final: 0.9026 (mtpp) REVERT: T 143 LYS cc_start: 0.9200 (ttpp) cc_final: 0.8861 (tptt) REVERT: U 20 PHE cc_start: 0.8838 (t80) cc_final: 0.8489 (t80) REVERT: U 22 TYR cc_start: 0.9073 (t80) cc_final: 0.8804 (t80) REVERT: U 45 GLN cc_start: 0.8805 (tp-100) cc_final: 0.8480 (tp-100) REVERT: U 55 MET cc_start: 0.9004 (mmm) cc_final: 0.8775 (mmm) REVERT: V 22 TYR cc_start: 0.8865 (t80) cc_final: 0.8641 (t80) REVERT: V 36 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.9041 (tt0) REVERT: V 40 TYR cc_start: 0.8906 (m-10) cc_final: 0.8199 (m-10) REVERT: V 45 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8353 (tp-100) REVERT: V 152 ARG cc_start: 0.8747 (mmt-90) cc_final: 0.8364 (mmt-90) REVERT: W 22 TYR cc_start: 0.9039 (t80) cc_final: 0.8739 (t80) REVERT: X 110 GLN cc_start: 0.8337 (tm-30) cc_final: 0.8131 (tm-30) REVERT: X 143 LYS cc_start: 0.8900 (ttpt) cc_final: 0.8679 (ttpp) REVERT: Y 22 TYR cc_start: 0.9013 (t80) cc_final: 0.8624 (t80) REVERT: Z 45 GLN cc_start: 0.8747 (tp-100) cc_final: 0.8408 (tp-100) outliers start: 147 outliers final: 120 residues processed: 2066 average time/residue: 0.9551 time to fit residues: 3151.2883 Evaluate side-chains 2112 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1985 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 83 GLN Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain N residue 39 THR Chi-restraints excluded: chain N residue 47 THR Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 149 ILE Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 86 LYS Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain T residue 36 GLN Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 71 TYR Chi-restraints excluded: chain T residue 109 ASN Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain U residue 47 THR Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain U residue 113 ASN Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain V residue 36 GLN Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 148 THR Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 112 LEU Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 147 SER Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Z residue 36 GLN Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 50 LEU Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain Z residue 91 LEU Chi-restraints excluded: chain Z residue 113 ASN Chi-restraints excluded: chain Z residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 388 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 229 optimal weight: 0.9980 chunk 293 optimal weight: 6.9990 chunk 227 optimal weight: 7.9990 chunk 338 optimal weight: 9.9990 chunk 224 optimal weight: 4.9990 chunk 400 optimal weight: 9.9990 chunk 250 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 GLN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 ASN N 113 ASN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 33 GLN ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN ** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 113 ASN Y 109 ASN ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.7467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 32760 Z= 0.295 Angle : 0.619 8.590 44512 Z= 0.341 Chirality : 0.044 0.168 5304 Planarity : 0.003 0.033 5512 Dihedral : 5.462 59.580 4592 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 27.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.84 % Allowed : 35.58 % Favored : 59.59 % 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: -1.07 (0.12), residues: 4212 helix: 1.74 (0.13), residues: 1170 sheet: -1.45 (0.13), residues: 1144 loop : -1.81 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 92 PHE 0.025 0.002 PHE X 136 TYR 0.019 0.002 TYR X 40 ARG 0.005 0.001 ARG Q 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2158 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1992 time to evaluate : 3.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 72 PHE cc_start: 0.8778 (p90) cc_final: 0.8572 (p90) REVERT: I 119 LYS cc_start: 0.9362 (ttpp) cc_final: 0.8965 (mtpp) REVERT: I 136 PHE cc_start: 0.8782 (p90) cc_final: 0.8406 (p90) REVERT: B 22 TYR cc_start: 0.9230 (t80) cc_final: 0.8984 (t80) REVERT: B 36 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8904 (tt0) REVERT: B 40 TYR cc_start: 0.8633 (m-80) cc_final: 0.8015 (m-80) REVERT: B 45 GLN cc_start: 0.8975 (tp-100) cc_final: 0.8640 (tp-100) REVERT: C 45 GLN cc_start: 0.8909 (tp-100) cc_final: 0.8550 (tp-100) REVERT: E 45 GLN cc_start: 0.8953 (tp-100) cc_final: 0.8623 (tp-100) REVERT: H 45 GLN cc_start: 0.8939 (tp-100) cc_final: 0.8650 (tp-100) REVERT: K 20 PHE cc_start: 0.8955 (t80) cc_final: 0.8751 (t80) REVERT: K 45 GLN cc_start: 0.8921 (tp-100) cc_final: 0.8604 (tp-100) REVERT: L 45 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8539 (tp-100) REVERT: L 119 LYS cc_start: 0.9297 (ttpp) cc_final: 0.8987 (mtpp) REVERT: L 143 LYS cc_start: 0.9193 (ttpp) cc_final: 0.8935 (tptt) REVERT: P 29 PHE cc_start: 0.9011 (m-10) cc_final: 0.8780 (m-80) REVERT: P 147 SER cc_start: 0.9341 (m) cc_final: 0.9120 (p) REVERT: Q 25 LEU cc_start: 0.9125 (mt) cc_final: 0.8752 (mt) REVERT: Q 29 PHE cc_start: 0.9148 (m-10) cc_final: 0.8938 (m-10) REVERT: R 34 LYS cc_start: 0.9603 (tptt) cc_final: 0.9348 (mmmm) REVERT: S 25 LEU cc_start: 0.9243 (mt) cc_final: 0.9002 (mt) REVERT: S 34 LYS cc_start: 0.9527 (mmmt) cc_final: 0.9238 (mmmm) REVERT: T 36 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8784 (mm-40) REVERT: T 86 LYS cc_start: 0.8875 (tptt) cc_final: 0.8606 (tppt) REVERT: T 119 LYS cc_start: 0.9267 (ttpp) cc_final: 0.9006 (mtpp) REVERT: T 143 LYS cc_start: 0.9233 (ttpp) cc_final: 0.8887 (tptt) REVERT: U 20 PHE cc_start: 0.8857 (t80) cc_final: 0.8524 (t80) REVERT: U 22 TYR cc_start: 0.9141 (t80) cc_final: 0.8820 (t80) REVERT: U 45 GLN cc_start: 0.8825 (tp-100) cc_final: 0.8532 (tp-100) REVERT: V 22 TYR cc_start: 0.8888 (t80) cc_final: 0.8672 (t80) REVERT: V 45 GLN cc_start: 0.8607 (tp-100) cc_final: 0.8334 (tp-100) REVERT: W 22 TYR cc_start: 0.9063 (t80) cc_final: 0.8764 (t80) REVERT: W 147 SER cc_start: 0.9370 (m) cc_final: 0.9064 (p) REVERT: X 143 LYS cc_start: 0.8943 (ttpt) cc_final: 0.8704 (ttpp) REVERT: Y 22 TYR cc_start: 0.9043 (t80) cc_final: 0.8589 (t80) REVERT: Z 45 GLN cc_start: 0.8759 (tp-100) cc_final: 0.8393 (tp-100) outliers start: 166 outliers final: 151 residues processed: 2042 average time/residue: 0.8773 time to fit residues: 2835.6996 Evaluate side-chains 2114 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1961 time to evaluate : 4.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 49 ASN Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 83 GLN Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 113 ASN Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain N residue 39 THR Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 109 ASN Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain O residue 113 ASN Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 49 ASN Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 149 ILE Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 48 SER Chi-restraints excluded: chain R residue 49 ASN Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 36 GLN Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 71 TYR Chi-restraints excluded: chain T residue 109 ASN Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain T residue 113 ASN Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain U residue 47 THR Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain U residue 113 ASN Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain V residue 109 ASN Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain X residue 36 GLN Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain Y residue 112 LEU Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 147 SER Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 50 LEU Chi-restraints excluded: chain Z residue 91 LEU Chi-restraints excluded: chain Z residue 123 THR Chi-restraints excluded: chain Z residue 149 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 248 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 254 optimal weight: 1.9990 chunk 273 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 315 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 ASN ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 109 ASN ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.7677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 32760 Z= 0.351 Angle : 0.653 9.066 44512 Z= 0.363 Chirality : 0.044 0.184 5304 Planarity : 0.003 0.033 5512 Dihedral : 5.426 58.045 4589 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 31.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.16 % Allowed : 37.27 % Favored : 57.58 % 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: -1.17 (0.12), residues: 4212 helix: 1.69 (0.13), residues: 1170 sheet: -1.51 (0.13), residues: 1144 loop : -1.88 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 92 PHE 0.027 0.002 PHE O 136 TYR 0.022 0.002 TYR Z 57 ARG 0.006 0.001 ARG W 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2148 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1971 time to evaluate : 3.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 119 LYS cc_start: 0.9341 (ttpp) cc_final: 0.8967 (mtpp) REVERT: I 136 PHE cc_start: 0.8770 (p90) cc_final: 0.8458 (p90) REVERT: A 72 PHE cc_start: 0.8754 (p90) cc_final: 0.8427 (p90) REVERT: B 22 TYR cc_start: 0.9244 (t80) cc_final: 0.8988 (t80) REVERT: B 36 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.8931 (tt0) REVERT: B 40 TYR cc_start: 0.8665 (m-80) cc_final: 0.8076 (m-80) REVERT: B 45 GLN cc_start: 0.9049 (tp-100) cc_final: 0.8721 (tp-100) REVERT: B 111 GLN cc_start: 0.9015 (mp10) cc_final: 0.8765 (mm-40) REVERT: B 136 PHE cc_start: 0.8725 (p90) cc_final: 0.8405 (p90) REVERT: C 45 GLN cc_start: 0.8933 (tp-100) cc_final: 0.8578 (tp-100) REVERT: C 109 ASN cc_start: 0.6104 (OUTLIER) cc_final: 0.5895 (p0) REVERT: E 45 GLN cc_start: 0.8983 (tp-100) cc_final: 0.8641 (tp-100) REVERT: F 29 PHE cc_start: 0.9116 (m-10) cc_final: 0.8885 (m-80) REVERT: H 45 GLN cc_start: 0.8998 (tp-100) cc_final: 0.8684 (tp-100) REVERT: K 45 GLN cc_start: 0.8958 (tp-100) cc_final: 0.8622 (tp-100) REVERT: L 45 GLN cc_start: 0.8994 (tp-100) cc_final: 0.8631 (tp-100) REVERT: L 119 LYS cc_start: 0.9294 (ttpp) cc_final: 0.8955 (mtpp) REVERT: L 143 LYS cc_start: 0.9182 (ttpp) cc_final: 0.8912 (tptt) REVERT: M 83 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8387 (mm110) REVERT: P 30 PHE cc_start: 0.9360 (t80) cc_final: 0.9109 (t80) REVERT: Q 25 LEU cc_start: 0.9153 (mt) cc_final: 0.8775 (mt) REVERT: Q 29 PHE cc_start: 0.9172 (m-10) cc_final: 0.8953 (m-10) REVERT: Q 147 SER cc_start: 0.9360 (m) cc_final: 0.9139 (p) REVERT: R 86 LYS cc_start: 0.9303 (ttmm) cc_final: 0.8956 (tppt) REVERT: S 25 LEU cc_start: 0.9069 (mt) cc_final: 0.8835 (mt) REVERT: S 34 LYS cc_start: 0.9559 (mmmt) cc_final: 0.9308 (mmmm) REVERT: T 36 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8796 (mm-40) REVERT: T 119 LYS cc_start: 0.9287 (ttpp) cc_final: 0.9023 (mtpp) REVERT: T 143 LYS cc_start: 0.9282 (ttpp) cc_final: 0.8915 (tptt) REVERT: U 20 PHE cc_start: 0.8889 (t80) cc_final: 0.8549 (t80) REVERT: U 22 TYR cc_start: 0.9193 (t80) cc_final: 0.8875 (t80) REVERT: U 45 GLN cc_start: 0.8911 (tp-100) cc_final: 0.8635 (tp-100) REVERT: V 22 TYR cc_start: 0.8910 (t80) cc_final: 0.8698 (t80) REVERT: V 45 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8390 (tp-100) REVERT: W 22 TYR cc_start: 0.9097 (t80) cc_final: 0.8782 (t80) REVERT: W 119 LYS cc_start: 0.9338 (ttpp) cc_final: 0.9066 (tttp) REVERT: W 147 SER cc_start: 0.9373 (m) cc_final: 0.9068 (p) REVERT: X 143 LYS cc_start: 0.8984 (ttpt) cc_final: 0.8749 (ttpp) REVERT: Y 22 TYR cc_start: 0.9055 (t80) cc_final: 0.8602 (t80) REVERT: Z 45 GLN cc_start: 0.8847 (tp-100) cc_final: 0.8493 (tp-100) REVERT: Z 86 LYS cc_start: 0.8913 (ttmm) cc_final: 0.8566 (tppt) outliers start: 177 outliers final: 162 residues processed: 2020 average time/residue: 0.9359 time to fit residues: 3032.8299 Evaluate side-chains 2110 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1944 time to evaluate : 3.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 49 ASN Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 49 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 147 SER Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 83 GLN Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain M residue 113 ASN Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain N residue 39 THR Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 109 ASN Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain O residue 113 ASN Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 49 ASN Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 149 ILE Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 48 SER Chi-restraints excluded: chain R residue 49 ASN Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 149 ILE Chi-restraints excluded: chain T residue 36 GLN Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 109 ASN Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 149 ILE Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain U residue 113 ASN Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 113 ASN Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 48 SER Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 147 SER Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 50 LEU Chi-restraints excluded: chain Z residue 91 LEU Chi-restraints excluded: chain Z residue 123 THR Chi-restraints excluded: chain Z residue 149 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 364 optimal weight: 8.9990 chunk 384 optimal weight: 10.0000 chunk 350 optimal weight: 0.8980 chunk 373 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 293 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 337 optimal weight: 6.9990 chunk 353 optimal weight: 5.9990 chunk 372 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 ASN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 ASN ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 GLN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 ASN ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 113 ASN ** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 109 ASN ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.7949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 32760 Z= 0.363 Angle : 0.674 9.685 44512 Z= 0.374 Chirality : 0.044 0.209 5304 Planarity : 0.004 0.053 5512 Dihedral : 5.423 58.182 4586 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 33.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.48 % Allowed : 38.05 % Favored : 56.47 % 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: -1.26 (0.12), residues: 4212 helix: 1.59 (0.12), residues: 1170 sheet: -1.60 (0.13), residues: 1144 loop : -1.90 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 92 PHE 0.030 0.002 PHE T 29 TYR 0.023 0.002 TYR Z 57 ARG 0.006 0.001 ARG W 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2137 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1949 time to evaluate : 3.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 119 LYS cc_start: 0.9345 (ttpp) cc_final: 0.9029 (mtpp) REVERT: I 136 PHE cc_start: 0.8761 (p90) cc_final: 0.8422 (p90) REVERT: B 34 LYS cc_start: 0.9607 (tptt) cc_final: 0.9356 (mmmm) REVERT: B 36 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8882 (tt0) REVERT: B 40 TYR cc_start: 0.8627 (m-80) cc_final: 0.8099 (m-80) REVERT: B 45 GLN cc_start: 0.9074 (tp-100) cc_final: 0.8710 (tp-100) REVERT: C 45 GLN cc_start: 0.8940 (tp-100) cc_final: 0.8573 (tp-100) REVERT: E 45 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8585 (tp-100) REVERT: F 29 PHE cc_start: 0.9116 (m-10) cc_final: 0.8909 (m-80) REVERT: H 45 GLN cc_start: 0.9052 (tp-100) cc_final: 0.8676 (tp-100) REVERT: K 45 GLN cc_start: 0.8978 (tp-100) cc_final: 0.8642 (tp-100) REVERT: L 20 PHE cc_start: 0.8908 (t80) cc_final: 0.8695 (t80) REVERT: L 45 GLN cc_start: 0.9020 (tp-100) cc_final: 0.8677 (tp-100) REVERT: L 119 LYS cc_start: 0.9315 (ttpp) cc_final: 0.8980 (mtpp) REVERT: L 143 LYS cc_start: 0.9167 (ttpp) cc_final: 0.8916 (tptt) REVERT: P 22 TYR cc_start: 0.9109 (t80) cc_final: 0.8721 (t80) REVERT: P 30 PHE cc_start: 0.9360 (t80) cc_final: 0.9095 (t80) REVERT: Q 22 TYR cc_start: 0.9113 (t80) cc_final: 0.8848 (t80) REVERT: Q 25 LEU cc_start: 0.9179 (mt) cc_final: 0.8798 (mt) REVERT: Q 29 PHE cc_start: 0.9189 (m-10) cc_final: 0.8947 (m-10) REVERT: R 86 LYS cc_start: 0.9230 (ttmm) cc_final: 0.8897 (tppt) REVERT: S 25 LEU cc_start: 0.9089 (mt) cc_final: 0.8874 (mt) REVERT: S 30 PHE cc_start: 0.9396 (t80) cc_final: 0.9057 (t80) REVERT: T 36 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8807 (mm-40) REVERT: T 119 LYS cc_start: 0.9271 (ttpp) cc_final: 0.9026 (mtpp) REVERT: T 143 LYS cc_start: 0.9290 (ttpp) cc_final: 0.8932 (tptt) REVERT: U 22 TYR cc_start: 0.9205 (t80) cc_final: 0.8868 (t80) REVERT: U 45 GLN cc_start: 0.8943 (tp-100) cc_final: 0.8654 (tp-100) REVERT: V 45 GLN cc_start: 0.8637 (tp-100) cc_final: 0.8372 (tp-100) REVERT: W 22 TYR cc_start: 0.9139 (t80) cc_final: 0.8834 (t80) REVERT: W 147 SER cc_start: 0.9412 (m) cc_final: 0.9111 (p) REVERT: X 143 LYS cc_start: 0.8991 (ttpt) cc_final: 0.8768 (ttpp) REVERT: Y 22 TYR cc_start: 0.9100 (t80) cc_final: 0.8628 (t80) REVERT: Y 152 ARG cc_start: 0.8100 (mmt90) cc_final: 0.7857 (mmt90) REVERT: Z 45 GLN cc_start: 0.8842 (tp-100) cc_final: 0.8475 (tp-100) outliers start: 188 outliers final: 177 residues processed: 2002 average time/residue: 0.8599 time to fit residues: 2739.0129 Evaluate side-chains 2110 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1931 time to evaluate : 3.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 43 MET Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 49 ASN Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 147 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 49 ASN Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain M residue 113 ASN Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain N residue 39 THR Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 109 ASN Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain O residue 113 ASN Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 49 ASN Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain P residue 149 ILE Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 113 ASN Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 48 SER Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 149 ILE Chi-restraints excluded: chain T residue 36 GLN Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 109 ASN Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain T residue 113 ASN Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain U residue 47 THR Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain U residue 113 ASN Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 38 VAL Chi-restraints excluded: chain V residue 48 SER Chi-restraints excluded: chain V residue 109 ASN Chi-restraints excluded: chain V residue 123 THR Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 113 ASN Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 149 ILE Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 48 SER Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Z residue 47 THR Chi-restraints excluded: chain Z residue 50 LEU Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain Z residue 91 LEU Chi-restraints excluded: chain Z residue 123 THR Chi-restraints excluded: chain Z residue 138 LEU Chi-restraints excluded: chain Z residue 149 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 245 optimal weight: 7.9990 chunk 395 optimal weight: 0.6980 chunk 241 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 274 optimal weight: 0.8980 chunk 414 optimal weight: 0.8980 chunk 381 optimal weight: 0.7980 chunk 330 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 254 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 83 GLN K 83 GLN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 ASN ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 36 GLN ** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.8168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32760 Z= 0.209 Angle : 0.641 9.742 44512 Z= 0.344 Chirality : 0.045 0.175 5304 Planarity : 0.004 0.040 5512 Dihedral : 5.417 58.593 4586 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 28.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.58 % Allowed : 39.80 % Favored : 56.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.12), residues: 4212 helix: 2.02 (0.13), residues: 1170 sheet: -1.28 (0.14), residues: 1092 loop : -1.52 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 92 PHE 0.027 0.002 PHE Z 30 TYR 0.028 0.001 TYR F 40 ARG 0.007 0.001 ARG B 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2107 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1984 time to evaluate : 3.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 119 LYS cc_start: 0.9296 (ttpp) cc_final: 0.9004 (mtpp) REVERT: I 136 PHE cc_start: 0.8652 (p90) cc_final: 0.8377 (p90) REVERT: A 72 PHE cc_start: 0.8401 (p90) cc_final: 0.8187 (p90) REVERT: B 34 LYS cc_start: 0.9543 (tptt) cc_final: 0.9328 (mmmm) REVERT: B 45 GLN cc_start: 0.8793 (tp-100) cc_final: 0.8407 (tp-100) REVERT: B 112 LEU cc_start: 0.9155 (mm) cc_final: 0.8817 (mm) REVERT: C 45 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8343 (tp-100) REVERT: E 22 TYR cc_start: 0.9035 (t80) cc_final: 0.8126 (t80) REVERT: E 40 TYR cc_start: 0.8348 (m-10) cc_final: 0.7743 (m-10) REVERT: F 29 PHE cc_start: 0.9103 (m-10) cc_final: 0.8849 (m-80) REVERT: G 33 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8914 (mm-40) REVERT: H 45 GLN cc_start: 0.8831 (tp-100) cc_final: 0.8431 (tp-100) REVERT: K 45 GLN cc_start: 0.8711 (tp-100) cc_final: 0.8357 (tp-100) REVERT: L 45 GLN cc_start: 0.8863 (tp-100) cc_final: 0.8512 (tp-100) REVERT: L 119 LYS cc_start: 0.9313 (ttpp) cc_final: 0.9023 (mtpp) REVERT: L 143 LYS cc_start: 0.9134 (ttpp) cc_final: 0.8909 (tptt) REVERT: P 22 TYR cc_start: 0.9001 (t80) cc_final: 0.8653 (t80) REVERT: P 30 PHE cc_start: 0.9298 (t80) cc_final: 0.9080 (t80) REVERT: P 56 ILE cc_start: 0.9252 (mp) cc_final: 0.8873 (mp) REVERT: Q 22 TYR cc_start: 0.9041 (t80) cc_final: 0.8580 (t80) REVERT: Q 25 LEU cc_start: 0.9098 (mt) cc_final: 0.8689 (mt) REVERT: Q 29 PHE cc_start: 0.9127 (m-10) cc_final: 0.8840 (m-10) REVERT: R 86 LYS cc_start: 0.9036 (ttmm) cc_final: 0.8710 (tppt) REVERT: S 25 LEU cc_start: 0.9007 (mt) cc_final: 0.8786 (mt) REVERT: S 34 LYS cc_start: 0.9522 (mmmt) cc_final: 0.9273 (mmmm) REVERT: S 75 LYS cc_start: 0.8787 (ptmt) cc_final: 0.8585 (ttpp) REVERT: T 36 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8762 (mm-40) REVERT: T 119 LYS cc_start: 0.9242 (ttpp) cc_final: 0.9034 (mtpp) REVERT: T 143 LYS cc_start: 0.9217 (ttpp) cc_final: 0.8860 (tptt) REVERT: U 22 TYR cc_start: 0.9107 (t80) cc_final: 0.8840 (t80) REVERT: U 40 TYR cc_start: 0.8877 (m-10) cc_final: 0.8650 (m-10) REVERT: U 45 GLN cc_start: 0.8713 (tp-100) cc_final: 0.8359 (tp-100) REVERT: V 45 GLN cc_start: 0.8472 (tp-100) cc_final: 0.8099 (tp-100) REVERT: V 152 ARG cc_start: 0.8389 (mmt-90) cc_final: 0.8140 (mmt90) REVERT: W 22 TYR cc_start: 0.9037 (t80) cc_final: 0.8753 (t80) REVERT: W 30 PHE cc_start: 0.9390 (t80) cc_final: 0.9111 (t80) REVERT: W 45 GLN cc_start: 0.8937 (tp-100) cc_final: 0.8608 (tp-100) REVERT: W 147 SER cc_start: 0.9293 (m) cc_final: 0.9004 (p) REVERT: X 45 GLN cc_start: 0.8856 (tp-100) cc_final: 0.8263 (tp-100) REVERT: X 143 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8664 (ttpp) REVERT: Y 22 TYR cc_start: 0.8966 (t80) cc_final: 0.8445 (t80) REVERT: Y 25 LEU cc_start: 0.9512 (mt) cc_final: 0.9277 (mt) outliers start: 123 outliers final: 105 residues processed: 2017 average time/residue: 0.8610 time to fit residues: 2760.7957 Evaluate side-chains 2061 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1955 time to evaluate : 3.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 43 MET Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain J residue 36 GLN Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain O residue 36 GLN Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 138 LEU Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 36 GLN Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain T residue 113 ASN Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 57 TYR Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 151 THR Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 52 LEU Chi-restraints excluded: chain X residue 149 ILE Chi-restraints excluded: chain X residue 151 THR Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Z residue 91 LEU Chi-restraints excluded: chain Z residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 262 optimal weight: 3.9990 chunk 351 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 304 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 330 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 339 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.095499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.084313 restraints weight = 292595.729| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 5.50 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.8383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32760 Z= 0.206 Angle : 0.645 12.389 44512 Z= 0.344 Chirality : 0.045 0.176 5304 Planarity : 0.004 0.043 5512 Dihedral : 5.533 68.756 4584 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 29.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.06 % Allowed : 41.00 % Favored : 55.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.12), residues: 4212 helix: 2.05 (0.13), residues: 1170 sheet: -1.14 (0.15), residues: 1092 loop : -1.49 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 92 PHE 0.033 0.002 PHE K 29 TYR 0.031 0.001 TYR M 73 ARG 0.007 0.001 ARG B 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35097.11 seconds wall clock time: 601 minutes 15.29 seconds (36075.29 seconds total)