Starting phenix.real_space_refine on Thu Mar 14 11:40:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6te9_10477/03_2024/6te9_10477.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6te9_10477/03_2024/6te9_10477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6te9_10477/03_2024/6te9_10477.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6te9_10477/03_2024/6te9_10477.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6te9_10477/03_2024/6te9_10477.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6te9_10477/03_2024/6te9_10477.pdb" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 270 5.16 5 C 42576 2.51 5 N 11988 2.21 5 O 12072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 61": "NH1" <-> "NH2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 324": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 320": "NH1" <-> "NH2" Residue "B TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B ARG 333": "NH1" <-> "NH2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D ARG 186": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "E ARG 5": "NH1" <-> "NH2" Residue "E ARG 47": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 73": "NH1" <-> "NH2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "G ARG 28": "NH1" <-> "NH2" Residue "G ARG 31": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 80": "NH1" <-> "NH2" Residue "G ASP 97": "OD1" <-> "OD2" Residue "G PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 61": "NH1" <-> "NH2" Residue "H ARG 64": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H ARG 113": "NH1" <-> "NH2" Residue "H ARG 115": "NH1" <-> "NH2" Residue "H ARG 186": "NH1" <-> "NH2" Residue "H ARG 188": "NH1" <-> "NH2" Residue "I ARG 38": "NH1" <-> "NH2" Residue "I ARG 44": "NH1" <-> "NH2" Residue "I ARG 51": "NH1" <-> "NH2" Residue "I ARG 95": "NH1" <-> "NH2" Residue "I ARG 103": "NH1" <-> "NH2" Residue "I ARG 139": "NH1" <-> "NH2" Residue "I ARG 220": "NH1" <-> "NH2" Residue "I ARG 320": "NH1" <-> "NH2" Residue "I TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 324": "NH1" <-> "NH2" Residue "I ARG 333": "NH1" <-> "NH2" Residue "I ARG 372": "NH1" <-> "NH2" Residue "J ARG 38": "NH1" <-> "NH2" Residue "J ARG 44": "NH1" <-> "NH2" Residue "J ARG 51": "NH1" <-> "NH2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 103": "NH1" <-> "NH2" Residue "J ARG 139": "NH1" <-> "NH2" Residue "J ARG 220": "NH1" <-> "NH2" Residue "J ARG 320": "NH1" <-> "NH2" Residue "J TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 324": "NH1" <-> "NH2" Residue "J ARG 333": "NH1" <-> "NH2" Residue "J ARG 372": "NH1" <-> "NH2" Residue "K ARG 24": "NH1" <-> "NH2" Residue "K ARG 61": "NH1" <-> "NH2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K ARG 90": "NH1" <-> "NH2" Residue "K ARG 113": "NH1" <-> "NH2" Residue "K ARG 115": "NH1" <-> "NH2" Residue "K ARG 131": "NH1" <-> "NH2" Residue "K ARG 186": "NH1" <-> "NH2" Residue "K ARG 188": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 101": "NH1" <-> "NH2" Residue "M ARG 5": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M ARG 72": "NH1" <-> "NH2" Residue "M ARG 73": "NH1" <-> "NH2" Residue "M ARG 75": "NH1" <-> "NH2" Residue "M ARG 81": "NH1" <-> "NH2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "N ARG 28": "NH1" <-> "NH2" Residue "N ARG 31": "NH1" <-> "NH2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 60": "NH1" <-> "NH2" Residue "N ARG 80": "NH1" <-> "NH2" Residue "N ASP 97": "OD1" <-> "OD2" Residue "N PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 61": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "O ARG 113": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 186": "NH1" <-> "NH2" Residue "O ARG 188": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 44": "NH1" <-> "NH2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ARG 95": "NH1" <-> "NH2" Residue "P ARG 103": "NH1" <-> "NH2" Residue "P ARG 139": "NH1" <-> "NH2" Residue "P ARG 220": "NH1" <-> "NH2" Residue "P ARG 320": "NH1" <-> "NH2" Residue "P TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 324": "NH1" <-> "NH2" Residue "P ARG 333": "NH1" <-> "NH2" Residue "P ARG 372": "NH1" <-> "NH2" Residue "Q ARG 38": "NH1" <-> "NH2" Residue "Q ARG 44": "NH1" <-> "NH2" Residue "Q ARG 51": "NH1" <-> "NH2" Residue "Q ARG 95": "NH1" <-> "NH2" Residue "Q ARG 103": "NH1" <-> "NH2" Residue "Q ARG 139": "NH1" <-> "NH2" Residue "Q ARG 220": "NH1" <-> "NH2" Residue "Q ARG 320": "NH1" <-> "NH2" Residue "Q TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 324": "NH1" <-> "NH2" Residue "Q ARG 333": "NH1" <-> "NH2" Residue "Q ARG 372": "NH1" <-> "NH2" Residue "R ARG 24": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R ARG 64": "NH1" <-> "NH2" Residue "R ARG 90": "NH1" <-> "NH2" Residue "R ARG 113": "NH1" <-> "NH2" Residue "R ARG 115": "NH1" <-> "NH2" Residue "R ARG 131": "NH1" <-> "NH2" Residue "R ARG 186": "NH1" <-> "NH2" Residue "R ARG 188": "NH1" <-> "NH2" Residue "S ARG 18": "NH1" <-> "NH2" Residue "S TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 101": "NH1" <-> "NH2" Residue "T ARG 5": "NH1" <-> "NH2" Residue "T ARG 47": "NH1" <-> "NH2" Residue "T ARG 72": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "T ARG 75": "NH1" <-> "NH2" Residue "T ARG 81": "NH1" <-> "NH2" Residue "T ARG 97": "NH1" <-> "NH2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U ARG 31": "NH1" <-> "NH2" Residue "U ARG 51": "NH1" <-> "NH2" Residue "U ARG 60": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "U ASP 97": "OD1" <-> "OD2" Residue "U PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 61": "NH1" <-> "NH2" Residue "V ARG 64": "NH1" <-> "NH2" Residue "V ARG 71": "NH1" <-> "NH2" Residue "V ARG 113": "NH1" <-> "NH2" Residue "V ARG 115": "NH1" <-> "NH2" Residue "V ARG 186": "NH1" <-> "NH2" Residue "V ARG 188": "NH1" <-> "NH2" Residue "W ARG 38": "NH1" <-> "NH2" Residue "W ARG 44": "NH1" <-> "NH2" Residue "W ARG 51": "NH1" <-> "NH2" Residue "W ARG 95": "NH1" <-> "NH2" Residue "W ARG 103": "NH1" <-> "NH2" Residue "W ARG 139": "NH1" <-> "NH2" Residue "W ARG 220": "NH1" <-> "NH2" Residue "W ARG 320": "NH1" <-> "NH2" Residue "W TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 324": "NH1" <-> "NH2" Residue "W ARG 333": "NH1" <-> "NH2" Residue "W ARG 372": "NH1" <-> "NH2" Residue "X ARG 38": "NH1" <-> "NH2" Residue "X ARG 44": "NH1" <-> "NH2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X ARG 95": "NH1" <-> "NH2" Residue "X ARG 103": "NH1" <-> "NH2" Residue "X ARG 139": "NH1" <-> "NH2" Residue "X ARG 220": "NH1" <-> "NH2" Residue "X ARG 320": "NH1" <-> "NH2" Residue "X TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 324": "NH1" <-> "NH2" Residue "X ARG 333": "NH1" <-> "NH2" Residue "X ARG 372": "NH1" <-> "NH2" Residue "Y ARG 24": "NH1" <-> "NH2" Residue "Y ARG 61": "NH1" <-> "NH2" Residue "Y ARG 64": "NH1" <-> "NH2" Residue "Y ARG 90": "NH1" <-> "NH2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 131": "NH1" <-> "NH2" Residue "Y ARG 186": "NH1" <-> "NH2" Residue "Y ARG 188": "NH1" <-> "NH2" Residue "Z ARG 18": "NH1" <-> "NH2" Residue "Z TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 101": "NH1" <-> "NH2" Residue "0 ARG 5": "NH1" <-> "NH2" Residue "0 ARG 47": "NH1" <-> "NH2" Residue "0 ARG 72": "NH1" <-> "NH2" Residue "0 ARG 73": "NH1" <-> "NH2" Residue "0 ARG 75": "NH1" <-> "NH2" Residue "0 ARG 81": "NH1" <-> "NH2" Residue "0 ARG 97": "NH1" <-> "NH2" Residue "1 ARG 28": "NH1" <-> "NH2" Residue "1 ARG 31": "NH1" <-> "NH2" Residue "1 ARG 51": "NH1" <-> "NH2" Residue "1 ARG 60": "NH1" <-> "NH2" Residue "1 ARG 80": "NH1" <-> "NH2" Residue "1 ASP 97": "OD1" <-> "OD2" Residue "1 PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 61": "NH1" <-> "NH2" Residue "2 ARG 64": "NH1" <-> "NH2" Residue "2 ARG 71": "NH1" <-> "NH2" Residue "2 ARG 113": "NH1" <-> "NH2" Residue "2 ARG 115": "NH1" <-> "NH2" Residue "2 ARG 186": "NH1" <-> "NH2" Residue "2 ARG 188": "NH1" <-> "NH2" Residue "3 ARG 38": "NH1" <-> "NH2" Residue "3 ARG 44": "NH1" <-> "NH2" Residue "3 ARG 51": "NH1" <-> "NH2" Residue "3 ARG 95": "NH1" <-> "NH2" Residue "3 ARG 103": "NH1" <-> "NH2" Residue "3 ARG 139": "NH1" <-> "NH2" Residue "3 ARG 220": "NH1" <-> "NH2" Residue "3 ARG 320": "NH1" <-> "NH2" Residue "3 TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 324": "NH1" <-> "NH2" Residue "3 ARG 333": "NH1" <-> "NH2" Residue "3 ARG 372": "NH1" <-> "NH2" Residue "4 ARG 38": "NH1" <-> "NH2" Residue "4 ARG 44": "NH1" <-> "NH2" Residue "4 ARG 51": "NH1" <-> "NH2" Residue "4 ARG 95": "NH1" <-> "NH2" Residue "4 ARG 103": "NH1" <-> "NH2" Residue "4 ARG 139": "NH1" <-> "NH2" Residue "4 ARG 220": "NH1" <-> "NH2" Residue "4 ARG 320": "NH1" <-> "NH2" Residue "4 TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 324": "NH1" <-> "NH2" Residue "4 ARG 333": "NH1" <-> "NH2" Residue "4 ARG 372": "NH1" <-> "NH2" Residue "5 ARG 24": "NH1" <-> "NH2" Residue "5 ARG 61": "NH1" <-> "NH2" Residue "5 ARG 64": "NH1" <-> "NH2" Residue "5 ARG 90": "NH1" <-> "NH2" Residue "5 ARG 113": "NH1" <-> "NH2" Residue "5 ARG 115": "NH1" <-> "NH2" Residue "5 ARG 131": "NH1" <-> "NH2" Residue "5 ARG 186": "NH1" <-> "NH2" Residue "5 ARG 188": "NH1" <-> "NH2" Residue "6 ARG 18": "NH1" <-> "NH2" Residue "6 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 101": "NH1" <-> "NH2" Residue "7 ARG 5": "NH1" <-> "NH2" Residue "7 ARG 47": "NH1" <-> "NH2" Residue "7 ARG 72": "NH1" <-> "NH2" Residue "7 ARG 73": "NH1" <-> "NH2" Residue "7 ARG 75": "NH1" <-> "NH2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 ARG 97": "NH1" <-> "NH2" Residue "8 ARG 28": "NH1" <-> "NH2" Residue "8 ARG 31": "NH1" <-> "NH2" Residue "8 ARG 51": "NH1" <-> "NH2" Residue "8 ARG 60": "NH1" <-> "NH2" Residue "8 ARG 80": "NH1" <-> "NH2" Residue "8 ASP 97": "OD1" <-> "OD2" Residue "8 PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 61": "NH1" <-> "NH2" Residue "9 ARG 64": "NH1" <-> "NH2" Residue "9 ARG 71": "NH1" <-> "NH2" Residue "9 ARG 113": "NH1" <-> "NH2" Residue "9 ARG 115": "NH1" <-> "NH2" Residue "9 ARG 186": "NH1" <-> "NH2" Residue "9 ARG 188": "NH1" <-> "NH2" Residue "a ARG 38": "NH1" <-> "NH2" Residue "a ARG 44": "NH1" <-> "NH2" Residue "a ARG 51": "NH1" <-> "NH2" Residue "a ARG 95": "NH1" <-> "NH2" Residue "a ARG 103": "NH1" <-> "NH2" Residue "a ARG 139": "NH1" <-> "NH2" Residue "a ARG 220": "NH1" <-> "NH2" Residue "a ARG 320": "NH1" <-> "NH2" Residue "a TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 324": "NH1" <-> "NH2" Residue "a ARG 333": "NH1" <-> "NH2" Residue "a ARG 372": "NH1" <-> "NH2" Residue "b ARG 38": "NH1" <-> "NH2" Residue "b ARG 44": "NH1" <-> "NH2" Residue "b ARG 51": "NH1" <-> "NH2" Residue "b ARG 95": "NH1" <-> "NH2" Residue "b ARG 103": "NH1" <-> "NH2" Residue "b ARG 139": "NH1" <-> "NH2" Residue "b ARG 220": "NH1" <-> "NH2" Residue "b ARG 320": "NH1" <-> "NH2" Residue "b TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 324": "NH1" <-> "NH2" Residue "b ARG 333": "NH1" <-> "NH2" Residue "b ARG 372": "NH1" <-> "NH2" Residue "c ARG 24": "NH1" <-> "NH2" Residue "c ARG 61": "NH1" <-> "NH2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "c ARG 90": "NH1" <-> "NH2" Residue "c ARG 113": "NH1" <-> "NH2" Residue "c ARG 115": "NH1" <-> "NH2" Residue "c ARG 131": "NH1" <-> "NH2" Residue "c ARG 186": "NH1" <-> "NH2" Residue "c ARG 188": "NH1" <-> "NH2" Residue "d ARG 18": "NH1" <-> "NH2" Residue "d TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 101": "NH1" <-> "NH2" Residue "e ARG 5": "NH1" <-> "NH2" Residue "e ARG 47": "NH1" <-> "NH2" Residue "e ARG 72": "NH1" <-> "NH2" Residue "e ARG 73": "NH1" <-> "NH2" Residue "e ARG 75": "NH1" <-> "NH2" Residue "e ARG 81": "NH1" <-> "NH2" Residue "e ARG 97": "NH1" <-> "NH2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ARG 31": "NH1" <-> "NH2" Residue "f ARG 51": "NH1" <-> "NH2" Residue "f ARG 60": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ASP 97": "OD1" <-> "OD2" Residue "f PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 66906 Number of models: 1 Model: "" Number of chains: 42 Chain: "C" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1450 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2723 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 28, 'TRANS': 331} Chain breaks: 1 Chain: "B" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2723 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 28, 'TRANS': 331} Chain breaks: 1 Chain: "D" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1456 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain breaks: 1 Chain: "F" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "E" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "G" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "H" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1450 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2723 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 28, 'TRANS': 331} Chain breaks: 1 Chain: "J" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2723 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 28, 'TRANS': 331} Chain breaks: 1 Chain: "K" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1456 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain breaks: 1 Chain: "L" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "M" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "N" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "O" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1450 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2723 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 28, 'TRANS': 331} Chain breaks: 1 Chain: "Q" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2723 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 28, 'TRANS': 331} Chain breaks: 1 Chain: "R" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1456 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain breaks: 1 Chain: "S" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "T" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "U" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "V" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1450 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2723 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 28, 'TRANS': 331} Chain breaks: 1 Chain: "X" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2723 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 28, 'TRANS': 331} Chain breaks: 1 Chain: "Y" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1456 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain breaks: 1 Chain: "Z" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "0" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "1" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "2" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1450 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2723 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 28, 'TRANS': 331} Chain breaks: 1 Chain: "4" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2723 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 28, 'TRANS': 331} Chain breaks: 1 Chain: "5" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1456 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain breaks: 1 Chain: "6" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "7" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "8" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Chain: "9" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1450 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2723 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 28, 'TRANS': 331} Chain breaks: 1 Chain: "b" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2723 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 28, 'TRANS': 331} Chain breaks: 1 Chain: "c" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1456 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain breaks: 1 Chain: "d" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "e" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "f" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 972 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Time building chain proxies: 27.69, per 1000 atoms: 0.41 Number of scatterers: 66906 At special positions: 0 Unit cell: (156.261, 154.135, 248.742, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 270 16.00 O 12072 8.00 N 11988 7.00 C 42576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.36 Conformation dependent library (CDL) restraints added in 9.4 seconds 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16020 Finding SS restraints... Secondary structure from input PDB file: 276 helices and 102 sheets defined 35.2% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.02 Creating SS restraints... Processing helix chain 'C' and resid 15 through 25 removed outlier: 3.809A pdb=" N ASP C 21 " --> pdb=" O ALA C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 55 removed outlier: 3.753A pdb=" N ALA C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 147 removed outlier: 3.560A pdb=" N ALA C 146 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 147 " --> pdb=" O TRP C 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 143 through 147' Processing helix chain 'C' and resid 148 through 165 removed outlier: 3.749A pdb=" N GLN C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 185 removed outlier: 3.678A pdb=" N LEU C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.727A pdb=" N ILE A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 54 removed outlier: 4.183A pdb=" N ARG A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 72 removed outlier: 3.725A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 96 removed outlier: 3.522A pdb=" N ARG A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 118 removed outlier: 3.662A pdb=" N LEU A 116 " --> pdb=" O GLY A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 3.817A pdb=" N ALA A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 217 removed outlier: 3.691A pdb=" N ASP A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 282 through 298 removed outlier: 3.536A pdb=" N ARG A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.667A pdb=" N ILE A 304 " --> pdb=" O PRO A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 removed outlier: 3.533A pdb=" N THR A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.538A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRP A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 359 through 362 Processing helix chain 'A' and resid 363 through 375 removed outlier: 3.645A pdb=" N GLN A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 389 removed outlier: 3.694A pdb=" N VAL A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 removed outlier: 3.725A pdb=" N VAL B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B 33 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 34 " --> pdb=" O VAL B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.565A pdb=" N MET B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG B 51 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 72 removed outlier: 3.727A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 72 " --> pdb=" O ALA B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 96 removed outlier: 3.533A pdb=" N ARG B 96 " --> pdb=" O ASP B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 118 removed outlier: 3.687A pdb=" N LEU B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 removed outlier: 3.896A pdb=" N ALA B 196 " --> pdb=" O SER B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 217 removed outlier: 3.650A pdb=" N ASP B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 Processing helix chain 'B' and resid 282 through 298 removed outlier: 3.703A pdb=" N ARG B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 removed outlier: 3.657A pdb=" N ILE B 304 " --> pdb=" O PRO B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 326 removed outlier: 3.515A pdb=" N ARG B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 342 removed outlier: 3.509A pdb=" N ALA B 336 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 359 through 362 Processing helix chain 'B' and resid 363 through 375 removed outlier: 3.639A pdb=" N GLN B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 389 removed outlier: 4.335A pdb=" N LEU B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 23 removed outlier: 3.817A pdb=" N ASP D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 55 removed outlier: 3.887A pdb=" N LEU D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 147 removed outlier: 3.612A pdb=" N ALA D 146 " --> pdb=" O SER D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 165 removed outlier: 3.733A pdb=" N GLN D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 185 removed outlier: 3.703A pdb=" N LEU D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 17 removed outlier: 3.866A pdb=" N GLN F 10 " --> pdb=" O ALA F 6 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA F 11 " --> pdb=" O GLY F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 removed outlier: 3.718A pdb=" N ALA F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 85 removed outlier: 3.593A pdb=" N ARG G 80 " --> pdb=" O ASP G 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 25 removed outlier: 3.809A pdb=" N ASP H 21 " --> pdb=" O ALA H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 55 removed outlier: 3.753A pdb=" N ALA H 45 " --> pdb=" O SER H 41 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY H 52 " --> pdb=" O ALA H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 147 removed outlier: 3.560A pdb=" N ALA H 146 " --> pdb=" O SER H 143 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU H 147 " --> pdb=" O TRP H 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 143 through 147' Processing helix chain 'H' and resid 148 through 165 removed outlier: 3.749A pdb=" N GLN H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 185 removed outlier: 3.678A pdb=" N LEU H 183 " --> pdb=" O GLY H 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 35 removed outlier: 3.727A pdb=" N ILE I 29 " --> pdb=" O VAL I 25 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET I 32 " --> pdb=" O ARG I 28 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA I 33 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER I 34 " --> pdb=" O VAL I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 46 No H-bonds generated for 'chain 'I' and resid 44 through 46' Processing helix chain 'I' and resid 47 through 54 removed outlier: 4.183A pdb=" N ARG I 51 " --> pdb=" O VAL I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 72 removed outlier: 3.725A pdb=" N VAL I 64 " --> pdb=" O GLY I 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA I 70 " --> pdb=" O LEU I 66 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA I 72 " --> pdb=" O ALA I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 96 removed outlier: 3.522A pdb=" N ARG I 96 " --> pdb=" O ASP I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 118 removed outlier: 3.662A pdb=" N LEU I 116 " --> pdb=" O GLY I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 197 removed outlier: 3.817A pdb=" N ALA I 196 " --> pdb=" O SER I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 217 removed outlier: 3.691A pdb=" N ASP I 202 " --> pdb=" O ALA I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 250 Processing helix chain 'I' and resid 282 through 298 removed outlier: 3.536A pdb=" N ARG I 291 " --> pdb=" O ALA I 287 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA I 294 " --> pdb=" O ALA I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 305 removed outlier: 3.667A pdb=" N ILE I 304 " --> pdb=" O PRO I 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 317 through 326 removed outlier: 3.533A pdb=" N THR I 326 " --> pdb=" O PHE I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 342 removed outlier: 3.537A pdb=" N ALA I 337 " --> pdb=" O ARG I 333 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TRP I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 343 through 345 No H-bonds generated for 'chain 'I' and resid 343 through 345' Processing helix chain 'I' and resid 359 through 362 Processing helix chain 'I' and resid 363 through 375 removed outlier: 3.645A pdb=" N GLN I 368 " --> pdb=" O VAL I 364 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU I 369 " --> pdb=" O GLU I 365 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG I 372 " --> pdb=" O GLN I 368 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 389 removed outlier: 3.694A pdb=" N VAL I 386 " --> pdb=" O SER I 382 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU I 387 " --> pdb=" O GLU I 383 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 35 removed outlier: 3.725A pdb=" N VAL J 30 " --> pdb=" O THR J 26 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA J 33 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER J 34 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 54 removed outlier: 3.565A pdb=" N MET J 50 " --> pdb=" O THR J 46 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG J 51 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 72 removed outlier: 3.727A pdb=" N VAL J 64 " --> pdb=" O GLY J 60 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA J 70 " --> pdb=" O LEU J 66 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA J 72 " --> pdb=" O ALA J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 96 removed outlier: 3.533A pdb=" N ARG J 96 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 118 removed outlier: 3.687A pdb=" N LEU J 116 " --> pdb=" O GLY J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 192 through 197 removed outlier: 3.896A pdb=" N ALA J 196 " --> pdb=" O SER J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 217 removed outlier: 3.650A pdb=" N ASP J 202 " --> pdb=" O ALA J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 250 Processing helix chain 'J' and resid 282 through 298 removed outlier: 3.703A pdb=" N ARG J 291 " --> pdb=" O ALA J 287 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA J 294 " --> pdb=" O ALA J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 305 removed outlier: 3.657A pdb=" N ILE J 304 " --> pdb=" O PRO J 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 326 removed outlier: 3.515A pdb=" N ARG J 324 " --> pdb=" O ARG J 320 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR J 326 " --> pdb=" O PHE J 322 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 342 removed outlier: 3.509A pdb=" N ALA J 336 " --> pdb=" O THR J 332 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP J 340 " --> pdb=" O ALA J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 345 No H-bonds generated for 'chain 'J' and resid 343 through 345' Processing helix chain 'J' and resid 359 through 362 Processing helix chain 'J' and resid 363 through 375 removed outlier: 3.639A pdb=" N GLN J 368 " --> pdb=" O VAL J 364 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU J 369 " --> pdb=" O GLU J 365 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG J 372 " --> pdb=" O GLN J 368 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE J 373 " --> pdb=" O LEU J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 381 through 389 removed outlier: 4.335A pdb=" N LEU J 387 " --> pdb=" O GLU J 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 23 removed outlier: 3.817A pdb=" N ASP K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 55 removed outlier: 3.887A pdb=" N LEU K 40 " --> pdb=" O ASP K 36 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER K 41 " --> pdb=" O ALA K 37 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA K 45 " --> pdb=" O SER K 41 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 147 removed outlier: 3.611A pdb=" N ALA K 146 " --> pdb=" O SER K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 165 removed outlier: 3.733A pdb=" N GLN K 161 " --> pdb=" O LEU K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 185 removed outlier: 3.703A pdb=" N LEU K 183 " --> pdb=" O GLY K 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 17 removed outlier: 3.866A pdb=" N GLN L 10 " --> pdb=" O ALA L 6 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA L 11 " --> pdb=" O GLY L 7 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 93 removed outlier: 3.718A pdb=" N ALA L 83 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 85 removed outlier: 3.593A pdb=" N ARG N 80 " --> pdb=" O ASP N 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 25 removed outlier: 3.809A pdb=" N ASP O 21 " --> pdb=" O ALA O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 55 removed outlier: 3.753A pdb=" N ALA O 45 " --> pdb=" O SER O 41 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY O 52 " --> pdb=" O ALA O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 147 removed outlier: 3.560A pdb=" N ALA O 146 " --> pdb=" O SER O 143 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU O 147 " --> pdb=" O TRP O 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 143 through 147' Processing helix chain 'O' and resid 148 through 165 removed outlier: 3.749A pdb=" N GLN O 161 " --> pdb=" O LEU O 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 185 removed outlier: 3.678A pdb=" N LEU O 183 " --> pdb=" O GLY O 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 35 removed outlier: 3.727A pdb=" N ILE P 29 " --> pdb=" O VAL P 25 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET P 32 " --> pdb=" O ARG P 28 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA P 33 " --> pdb=" O ILE P 29 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER P 34 " --> pdb=" O VAL P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 46 No H-bonds generated for 'chain 'P' and resid 44 through 46' Processing helix chain 'P' and resid 47 through 54 removed outlier: 4.183A pdb=" N ARG P 51 " --> pdb=" O VAL P 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 72 removed outlier: 3.725A pdb=" N VAL P 64 " --> pdb=" O GLY P 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA P 70 " --> pdb=" O LEU P 66 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA P 72 " --> pdb=" O ALA P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 96 removed outlier: 3.522A pdb=" N ARG P 96 " --> pdb=" O ASP P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 118 removed outlier: 3.662A pdb=" N LEU P 116 " --> pdb=" O GLY P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 197 removed outlier: 3.817A pdb=" N ALA P 196 " --> pdb=" O SER P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 197 through 217 removed outlier: 3.691A pdb=" N ASP P 202 " --> pdb=" O ALA P 198 " (cutoff:3.500A) Processing helix chain 'P' and resid 237 through 250 Processing helix chain 'P' and resid 282 through 298 removed outlier: 3.536A pdb=" N ARG P 291 " --> pdb=" O ALA P 287 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA P 294 " --> pdb=" O ALA P 290 " (cutoff:3.500A) Processing helix chain 'P' and resid 300 through 305 removed outlier: 3.667A pdb=" N ILE P 304 " --> pdb=" O PRO P 300 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 326 removed outlier: 3.533A pdb=" N THR P 326 " --> pdb=" O PHE P 322 " (cutoff:3.500A) Processing helix chain 'P' and resid 327 through 342 removed outlier: 3.538A pdb=" N ALA P 337 " --> pdb=" O ARG P 333 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TRP P 340 " --> pdb=" O ALA P 336 " (cutoff:3.500A) Processing helix chain 'P' and resid 343 through 345 No H-bonds generated for 'chain 'P' and resid 343 through 345' Processing helix chain 'P' and resid 359 through 362 Processing helix chain 'P' and resid 363 through 375 removed outlier: 3.645A pdb=" N GLN P 368 " --> pdb=" O VAL P 364 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU P 369 " --> pdb=" O GLU P 365 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG P 372 " --> pdb=" O GLN P 368 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE P 373 " --> pdb=" O LEU P 369 " (cutoff:3.500A) Processing helix chain 'P' and resid 381 through 389 removed outlier: 3.694A pdb=" N VAL P 386 " --> pdb=" O SER P 382 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU P 387 " --> pdb=" O GLU P 383 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 35 removed outlier: 3.725A pdb=" N VAL Q 30 " --> pdb=" O THR Q 26 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET Q 32 " --> pdb=" O ARG Q 28 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA Q 33 " --> pdb=" O ILE Q 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER Q 34 " --> pdb=" O VAL Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 54 removed outlier: 3.565A pdb=" N MET Q 50 " --> pdb=" O THR Q 46 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG Q 51 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 72 removed outlier: 3.727A pdb=" N VAL Q 64 " --> pdb=" O GLY Q 60 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA Q 70 " --> pdb=" O LEU Q 66 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 96 removed outlier: 3.533A pdb=" N ARG Q 96 " --> pdb=" O ASP Q 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 118 removed outlier: 3.686A pdb=" N LEU Q 116 " --> pdb=" O GLY Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 192 through 197 removed outlier: 3.896A pdb=" N ALA Q 196 " --> pdb=" O SER Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 197 through 217 removed outlier: 3.650A pdb=" N ASP Q 202 " --> pdb=" O ALA Q 198 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 250 Processing helix chain 'Q' and resid 282 through 298 removed outlier: 3.703A pdb=" N ARG Q 291 " --> pdb=" O ALA Q 287 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA Q 294 " --> pdb=" O ALA Q 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 300 through 305 removed outlier: 3.657A pdb=" N ILE Q 304 " --> pdb=" O PRO Q 300 " (cutoff:3.500A) Processing helix chain 'Q' and resid 317 through 326 removed outlier: 3.515A pdb=" N ARG Q 324 " --> pdb=" O ARG Q 320 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR Q 326 " --> pdb=" O PHE Q 322 " (cutoff:3.500A) Processing helix chain 'Q' and resid 327 through 342 removed outlier: 3.509A pdb=" N ALA Q 336 " --> pdb=" O THR Q 332 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP Q 340 " --> pdb=" O ALA Q 336 " (cutoff:3.500A) Processing helix chain 'Q' and resid 343 through 345 No H-bonds generated for 'chain 'Q' and resid 343 through 345' Processing helix chain 'Q' and resid 359 through 362 Processing helix chain 'Q' and resid 363 through 375 removed outlier: 3.639A pdb=" N GLN Q 368 " --> pdb=" O VAL Q 364 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU Q 369 " --> pdb=" O GLU Q 365 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG Q 372 " --> pdb=" O GLN Q 368 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE Q 373 " --> pdb=" O LEU Q 369 " (cutoff:3.500A) Processing helix chain 'Q' and resid 381 through 389 removed outlier: 4.335A pdb=" N LEU Q 387 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 23 removed outlier: 3.817A pdb=" N ASP R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 55 removed outlier: 3.888A pdb=" N LEU R 40 " --> pdb=" O ASP R 36 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER R 41 " --> pdb=" O ALA R 37 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY R 52 " --> pdb=" O ALA R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 147 removed outlier: 3.612A pdb=" N ALA R 146 " --> pdb=" O SER R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 165 removed outlier: 3.733A pdb=" N GLN R 161 " --> pdb=" O LEU R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 185 removed outlier: 3.703A pdb=" N LEU R 183 " --> pdb=" O GLY R 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 17 removed outlier: 3.866A pdb=" N GLN S 10 " --> pdb=" O ALA S 6 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA S 11 " --> pdb=" O GLY S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 93 removed outlier: 3.718A pdb=" N ALA S 83 " --> pdb=" O ALA S 79 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 85 removed outlier: 3.593A pdb=" N ARG U 80 " --> pdb=" O ASP U 76 " (cutoff:3.500A) Processing helix chain 'V' and resid 15 through 25 removed outlier: 3.809A pdb=" N ASP V 21 " --> pdb=" O ALA V 17 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 55 removed outlier: 3.753A pdb=" N ALA V 45 " --> pdb=" O SER V 41 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY V 52 " --> pdb=" O ALA V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 143 through 147 removed outlier: 3.560A pdb=" N ALA V 146 " --> pdb=" O SER V 143 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU V 147 " --> pdb=" O TRP V 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 143 through 147' Processing helix chain 'V' and resid 148 through 165 removed outlier: 3.749A pdb=" N GLN V 161 " --> pdb=" O LEU V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 179 through 185 removed outlier: 3.678A pdb=" N LEU V 183 " --> pdb=" O GLY V 179 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 35 removed outlier: 3.727A pdb=" N ILE W 29 " --> pdb=" O VAL W 25 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET W 32 " --> pdb=" O ARG W 28 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA W 33 " --> pdb=" O ILE W 29 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER W 34 " --> pdb=" O VAL W 30 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 46 No H-bonds generated for 'chain 'W' and resid 44 through 46' Processing helix chain 'W' and resid 47 through 54 removed outlier: 4.183A pdb=" N ARG W 51 " --> pdb=" O VAL W 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 57 through 72 removed outlier: 3.725A pdb=" N VAL W 64 " --> pdb=" O GLY W 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA W 70 " --> pdb=" O LEU W 66 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA W 72 " --> pdb=" O ALA W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 90 through 96 removed outlier: 3.522A pdb=" N ARG W 96 " --> pdb=" O ASP W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 102 through 118 removed outlier: 3.662A pdb=" N LEU W 116 " --> pdb=" O GLY W 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 192 through 197 removed outlier: 3.817A pdb=" N ALA W 196 " --> pdb=" O SER W 192 " (cutoff:3.500A) Processing helix chain 'W' and resid 197 through 217 removed outlier: 3.691A pdb=" N ASP W 202 " --> pdb=" O ALA W 198 " (cutoff:3.500A) Processing helix chain 'W' and resid 237 through 250 Processing helix chain 'W' and resid 282 through 298 removed outlier: 3.536A pdb=" N ARG W 291 " --> pdb=" O ALA W 287 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA W 294 " --> pdb=" O ALA W 290 " (cutoff:3.500A) Processing helix chain 'W' and resid 300 through 305 removed outlier: 3.667A pdb=" N ILE W 304 " --> pdb=" O PRO W 300 " (cutoff:3.500A) Processing helix chain 'W' and resid 317 through 326 removed outlier: 3.533A pdb=" N THR W 326 " --> pdb=" O PHE W 322 " (cutoff:3.500A) Processing helix chain 'W' and resid 327 through 342 removed outlier: 3.538A pdb=" N ALA W 337 " --> pdb=" O ARG W 333 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRP W 340 " --> pdb=" O ALA W 336 " (cutoff:3.500A) Processing helix chain 'W' and resid 343 through 345 No H-bonds generated for 'chain 'W' and resid 343 through 345' Processing helix chain 'W' and resid 359 through 362 Processing helix chain 'W' and resid 363 through 375 removed outlier: 3.645A pdb=" N GLN W 368 " --> pdb=" O VAL W 364 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU W 369 " --> pdb=" O GLU W 365 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG W 372 " --> pdb=" O GLN W 368 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE W 373 " --> pdb=" O LEU W 369 " (cutoff:3.500A) Processing helix chain 'W' and resid 381 through 389 removed outlier: 3.694A pdb=" N VAL W 386 " --> pdb=" O SER W 382 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU W 387 " --> pdb=" O GLU W 383 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 35 removed outlier: 3.725A pdb=" N VAL X 30 " --> pdb=" O THR X 26 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET X 32 " --> pdb=" O ARG X 28 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA X 33 " --> pdb=" O ILE X 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER X 34 " --> pdb=" O VAL X 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 45 through 54 removed outlier: 3.565A pdb=" N MET X 50 " --> pdb=" O THR X 46 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG X 51 " --> pdb=" O VAL X 47 " (cutoff:3.500A) Processing helix chain 'X' and resid 57 through 72 removed outlier: 3.727A pdb=" N VAL X 64 " --> pdb=" O GLY X 60 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA X 70 " --> pdb=" O LEU X 66 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA X 72 " --> pdb=" O ALA X 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 90 through 96 removed outlier: 3.533A pdb=" N ARG X 96 " --> pdb=" O ASP X 92 " (cutoff:3.500A) Processing helix chain 'X' and resid 102 through 118 removed outlier: 3.687A pdb=" N LEU X 116 " --> pdb=" O GLY X 112 " (cutoff:3.500A) Processing helix chain 'X' and resid 192 through 197 removed outlier: 3.896A pdb=" N ALA X 196 " --> pdb=" O SER X 192 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 217 removed outlier: 3.650A pdb=" N ASP X 202 " --> pdb=" O ALA X 198 " (cutoff:3.500A) Processing helix chain 'X' and resid 237 through 250 Processing helix chain 'X' and resid 282 through 298 removed outlier: 3.703A pdb=" N ARG X 291 " --> pdb=" O ALA X 287 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA X 294 " --> pdb=" O ALA X 290 " (cutoff:3.500A) Processing helix chain 'X' and resid 300 through 305 removed outlier: 3.657A pdb=" N ILE X 304 " --> pdb=" O PRO X 300 " (cutoff:3.500A) Processing helix chain 'X' and resid 317 through 326 removed outlier: 3.515A pdb=" N ARG X 324 " --> pdb=" O ARG X 320 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR X 326 " --> pdb=" O PHE X 322 " (cutoff:3.500A) Processing helix chain 'X' and resid 327 through 342 removed outlier: 3.509A pdb=" N ALA X 336 " --> pdb=" O THR X 332 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP X 340 " --> pdb=" O ALA X 336 " (cutoff:3.500A) Processing helix chain 'X' and resid 343 through 345 No H-bonds generated for 'chain 'X' and resid 343 through 345' Processing helix chain 'X' and resid 359 through 362 Processing helix chain 'X' and resid 363 through 375 removed outlier: 3.639A pdb=" N GLN X 368 " --> pdb=" O VAL X 364 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU X 369 " --> pdb=" O GLU X 365 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG X 372 " --> pdb=" O GLN X 368 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE X 373 " --> pdb=" O LEU X 369 " (cutoff:3.500A) Processing helix chain 'X' and resid 381 through 389 removed outlier: 4.335A pdb=" N LEU X 387 " --> pdb=" O GLU X 383 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 23 removed outlier: 3.817A pdb=" N ASP Y 21 " --> pdb=" O ALA Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 55 removed outlier: 3.887A pdb=" N LEU Y 40 " --> pdb=" O ASP Y 36 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER Y 41 " --> pdb=" O ALA Y 37 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA Y 45 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA Y 49 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY Y 52 " --> pdb=" O ALA Y 48 " (cutoff:3.500A) Processing helix chain 'Y' and resid 143 through 147 removed outlier: 3.612A pdb=" N ALA Y 146 " --> pdb=" O SER Y 143 " (cutoff:3.500A) Processing helix chain 'Y' and resid 148 through 165 removed outlier: 3.733A pdb=" N GLN Y 161 " --> pdb=" O LEU Y 157 " (cutoff:3.500A) Processing helix chain 'Y' and resid 179 through 185 removed outlier: 3.703A pdb=" N LEU Y 183 " --> pdb=" O GLY Y 179 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 17 removed outlier: 3.866A pdb=" N GLN Z 10 " --> pdb=" O ALA Z 6 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA Z 11 " --> pdb=" O GLY Z 7 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 93 removed outlier: 3.718A pdb=" N ALA Z 83 " --> pdb=" O ALA Z 79 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 85 removed outlier: 3.593A pdb=" N ARG 1 80 " --> pdb=" O ASP 1 76 " (cutoff:3.500A) Processing helix chain '2' and resid 15 through 25 removed outlier: 3.809A pdb=" N ASP 2 21 " --> pdb=" O ALA 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 35 through 55 removed outlier: 3.753A pdb=" N ALA 2 45 " --> pdb=" O SER 2 41 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY 2 52 " --> pdb=" O ALA 2 48 " (cutoff:3.500A) Processing helix chain '2' and resid 143 through 147 removed outlier: 3.560A pdb=" N ALA 2 146 " --> pdb=" O SER 2 143 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU 2 147 " --> pdb=" O TRP 2 144 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 143 through 147' Processing helix chain '2' and resid 148 through 165 removed outlier: 3.749A pdb=" N GLN 2 161 " --> pdb=" O LEU 2 157 " (cutoff:3.500A) Processing helix chain '2' and resid 179 through 185 removed outlier: 3.678A pdb=" N LEU 2 183 " --> pdb=" O GLY 2 179 " (cutoff:3.500A) Processing helix chain '3' and resid 25 through 35 removed outlier: 3.727A pdb=" N ILE 3 29 " --> pdb=" O VAL 3 25 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET 3 32 " --> pdb=" O ARG 3 28 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA 3 33 " --> pdb=" O ILE 3 29 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER 3 34 " --> pdb=" O VAL 3 30 " (cutoff:3.500A) Processing helix chain '3' and resid 44 through 46 No H-bonds generated for 'chain '3' and resid 44 through 46' Processing helix chain '3' and resid 47 through 54 removed outlier: 4.183A pdb=" N ARG 3 51 " --> pdb=" O VAL 3 47 " (cutoff:3.500A) Processing helix chain '3' and resid 57 through 72 removed outlier: 3.725A pdb=" N VAL 3 64 " --> pdb=" O GLY 3 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA 3 70 " --> pdb=" O LEU 3 66 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA 3 72 " --> pdb=" O ALA 3 68 " (cutoff:3.500A) Processing helix chain '3' and resid 90 through 96 removed outlier: 3.522A pdb=" N ARG 3 96 " --> pdb=" O ASP 3 92 " (cutoff:3.500A) Processing helix chain '3' and resid 102 through 118 removed outlier: 3.662A pdb=" N LEU 3 116 " --> pdb=" O GLY 3 112 " (cutoff:3.500A) Processing helix chain '3' and resid 192 through 197 removed outlier: 3.817A pdb=" N ALA 3 196 " --> pdb=" O SER 3 192 " (cutoff:3.500A) Processing helix chain '3' and resid 197 through 217 removed outlier: 3.691A pdb=" N ASP 3 202 " --> pdb=" O ALA 3 198 " (cutoff:3.500A) Processing helix chain '3' and resid 237 through 250 Processing helix chain '3' and resid 282 through 298 removed outlier: 3.536A pdb=" N ARG 3 291 " --> pdb=" O ALA 3 287 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA 3 294 " --> pdb=" O ALA 3 290 " (cutoff:3.500A) Processing helix chain '3' and resid 300 through 305 removed outlier: 3.667A pdb=" N ILE 3 304 " --> pdb=" O PRO 3 300 " (cutoff:3.500A) Processing helix chain '3' and resid 317 through 326 removed outlier: 3.533A pdb=" N THR 3 326 " --> pdb=" O PHE 3 322 " (cutoff:3.500A) Processing helix chain '3' and resid 327 through 342 removed outlier: 3.537A pdb=" N ALA 3 337 " --> pdb=" O ARG 3 333 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TRP 3 340 " --> pdb=" O ALA 3 336 " (cutoff:3.500A) Processing helix chain '3' and resid 343 through 345 No H-bonds generated for 'chain '3' and resid 343 through 345' Processing helix chain '3' and resid 359 through 362 Processing helix chain '3' and resid 363 through 375 removed outlier: 3.645A pdb=" N GLN 3 368 " --> pdb=" O VAL 3 364 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU 3 369 " --> pdb=" O GLU 3 365 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG 3 372 " --> pdb=" O GLN 3 368 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE 3 373 " --> pdb=" O LEU 3 369 " (cutoff:3.500A) Processing helix chain '3' and resid 381 through 389 removed outlier: 3.694A pdb=" N VAL 3 386 " --> pdb=" O SER 3 382 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU 3 387 " --> pdb=" O GLU 3 383 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 35 removed outlier: 3.725A pdb=" N VAL 4 30 " --> pdb=" O THR 4 26 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET 4 32 " --> pdb=" O ARG 4 28 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA 4 33 " --> pdb=" O ILE 4 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER 4 34 " --> pdb=" O VAL 4 30 " (cutoff:3.500A) Processing helix chain '4' and resid 45 through 54 removed outlier: 3.565A pdb=" N MET 4 50 " --> pdb=" O THR 4 46 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG 4 51 " --> pdb=" O VAL 4 47 " (cutoff:3.500A) Processing helix chain '4' and resid 57 through 72 removed outlier: 3.727A pdb=" N VAL 4 64 " --> pdb=" O GLY 4 60 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA 4 70 " --> pdb=" O LEU 4 66 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA 4 72 " --> pdb=" O ALA 4 68 " (cutoff:3.500A) Processing helix chain '4' and resid 90 through 96 removed outlier: 3.533A pdb=" N ARG 4 96 " --> pdb=" O ASP 4 92 " (cutoff:3.500A) Processing helix chain '4' and resid 102 through 118 removed outlier: 3.687A pdb=" N LEU 4 116 " --> pdb=" O GLY 4 112 " (cutoff:3.500A) Processing helix chain '4' and resid 192 through 197 removed outlier: 3.896A pdb=" N ALA 4 196 " --> pdb=" O SER 4 192 " (cutoff:3.500A) Processing helix chain '4' and resid 197 through 217 removed outlier: 3.650A pdb=" N ASP 4 202 " --> pdb=" O ALA 4 198 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 250 Processing helix chain '4' and resid 282 through 298 removed outlier: 3.703A pdb=" N ARG 4 291 " --> pdb=" O ALA 4 287 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA 4 294 " --> pdb=" O ALA 4 290 " (cutoff:3.500A) Processing helix chain '4' and resid 300 through 305 removed outlier: 3.657A pdb=" N ILE 4 304 " --> pdb=" O PRO 4 300 " (cutoff:3.500A) Processing helix chain '4' and resid 317 through 326 removed outlier: 3.515A pdb=" N ARG 4 324 " --> pdb=" O ARG 4 320 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR 4 326 " --> pdb=" O PHE 4 322 " (cutoff:3.500A) Processing helix chain '4' and resid 327 through 342 removed outlier: 3.509A pdb=" N ALA 4 336 " --> pdb=" O THR 4 332 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP 4 340 " --> pdb=" O ALA 4 336 " (cutoff:3.500A) Processing helix chain '4' and resid 343 through 345 No H-bonds generated for 'chain '4' and resid 343 through 345' Processing helix chain '4' and resid 359 through 362 Processing helix chain '4' and resid 363 through 375 removed outlier: 3.639A pdb=" N GLN 4 368 " --> pdb=" O VAL 4 364 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU 4 369 " --> pdb=" O GLU 4 365 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG 4 372 " --> pdb=" O GLN 4 368 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE 4 373 " --> pdb=" O LEU 4 369 " (cutoff:3.500A) Processing helix chain '4' and resid 381 through 389 removed outlier: 4.335A pdb=" N LEU 4 387 " --> pdb=" O GLU 4 383 " (cutoff:3.500A) Processing helix chain '5' and resid 15 through 23 removed outlier: 3.817A pdb=" N ASP 5 21 " --> pdb=" O ALA 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 35 through 55 removed outlier: 3.887A pdb=" N LEU 5 40 " --> pdb=" O ASP 5 36 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER 5 41 " --> pdb=" O ALA 5 37 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA 5 45 " --> pdb=" O SER 5 41 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY 5 52 " --> pdb=" O ALA 5 48 " (cutoff:3.500A) Processing helix chain '5' and resid 143 through 147 removed outlier: 3.611A pdb=" N ALA 5 146 " --> pdb=" O SER 5 143 " (cutoff:3.500A) Processing helix chain '5' and resid 148 through 165 removed outlier: 3.733A pdb=" N GLN 5 161 " --> pdb=" O LEU 5 157 " (cutoff:3.500A) Processing helix chain '5' and resid 179 through 185 removed outlier: 3.703A pdb=" N LEU 5 183 " --> pdb=" O GLY 5 179 " (cutoff:3.500A) Processing helix chain '6' and resid 5 through 17 removed outlier: 3.866A pdb=" N GLN 6 10 " --> pdb=" O ALA 6 6 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA 6 11 " --> pdb=" O GLY 6 7 " (cutoff:3.500A) Processing helix chain '6' and resid 79 through 93 removed outlier: 3.718A pdb=" N ALA 6 83 " --> pdb=" O ALA 6 79 " (cutoff:3.500A) Processing helix chain '8' and resid 75 through 85 removed outlier: 3.593A pdb=" N ARG 8 80 " --> pdb=" O ASP 8 76 " (cutoff:3.500A) Processing helix chain '9' and resid 15 through 25 removed outlier: 3.809A pdb=" N ASP 9 21 " --> pdb=" O ALA 9 17 " (cutoff:3.500A) Processing helix chain '9' and resid 35 through 55 removed outlier: 3.753A pdb=" N ALA 9 45 " --> pdb=" O SER 9 41 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY 9 52 " --> pdb=" O ALA 9 48 " (cutoff:3.500A) Processing helix chain '9' and resid 143 through 147 removed outlier: 3.560A pdb=" N ALA 9 146 " --> pdb=" O SER 9 143 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU 9 147 " --> pdb=" O TRP 9 144 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 143 through 147' Processing helix chain '9' and resid 148 through 165 removed outlier: 3.749A pdb=" N GLN 9 161 " --> pdb=" O LEU 9 157 " (cutoff:3.500A) Processing helix chain '9' and resid 179 through 185 removed outlier: 3.678A pdb=" N LEU 9 183 " --> pdb=" O GLY 9 179 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 35 removed outlier: 3.727A pdb=" N ILE a 29 " --> pdb=" O VAL a 25 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET a 32 " --> pdb=" O ARG a 28 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA a 33 " --> pdb=" O ILE a 29 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER a 34 " --> pdb=" O VAL a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 46 No H-bonds generated for 'chain 'a' and resid 44 through 46' Processing helix chain 'a' and resid 47 through 54 removed outlier: 4.183A pdb=" N ARG a 51 " --> pdb=" O VAL a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 72 removed outlier: 3.725A pdb=" N VAL a 64 " --> pdb=" O GLY a 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA a 70 " --> pdb=" O LEU a 66 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA a 72 " --> pdb=" O ALA a 68 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 96 removed outlier: 3.522A pdb=" N ARG a 96 " --> pdb=" O ASP a 92 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 118 removed outlier: 3.662A pdb=" N LEU a 116 " --> pdb=" O GLY a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 192 through 197 removed outlier: 3.817A pdb=" N ALA a 196 " --> pdb=" O SER a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 197 through 217 removed outlier: 3.691A pdb=" N ASP a 202 " --> pdb=" O ALA a 198 " (cutoff:3.500A) Processing helix chain 'a' and resid 237 through 250 Processing helix chain 'a' and resid 282 through 298 removed outlier: 3.536A pdb=" N ARG a 291 " --> pdb=" O ALA a 287 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA a 294 " --> pdb=" O ALA a 290 " (cutoff:3.500A) Processing helix chain 'a' and resid 300 through 305 removed outlier: 3.667A pdb=" N ILE a 304 " --> pdb=" O PRO a 300 " (cutoff:3.500A) Processing helix chain 'a' and resid 317 through 326 removed outlier: 3.533A pdb=" N THR a 326 " --> pdb=" O PHE a 322 " (cutoff:3.500A) Processing helix chain 'a' and resid 327 through 342 removed outlier: 3.538A pdb=" N ALA a 337 " --> pdb=" O ARG a 333 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TRP a 340 " --> pdb=" O ALA a 336 " (cutoff:3.500A) Processing helix chain 'a' and resid 343 through 345 No H-bonds generated for 'chain 'a' and resid 343 through 345' Processing helix chain 'a' and resid 359 through 362 Processing helix chain 'a' and resid 363 through 375 removed outlier: 3.645A pdb=" N GLN a 368 " --> pdb=" O VAL a 364 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU a 369 " --> pdb=" O GLU a 365 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG a 372 " --> pdb=" O GLN a 368 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE a 373 " --> pdb=" O LEU a 369 " (cutoff:3.500A) Processing helix chain 'a' and resid 381 through 389 removed outlier: 3.694A pdb=" N VAL a 386 " --> pdb=" O SER a 382 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU a 387 " --> pdb=" O GLU a 383 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 35 removed outlier: 3.725A pdb=" N VAL b 30 " --> pdb=" O THR b 26 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET b 32 " --> pdb=" O ARG b 28 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA b 33 " --> pdb=" O ILE b 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER b 34 " --> pdb=" O VAL b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 45 through 54 removed outlier: 3.565A pdb=" N MET b 50 " --> pdb=" O THR b 46 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG b 51 " --> pdb=" O VAL b 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 72 removed outlier: 3.727A pdb=" N VAL b 64 " --> pdb=" O GLY b 60 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA b 70 " --> pdb=" O LEU b 66 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA b 72 " --> pdb=" O ALA b 68 " (cutoff:3.500A) Processing helix chain 'b' and resid 90 through 96 removed outlier: 3.533A pdb=" N ARG b 96 " --> pdb=" O ASP b 92 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 118 removed outlier: 3.686A pdb=" N LEU b 116 " --> pdb=" O GLY b 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 192 through 197 removed outlier: 3.896A pdb=" N ALA b 196 " --> pdb=" O SER b 192 " (cutoff:3.500A) Processing helix chain 'b' and resid 197 through 217 removed outlier: 3.650A pdb=" N ASP b 202 " --> pdb=" O ALA b 198 " (cutoff:3.500A) Processing helix chain 'b' and resid 237 through 250 Processing helix chain 'b' and resid 282 through 298 removed outlier: 3.703A pdb=" N ARG b 291 " --> pdb=" O ALA b 287 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA b 294 " --> pdb=" O ALA b 290 " (cutoff:3.500A) Processing helix chain 'b' and resid 300 through 305 removed outlier: 3.657A pdb=" N ILE b 304 " --> pdb=" O PRO b 300 " (cutoff:3.500A) Processing helix chain 'b' and resid 317 through 326 removed outlier: 3.515A pdb=" N ARG b 324 " --> pdb=" O ARG b 320 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR b 326 " --> pdb=" O PHE b 322 " (cutoff:3.500A) Processing helix chain 'b' and resid 327 through 342 removed outlier: 3.509A pdb=" N ALA b 336 " --> pdb=" O THR b 332 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP b 340 " --> pdb=" O ALA b 336 " (cutoff:3.500A) Processing helix chain 'b' and resid 343 through 345 No H-bonds generated for 'chain 'b' and resid 343 through 345' Processing helix chain 'b' and resid 359 through 362 Processing helix chain 'b' and resid 363 through 375 removed outlier: 3.639A pdb=" N GLN b 368 " --> pdb=" O VAL b 364 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU b 369 " --> pdb=" O GLU b 365 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG b 372 " --> pdb=" O GLN b 368 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE b 373 " --> pdb=" O LEU b 369 " (cutoff:3.500A) Processing helix chain 'b' and resid 381 through 389 removed outlier: 4.335A pdb=" N LEU b 387 " --> pdb=" O GLU b 383 " (cutoff:3.500A) Processing helix chain 'c' and resid 15 through 23 removed outlier: 3.817A pdb=" N ASP c 21 " --> pdb=" O ALA c 17 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 55 removed outlier: 3.888A pdb=" N LEU c 40 " --> pdb=" O ASP c 36 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER c 41 " --> pdb=" O ALA c 37 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA c 45 " --> pdb=" O SER c 41 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY c 52 " --> pdb=" O ALA c 48 " (cutoff:3.500A) Processing helix chain 'c' and resid 143 through 147 removed outlier: 3.612A pdb=" N ALA c 146 " --> pdb=" O SER c 143 " (cutoff:3.500A) Processing helix chain 'c' and resid 148 through 165 removed outlier: 3.733A pdb=" N GLN c 161 " --> pdb=" O LEU c 157 " (cutoff:3.500A) Processing helix chain 'c' and resid 179 through 185 removed outlier: 3.703A pdb=" N LEU c 183 " --> pdb=" O GLY c 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 17 removed outlier: 3.866A pdb=" N GLN d 10 " --> pdb=" O ALA d 6 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA d 11 " --> pdb=" O GLY d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 79 through 93 removed outlier: 3.718A pdb=" N ALA d 83 " --> pdb=" O ALA d 79 " (cutoff:3.500A) Processing helix chain 'f' and resid 75 through 85 removed outlier: 3.593A pdb=" N ARG f 80 " --> pdb=" O ASP f 76 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.706A pdb=" N ASN C 4 " --> pdb=" O ARG C 64 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG C 61 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR C 137 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL C 86 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 76 through 77 Processing sheet with id= 3, first strand: chain 'A' and resid 134 through 137 removed outlier: 3.803A pdb=" N GLU A 134 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 125 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS A 177 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 143 through 146 removed outlier: 3.700A pdb=" N GLY A 155 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 225 through 227 Processing sheet with id= 6, first strand: chain 'B' and resid 76 through 77 removed outlier: 3.502A pdb=" N LYS B 353 " --> pdb=" O ILE B 77 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 134 through 137 removed outlier: 3.687A pdb=" N GLU B 134 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS B 177 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 143 through 146 removed outlier: 3.881A pdb=" N GLY B 155 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 225 through 227 Processing sheet with id= 10, first strand: chain 'D' and resid 4 through 5 removed outlier: 6.988A pdb=" N THR D 137 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL D 86 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 91 through 92 Processing sheet with id= 12, first strand: chain 'F' and resid 31 through 32 removed outlier: 7.266A pdb=" N TYR F 32 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ARG F 130 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU F 107 " --> pdb=" O ARG F 130 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG F 132 " --> pdb=" O VAL F 105 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 31 through 32 removed outlier: 7.266A pdb=" N TYR F 32 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG F 123 " --> pdb=" O THR F 73 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N MET F 122 " --> pdb=" O VAL F 117 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 85 through 88 removed outlier: 3.695A pdb=" N LEU E 12 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY E 33 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLU E 14 " --> pdb=" O ALA E 31 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ALA E 31 " --> pdb=" O GLU E 14 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N TRP E 36 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG E 64 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 17 through 19 Processing sheet with id= 16, first strand: chain 'E' and resid 45 through 48 Processing sheet with id= 17, first strand: chain 'G' and resid 22 through 23 removed outlier: 3.539A pdb=" N LEU G 10 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE G 107 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA G 127 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA G 62 " --> pdb=" O SER G 128 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.706A pdb=" N ASN H 4 " --> pdb=" O ARG H 64 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG H 61 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR H 137 " --> pdb=" O VAL H 86 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL H 86 " --> pdb=" O THR H 137 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'I' and resid 76 through 77 Processing sheet with id= 20, first strand: chain 'I' and resid 134 through 137 removed outlier: 3.802A pdb=" N GLU I 134 " --> pdb=" O VAL I 125 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL I 125 " --> pdb=" O GLU I 134 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS I 177 " --> pdb=" O LEU I 122 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 143 through 146 removed outlier: 3.700A pdb=" N GLY I 155 " --> pdb=" O VAL I 146 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'I' and resid 225 through 227 Processing sheet with id= 23, first strand: chain 'J' and resid 76 through 77 removed outlier: 3.502A pdb=" N LYS J 353 " --> pdb=" O ILE J 77 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 134 through 137 removed outlier: 3.687A pdb=" N GLU J 134 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS J 177 " --> pdb=" O LEU J 122 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 143 through 146 removed outlier: 3.882A pdb=" N GLY J 155 " --> pdb=" O VAL J 146 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 225 through 227 Processing sheet with id= 27, first strand: chain 'K' and resid 4 through 5 removed outlier: 6.988A pdb=" N THR K 137 " --> pdb=" O VAL K 86 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL K 86 " --> pdb=" O THR K 137 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'K' and resid 91 through 92 Processing sheet with id= 29, first strand: chain 'L' and resid 31 through 32 removed outlier: 7.267A pdb=" N TYR L 32 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG L 130 " --> pdb=" O LEU L 107 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU L 107 " --> pdb=" O ARG L 130 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG L 132 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'L' and resid 31 through 32 removed outlier: 7.267A pdb=" N TYR L 32 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG L 123 " --> pdb=" O THR L 73 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N MET L 122 " --> pdb=" O VAL L 117 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'M' and resid 85 through 88 removed outlier: 3.695A pdb=" N LEU M 12 " --> pdb=" O GLY M 33 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY M 33 " --> pdb=" O LEU M 12 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLU M 14 " --> pdb=" O ALA M 31 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ALA M 31 " --> pdb=" O GLU M 14 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TRP M 36 " --> pdb=" O ARG M 64 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG M 64 " --> pdb=" O TRP M 36 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'M' and resid 17 through 19 Processing sheet with id= 33, first strand: chain 'M' and resid 45 through 48 Processing sheet with id= 34, first strand: chain 'N' and resid 22 through 23 removed outlier: 3.538A pdb=" N LEU N 10 " --> pdb=" O ILE N 94 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE N 107 " --> pdb=" O ALA N 127 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA N 127 " --> pdb=" O ILE N 107 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA N 62 " --> pdb=" O SER N 128 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'O' and resid 4 through 5 removed outlier: 3.706A pdb=" N ASN O 4 " --> pdb=" O ARG O 64 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG O 61 " --> pdb=" O ALA O 138 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR O 137 " --> pdb=" O VAL O 86 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL O 86 " --> pdb=" O THR O 137 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'P' and resid 76 through 77 Processing sheet with id= 37, first strand: chain 'P' and resid 134 through 137 removed outlier: 3.803A pdb=" N GLU P 134 " --> pdb=" O VAL P 125 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL P 125 " --> pdb=" O GLU P 134 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS P 177 " --> pdb=" O LEU P 122 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'P' and resid 143 through 146 removed outlier: 3.699A pdb=" N GLY P 155 " --> pdb=" O VAL P 146 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'P' and resid 225 through 227 Processing sheet with id= 40, first strand: chain 'Q' and resid 76 through 77 removed outlier: 3.502A pdb=" N LYS Q 353 " --> pdb=" O ILE Q 77 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'Q' and resid 134 through 137 removed outlier: 3.686A pdb=" N GLU Q 134 " --> pdb=" O VAL Q 125 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS Q 177 " --> pdb=" O LEU Q 122 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'Q' and resid 143 through 146 removed outlier: 3.882A pdb=" N GLY Q 155 " --> pdb=" O VAL Q 146 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Q' and resid 225 through 227 Processing sheet with id= 44, first strand: chain 'R' and resid 4 through 5 removed outlier: 6.988A pdb=" N THR R 137 " --> pdb=" O VAL R 86 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL R 86 " --> pdb=" O THR R 137 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'R' and resid 91 through 92 Processing sheet with id= 46, first strand: chain 'S' and resid 31 through 32 removed outlier: 7.266A pdb=" N TYR S 32 " --> pdb=" O LEU S 47 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG S 130 " --> pdb=" O LEU S 107 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU S 107 " --> pdb=" O ARG S 130 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ARG S 132 " --> pdb=" O VAL S 105 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'S' and resid 31 through 32 removed outlier: 7.266A pdb=" N TYR S 32 " --> pdb=" O LEU S 47 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG S 123 " --> pdb=" O THR S 73 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N MET S 122 " --> pdb=" O VAL S 117 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'T' and resid 85 through 88 removed outlier: 3.695A pdb=" N LEU T 12 " --> pdb=" O GLY T 33 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY T 33 " --> pdb=" O LEU T 12 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLU T 14 " --> pdb=" O ALA T 31 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ALA T 31 " --> pdb=" O GLU T 14 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N TRP T 36 " --> pdb=" O ARG T 64 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG T 64 " --> pdb=" O TRP T 36 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'T' and resid 17 through 19 Processing sheet with id= 50, first strand: chain 'T' and resid 45 through 48 Processing sheet with id= 51, first strand: chain 'U' and resid 22 through 23 removed outlier: 3.538A pdb=" N LEU U 10 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE U 107 " --> pdb=" O ALA U 127 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA U 127 " --> pdb=" O ILE U 107 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA U 62 " --> pdb=" O SER U 128 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'V' and resid 4 through 5 removed outlier: 3.706A pdb=" N ASN V 4 " --> pdb=" O ARG V 64 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG V 61 " --> pdb=" O ALA V 138 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR V 137 " --> pdb=" O VAL V 86 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL V 86 " --> pdb=" O THR V 137 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'W' and resid 76 through 77 Processing sheet with id= 54, first strand: chain 'W' and resid 134 through 137 removed outlier: 3.803A pdb=" N GLU W 134 " --> pdb=" O VAL W 125 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL W 125 " --> pdb=" O GLU W 134 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS W 177 " --> pdb=" O LEU W 122 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'W' and resid 143 through 146 removed outlier: 3.700A pdb=" N GLY W 155 " --> pdb=" O VAL W 146 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'W' and resid 225 through 227 Processing sheet with id= 57, first strand: chain 'X' and resid 76 through 77 removed outlier: 3.502A pdb=" N LYS X 353 " --> pdb=" O ILE X 77 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'X' and resid 134 through 137 removed outlier: 3.687A pdb=" N GLU X 134 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS X 177 " --> pdb=" O LEU X 122 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'X' and resid 143 through 146 removed outlier: 3.881A pdb=" N GLY X 155 " --> pdb=" O VAL X 146 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'X' and resid 225 through 227 Processing sheet with id= 61, first strand: chain 'Y' and resid 4 through 5 removed outlier: 6.988A pdb=" N THR Y 137 " --> pdb=" O VAL Y 86 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL Y 86 " --> pdb=" O THR Y 137 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Y' and resid 91 through 92 Processing sheet with id= 63, first strand: chain 'Z' and resid 31 through 32 removed outlier: 7.266A pdb=" N TYR Z 32 " --> pdb=" O LEU Z 47 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ARG Z 130 " --> pdb=" O LEU Z 107 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU Z 107 " --> pdb=" O ARG Z 130 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG Z 132 " --> pdb=" O VAL Z 105 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Z' and resid 31 through 32 removed outlier: 7.266A pdb=" N TYR Z 32 " --> pdb=" O LEU Z 47 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG Z 123 " --> pdb=" O THR Z 73 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N MET Z 122 " --> pdb=" O VAL Z 117 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain '0' and resid 85 through 88 removed outlier: 3.695A pdb=" N LEU 0 12 " --> pdb=" O GLY 0 33 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY 0 33 " --> pdb=" O LEU 0 12 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLU 0 14 " --> pdb=" O ALA 0 31 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ALA 0 31 " --> pdb=" O GLU 0 14 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N TRP 0 36 " --> pdb=" O ARG 0 64 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG 0 64 " --> pdb=" O TRP 0 36 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain '0' and resid 17 through 19 Processing sheet with id= 67, first strand: chain '0' and resid 45 through 48 Processing sheet with id= 68, first strand: chain '1' and resid 22 through 23 removed outlier: 3.539A pdb=" N LEU 1 10 " --> pdb=" O ILE 1 94 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE 1 107 " --> pdb=" O ALA 1 127 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA 1 127 " --> pdb=" O ILE 1 107 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA 1 62 " --> pdb=" O SER 1 128 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '2' and resid 4 through 5 removed outlier: 3.706A pdb=" N ASN 2 4 " --> pdb=" O ARG 2 64 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG 2 61 " --> pdb=" O ALA 2 138 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR 2 137 " --> pdb=" O VAL 2 86 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL 2 86 " --> pdb=" O THR 2 137 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '3' and resid 76 through 77 Processing sheet with id= 71, first strand: chain '3' and resid 134 through 137 removed outlier: 3.802A pdb=" N GLU 3 134 " --> pdb=" O VAL 3 125 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL 3 125 " --> pdb=" O GLU 3 134 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS 3 177 " --> pdb=" O LEU 3 122 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain '3' and resid 143 through 146 removed outlier: 3.700A pdb=" N GLY 3 155 " --> pdb=" O VAL 3 146 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain '3' and resid 225 through 227 Processing sheet with id= 74, first strand: chain '4' and resid 76 through 77 removed outlier: 3.502A pdb=" N LYS 4 353 " --> pdb=" O ILE 4 77 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain '4' and resid 134 through 137 removed outlier: 3.687A pdb=" N GLU 4 134 " --> pdb=" O VAL 4 125 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS 4 177 " --> pdb=" O LEU 4 122 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain '4' and resid 143 through 146 removed outlier: 3.882A pdb=" N GLY 4 155 " --> pdb=" O VAL 4 146 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain '4' and resid 225 through 227 Processing sheet with id= 78, first strand: chain '5' and resid 4 through 5 removed outlier: 6.988A pdb=" N THR 5 137 " --> pdb=" O VAL 5 86 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL 5 86 " --> pdb=" O THR 5 137 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain '5' and resid 91 through 92 Processing sheet with id= 80, first strand: chain '6' and resid 31 through 32 removed outlier: 7.267A pdb=" N TYR 6 32 " --> pdb=" O LEU 6 47 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG 6 130 " --> pdb=" O LEU 6 107 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU 6 107 " --> pdb=" O ARG 6 130 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG 6 132 " --> pdb=" O VAL 6 105 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain '6' and resid 31 through 32 removed outlier: 7.267A pdb=" N TYR 6 32 " --> pdb=" O LEU 6 47 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG 6 123 " --> pdb=" O THR 6 73 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N MET 6 122 " --> pdb=" O VAL 6 117 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain '7' and resid 85 through 88 removed outlier: 3.695A pdb=" N LEU 7 12 " --> pdb=" O GLY 7 33 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY 7 33 " --> pdb=" O LEU 7 12 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLU 7 14 " --> pdb=" O ALA 7 31 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ALA 7 31 " --> pdb=" O GLU 7 14 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TRP 7 36 " --> pdb=" O ARG 7 64 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG 7 64 " --> pdb=" O TRP 7 36 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain '7' and resid 17 through 19 Processing sheet with id= 84, first strand: chain '7' and resid 45 through 48 Processing sheet with id= 85, first strand: chain '8' and resid 22 through 23 removed outlier: 3.538A pdb=" N LEU 8 10 " --> pdb=" O ILE 8 94 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE 8 107 " --> pdb=" O ALA 8 127 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA 8 127 " --> pdb=" O ILE 8 107 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA 8 62 " --> pdb=" O SER 8 128 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain '9' and resid 4 through 5 removed outlier: 3.706A pdb=" N ASN 9 4 " --> pdb=" O ARG 9 64 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG 9 61 " --> pdb=" O ALA 9 138 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR 9 137 " --> pdb=" O VAL 9 86 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL 9 86 " --> pdb=" O THR 9 137 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'a' and resid 76 through 77 Processing sheet with id= 88, first strand: chain 'a' and resid 134 through 137 removed outlier: 3.803A pdb=" N GLU a 134 " --> pdb=" O VAL a 125 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL a 125 " --> pdb=" O GLU a 134 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS a 177 " --> pdb=" O LEU a 122 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'a' and resid 143 through 146 removed outlier: 3.699A pdb=" N GLY a 155 " --> pdb=" O VAL a 146 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'a' and resid 225 through 227 Processing sheet with id= 91, first strand: chain 'b' and resid 76 through 77 removed outlier: 3.502A pdb=" N LYS b 353 " --> pdb=" O ILE b 77 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'b' and resid 134 through 137 removed outlier: 3.686A pdb=" N GLU b 134 " --> pdb=" O VAL b 125 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS b 177 " --> pdb=" O LEU b 122 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'b' and resid 143 through 146 removed outlier: 3.882A pdb=" N GLY b 155 " --> pdb=" O VAL b 146 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'b' and resid 225 through 227 Processing sheet with id= 95, first strand: chain 'c' and resid 4 through 5 removed outlier: 6.988A pdb=" N THR c 137 " --> pdb=" O VAL c 86 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL c 86 " --> pdb=" O THR c 137 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'c' and resid 91 through 92 Processing sheet with id= 97, first strand: chain 'd' and resid 31 through 32 removed outlier: 7.266A pdb=" N TYR d 32 " --> pdb=" O LEU d 47 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG d 130 " --> pdb=" O LEU d 107 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU d 107 " --> pdb=" O ARG d 130 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ARG d 132 " --> pdb=" O VAL d 105 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'd' and resid 31 through 32 removed outlier: 7.266A pdb=" N TYR d 32 " --> pdb=" O LEU d 47 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG d 123 " --> pdb=" O THR d 73 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N MET d 122 " --> pdb=" O VAL d 117 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'e' and resid 85 through 88 removed outlier: 3.695A pdb=" N LEU e 12 " --> pdb=" O GLY e 33 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY e 33 " --> pdb=" O LEU e 12 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLU e 14 " --> pdb=" O ALA e 31 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ALA e 31 " --> pdb=" O GLU e 14 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N TRP e 36 " --> pdb=" O ARG e 64 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG e 64 " --> pdb=" O TRP e 36 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'e' and resid 17 through 19 Processing sheet with id=101, first strand: chain 'e' and resid 45 through 48 Processing sheet with id=102, first strand: chain 'f' and resid 22 through 23 removed outlier: 3.538A pdb=" N LEU f 10 " --> pdb=" O ILE f 94 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE f 107 " --> pdb=" O ALA f 127 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA f 127 " --> pdb=" O ILE f 107 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA f 62 " --> pdb=" O SER f 128 " (cutoff:3.500A) 2340 hydrogen bonds defined for protein. 6696 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: -4179.28 Time building geometry restraints manager: 21.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22152 1.34 - 1.46: 13804 1.46 - 1.58: 31952 1.58 - 1.70: 6 1.70 - 1.82: 498 Bond restraints: 68412 Sorted by residual: bond pdb=" N PRO V 114 " pdb=" CD PRO V 114 " ideal model delta sigma weight residual 1.473 1.390 0.083 1.40e-02 5.10e+03 3.51e+01 bond pdb=" N PRO C 114 " pdb=" CD PRO C 114 " ideal model delta sigma weight residual 1.473 1.390 0.083 1.40e-02 5.10e+03 3.51e+01 bond pdb=" N PRO 9 114 " pdb=" CD PRO 9 114 " ideal model delta sigma weight residual 1.473 1.390 0.083 1.40e-02 5.10e+03 3.51e+01 bond pdb=" N PRO O 114 " pdb=" CD PRO O 114 " ideal model delta sigma weight residual 1.473 1.390 0.083 1.40e-02 5.10e+03 3.51e+01 bond pdb=" N PRO 2 114 " pdb=" CD PRO 2 114 " ideal model delta sigma weight residual 1.473 1.390 0.083 1.40e-02 5.10e+03 3.51e+01 ... (remaining 68407 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.76: 1810 104.76 - 112.73: 35072 112.73 - 120.70: 33182 120.70 - 128.67: 22270 128.67 - 136.64: 714 Bond angle restraints: 93048 Sorted by residual: angle pdb=" N VAL 2 132 " pdb=" CA VAL 2 132 " pdb=" C VAL 2 132 " ideal model delta sigma weight residual 110.05 100.23 9.82 1.09e+00 8.42e-01 8.12e+01 angle pdb=" N VAL H 132 " pdb=" CA VAL H 132 " pdb=" C VAL H 132 " ideal model delta sigma weight residual 110.05 100.23 9.82 1.09e+00 8.42e-01 8.12e+01 angle pdb=" N VAL V 132 " pdb=" CA VAL V 132 " pdb=" C VAL V 132 " ideal model delta sigma weight residual 110.05 100.23 9.82 1.09e+00 8.42e-01 8.11e+01 angle pdb=" N VAL C 132 " pdb=" CA VAL C 132 " pdb=" C VAL C 132 " ideal model delta sigma weight residual 110.05 100.23 9.82 1.09e+00 8.42e-01 8.11e+01 angle pdb=" N VAL O 132 " pdb=" CA VAL O 132 " pdb=" C VAL O 132 " ideal model delta sigma weight residual 110.05 100.24 9.81 1.09e+00 8.42e-01 8.09e+01 ... (remaining 93043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 38070 15.32 - 30.63: 1956 30.63 - 45.95: 480 45.95 - 61.27: 18 61.27 - 76.58: 60 Dihedral angle restraints: 40584 sinusoidal: 15546 harmonic: 25038 Sorted by residual: dihedral pdb=" CA ASP 3 279 " pdb=" C ASP 3 279 " pdb=" N MET 3 280 " pdb=" CA MET 3 280 " ideal model delta harmonic sigma weight residual 180.00 153.52 26.48 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA ASP I 279 " pdb=" C ASP I 279 " pdb=" N MET I 280 " pdb=" CA MET I 280 " ideal model delta harmonic sigma weight residual 180.00 153.52 26.48 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA ASP P 279 " pdb=" C ASP P 279 " pdb=" N MET P 280 " pdb=" CA MET P 280 " ideal model delta harmonic sigma weight residual 180.00 153.53 26.47 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 40581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 8232 0.086 - 0.171: 1742 0.171 - 0.257: 362 0.257 - 0.342: 44 0.342 - 0.428: 24 Chirality restraints: 10404 Sorted by residual: chirality pdb=" CB ILE 8 107 " pdb=" CA ILE 8 107 " pdb=" CG1 ILE 8 107 " pdb=" CG2 ILE 8 107 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CB ILE N 107 " pdb=" CA ILE N 107 " pdb=" CG1 ILE N 107 " pdb=" CG2 ILE N 107 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CB ILE f 107 " pdb=" CA ILE f 107 " pdb=" CG1 ILE f 107 " pdb=" CG2 ILE f 107 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.56e+00 ... (remaining 10401 not shown) Planarity restraints: 12192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU N 45 " -0.030 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" CD GLU N 45 " 0.104 2.00e-02 2.50e+03 pdb=" OE1 GLU N 45 " -0.038 2.00e-02 2.50e+03 pdb=" OE2 GLU N 45 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU 8 45 " 0.030 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" CD GLU 8 45 " -0.104 2.00e-02 2.50e+03 pdb=" OE1 GLU 8 45 " 0.038 2.00e-02 2.50e+03 pdb=" OE2 GLU 8 45 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU 1 45 " -0.030 2.00e-02 2.50e+03 6.00e-02 3.60e+01 pdb=" CD GLU 1 45 " 0.104 2.00e-02 2.50e+03 pdb=" OE1 GLU 1 45 " -0.038 2.00e-02 2.50e+03 pdb=" OE2 GLU 1 45 " -0.035 2.00e-02 2.50e+03 ... (remaining 12189 not shown) Histogram of nonbonded interaction distances: 0.89 - 1.69: 12 1.69 - 2.49: 384 2.49 - 3.30: 73406 3.30 - 4.10: 166106 4.10 - 4.90: 307050 Warning: very small nonbonded interaction distances. Nonbonded interactions: 546958 Sorted by model distance: nonbonded pdb=" OD2 ASP G 72 " pdb=" OD2 ASP f 97 " model vdw 0.891 3.040 nonbonded pdb=" OD2 ASP U 97 " pdb=" OD2 ASP 1 72 " model vdw 0.891 3.040 nonbonded pdb=" OD2 ASP N 97 " pdb=" OD2 ASP U 72 " model vdw 0.892 3.040 nonbonded pdb=" OD2 ASP 8 97 " pdb=" OD2 ASP f 72 " model vdw 0.892 3.040 nonbonded pdb=" OD2 ASP 1 97 " pdb=" OD2 ASP 8 72 " model vdw 0.892 3.040 ... (remaining 546953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '7' selection = chain 'E' selection = chain 'M' selection = chain 'T' selection = chain 'e' } ncs_group { reference = chain '1' selection = chain '8' selection = chain 'G' selection = chain 'N' selection = chain 'U' selection = chain 'f' } ncs_group { reference = chain '2' selection = (chain '5' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 121 or (resid 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 197)) selection = chain '9' selection = chain 'C' selection = (chain 'D' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 121 or (resid 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 197)) selection = chain 'H' selection = (chain 'K' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 121 or (resid 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 197)) selection = chain 'O' selection = (chain 'R' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 121 or (resid 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 197)) selection = chain 'V' selection = (chain 'Y' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 121 or (resid 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 197)) selection = (chain 'c' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 121 or (resid 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 197)) } ncs_group { reference = chain '3' selection = chain '4' selection = chain 'A' selection = chain 'B' selection = chain 'I' selection = chain 'J' selection = chain 'P' selection = chain 'Q' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain '6' selection = chain 'F' selection = chain 'L' selection = chain 'S' selection = chain 'Z' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.050 Extract box with map and model: 8.240 Check model and map are aligned: 0.720 Set scattering table: 0.470 Process input model: 131.260 Find NCS groups from input model: 3.110 Set up NCS constraints: 0.520 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 : 0.011 0.102 68412 Z= 0.737 Angle : 1.323 15.558 93048 Z= 0.725 Chirality : 0.077 0.428 10404 Planarity : 0.009 0.084 12192 Dihedral : 10.497 76.583 24564 Min Nonbonded Distance : 0.891 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.95 % Favored : 89.99 % Rotamer: Outliers : 0.82 % Allowed : 4.46 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.43 (0.07), residues: 8748 helix: -4.38 (0.05), residues: 2844 sheet: -2.68 (0.12), residues: 1500 loop : -3.39 (0.07), residues: 4404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.005 TRP B 370 HIS 0.012 0.002 HIS 9 167 PHE 0.055 0.004 PHE Z 78 TYR 0.035 0.004 TYR R 162 ARG 0.015 0.002 ARG c 186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2565 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 2511 time to evaluate : 5.678 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: C 39 LEU cc_start: 0.9461 (mt) cc_final: 0.9259 (mp) REVERT: C 189 THR cc_start: 0.9335 (m) cc_final: 0.9045 (p) REVERT: A 253 GLN cc_start: 0.9218 (mt0) cc_final: 0.9018 (mt0) REVERT: A 367 ASP cc_start: 0.8489 (m-30) cc_final: 0.8132 (m-30) REVERT: B 119 ASN cc_start: 0.9138 (m-40) cc_final: 0.8877 (m-40) REVERT: B 164 LYS cc_start: 0.8447 (mtpp) cc_final: 0.8059 (ttmm) REVERT: B 216 ASP cc_start: 0.7413 (t70) cc_final: 0.7175 (t0) REVERT: B 228 LYS cc_start: 0.9336 (mmpt) cc_final: 0.8993 (mmtt) REVERT: B 242 GLU cc_start: 0.7528 (mt-10) cc_final: 0.6931 (mt-10) REVERT: B 249 GLU cc_start: 0.8188 (tt0) cc_final: 0.7959 (tt0) REVERT: B 279 ASP cc_start: 0.8009 (m-30) cc_final: 0.7738 (m-30) REVERT: B 314 ASN cc_start: 0.7875 (p0) cc_final: 0.6735 (p0) REVERT: D 1 MET cc_start: 0.7492 (tmm) cc_final: 0.6496 (ttp) REVERT: D 21 ASP cc_start: 0.7727 (t0) cc_final: 0.7466 (t0) REVERT: D 163 TYR cc_start: 0.9217 (t80) cc_final: 0.8601 (t80) REVERT: F 73 THR cc_start: 0.9122 (m) cc_final: 0.8789 (p) REVERT: F 113 LYS cc_start: 0.8055 (tttm) cc_final: 0.7851 (tttp) REVERT: E 9 LEU cc_start: 0.9317 (tp) cc_final: 0.8860 (tp) REVERT: E 88 ARG cc_start: 0.8563 (mtm180) cc_final: 0.6477 (mmm160) REVERT: G 13 LEU cc_start: 0.9258 (mp) cc_final: 0.8935 (mp) REVERT: G 77 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8285 (tp30) REVERT: G 81 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8364 (tm-30) REVERT: G 98 PHE cc_start: 0.8053 (m-10) cc_final: 0.7487 (m-10) REVERT: G 117 ASN cc_start: 0.9167 (p0) cc_final: 0.8900 (p0) REVERT: G 123 GLU cc_start: 0.8235 (tp30) cc_final: 0.8022 (tp30) REVERT: H 189 THR cc_start: 0.9402 (m) cc_final: 0.9085 (p) REVERT: I 47 VAL cc_start: 0.8936 (p) cc_final: 0.8692 (m) REVERT: I 119 ASN cc_start: 0.9496 (m-40) cc_final: 0.9256 (m110) REVERT: I 215 LEU cc_start: 0.9572 (mt) cc_final: 0.9232 (mt) REVERT: I 249 GLU cc_start: 0.8306 (tt0) cc_final: 0.7978 (tt0) REVERT: I 271 LYS cc_start: 0.8804 (ttpt) cc_final: 0.8368 (ttpp) REVERT: I 273 MET cc_start: 0.8832 (mpt) cc_final: 0.8341 (mpp) REVERT: J 136 HIS cc_start: 0.8318 (m-70) cc_final: 0.8054 (m-70) REVERT: J 141 ASP cc_start: 0.8488 (m-30) cc_final: 0.8248 (m-30) REVERT: J 157 ASP cc_start: 0.8774 (m-30) cc_final: 0.8336 (m-30) REVERT: J 189 TYR cc_start: 0.9091 (m-80) cc_final: 0.8677 (m-10) REVERT: J 205 ASN cc_start: 0.8814 (m-40) cc_final: 0.8368 (m110) REVERT: J 216 ASP cc_start: 0.7503 (t70) cc_final: 0.7181 (t0) REVERT: J 256 ARG cc_start: 0.8100 (ptt90) cc_final: 0.7881 (ttp-110) REVERT: J 286 LYS cc_start: 0.9010 (ttpt) cc_final: 0.8699 (tttt) REVERT: J 314 ASN cc_start: 0.8033 (p0) cc_final: 0.7483 (p0) REVERT: J 367 ASP cc_start: 0.8315 (m-30) cc_final: 0.8113 (m-30) REVERT: K 21 ASP cc_start: 0.7707 (t0) cc_final: 0.7487 (t0) REVERT: K 80 ILE cc_start: 0.9283 (mm) cc_final: 0.8965 (tp) REVERT: L 15 GLN cc_start: 0.9003 (mm110) cc_final: 0.8720 (mm-40) REVERT: M 88 ARG cc_start: 0.8426 (mtm180) cc_final: 0.6377 (mmm160) REVERT: N 7 LYS cc_start: 0.8423 (mtpm) cc_final: 0.8049 (tmtt) REVERT: N 13 LEU cc_start: 0.9151 (mp) cc_final: 0.8856 (mp) REVERT: N 77 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8257 (tm-30) REVERT: N 81 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8252 (tm-30) REVERT: N 106 MET cc_start: 0.7529 (ptp) cc_final: 0.7246 (ptp) REVERT: N 123 GLU cc_start: 0.8142 (tp30) cc_final: 0.7874 (tp30) REVERT: O 105 TRP cc_start: 0.8897 (p-90) cc_final: 0.8315 (p-90) REVERT: O 189 THR cc_start: 0.9279 (m) cc_final: 0.8995 (p) REVERT: P 32 MET cc_start: 0.7102 (ptm) cc_final: 0.6583 (ppp) REVERT: P 156 TYR cc_start: 0.8587 (m-80) cc_final: 0.8371 (m-80) REVERT: P 164 LYS cc_start: 0.8791 (mtpp) cc_final: 0.8429 (ttmm) REVERT: P 244 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9256 (tm) REVERT: P 284 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8569 (tp30) REVERT: Q 119 ASN cc_start: 0.9097 (m-40) cc_final: 0.8865 (m-40) REVERT: Q 216 ASP cc_start: 0.7422 (t70) cc_final: 0.6862 (t0) REVERT: Q 242 GLU cc_start: 0.7537 (mt-10) cc_final: 0.6930 (mt-10) REVERT: Q 314 ASN cc_start: 0.8124 (p0) cc_final: 0.7569 (p0) REVERT: R 1 MET cc_start: 0.7555 (tmm) cc_final: 0.6604 (ttp) REVERT: R 21 ASP cc_start: 0.7881 (t0) cc_final: 0.7599 (t0) REVERT: R 131 ARG cc_start: 0.8095 (ptt-90) cc_final: 0.7882 (ptt90) REVERT: T 88 ARG cc_start: 0.8430 (mtm180) cc_final: 0.6460 (mmm160) REVERT: U 77 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8227 (tm-30) REVERT: U 123 GLU cc_start: 0.8052 (tp30) cc_final: 0.7698 (tp30) REVERT: V 189 THR cc_start: 0.9332 (m) cc_final: 0.9038 (p) REVERT: W 32 MET cc_start: 0.7103 (ptm) cc_final: 0.6731 (ppp) REVERT: W 65 LYS cc_start: 0.8367 (tttt) cc_final: 0.8150 (ttmt) REVERT: W 134 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7898 (mm-30) REVERT: W 164 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8629 (mtpp) REVERT: W 253 GLN cc_start: 0.9210 (mt0) cc_final: 0.9009 (mt0) REVERT: W 367 ASP cc_start: 0.8471 (m-30) cc_final: 0.8122 (m-30) REVERT: X 101 GLN cc_start: 0.8363 (tp-100) cc_final: 0.8129 (tt0) REVERT: X 119 ASN cc_start: 0.9144 (m-40) cc_final: 0.8875 (m-40) REVERT: X 216 ASP cc_start: 0.7408 (t70) cc_final: 0.7163 (t0) REVERT: X 228 LYS cc_start: 0.9339 (mmpt) cc_final: 0.9005 (mmtt) REVERT: X 242 GLU cc_start: 0.7522 (mt-10) cc_final: 0.6904 (mt-10) REVERT: X 249 GLU cc_start: 0.8165 (tt0) cc_final: 0.7882 (tt0) REVERT: X 279 ASP cc_start: 0.7998 (m-30) cc_final: 0.7725 (m-30) REVERT: X 284 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8167 (mm-30) REVERT: X 314 ASN cc_start: 0.7871 (p0) cc_final: 0.6701 (p0) REVERT: Y 1 MET cc_start: 0.7483 (tmm) cc_final: 0.6505 (ttp) REVERT: Y 21 ASP cc_start: 0.7725 (t0) cc_final: 0.7468 (t0) REVERT: Y 110 ASP cc_start: 0.8254 (t0) cc_final: 0.7871 (t0) REVERT: Y 163 TYR cc_start: 0.9219 (t80) cc_final: 0.8583 (t80) REVERT: Z 73 THR cc_start: 0.9128 (m) cc_final: 0.8813 (p) REVERT: 0 9 LEU cc_start: 0.9313 (tp) cc_final: 0.8850 (tp) REVERT: 0 88 ARG cc_start: 0.8574 (mtm180) cc_final: 0.6474 (mmm160) REVERT: 1 13 LEU cc_start: 0.9258 (mp) cc_final: 0.8883 (mp) REVERT: 1 81 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8382 (tm-30) REVERT: 1 98 PHE cc_start: 0.8041 (m-10) cc_final: 0.7476 (m-10) REVERT: 1 116 HIS cc_start: 0.8260 (p90) cc_final: 0.7999 (p-80) REVERT: 1 117 ASN cc_start: 0.9156 (p0) cc_final: 0.8860 (p0) REVERT: 1 123 GLU cc_start: 0.8248 (tp30) cc_final: 0.8048 (mt-10) REVERT: 2 167 HIS cc_start: 0.8018 (p-80) cc_final: 0.7818 (p-80) REVERT: 2 189 THR cc_start: 0.9401 (m) cc_final: 0.9094 (p) REVERT: 3 32 MET cc_start: 0.7156 (ptm) cc_final: 0.6726 (ppp) REVERT: 3 47 VAL cc_start: 0.8962 (p) cc_final: 0.8708 (m) REVERT: 3 101 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8413 (tt0) REVERT: 3 119 ASN cc_start: 0.9498 (m-40) cc_final: 0.9264 (m110) REVERT: 3 164 LYS cc_start: 0.8785 (mtpp) cc_final: 0.8543 (mtpt) REVERT: 3 215 LEU cc_start: 0.9576 (mt) cc_final: 0.9239 (mt) REVERT: 3 249 GLU cc_start: 0.8287 (tt0) cc_final: 0.7960 (tt0) REVERT: 3 271 LYS cc_start: 0.8825 (ttpt) cc_final: 0.8393 (ttpp) REVERT: 3 273 MET cc_start: 0.8834 (mpt) cc_final: 0.8358 (mpp) REVERT: 3 323 TYR cc_start: 0.8931 (m-80) cc_final: 0.8641 (m-80) REVERT: 4 101 GLN cc_start: 0.8357 (tp-100) cc_final: 0.8093 (tt0) REVERT: 4 136 HIS cc_start: 0.8314 (m-70) cc_final: 0.8036 (m-70) REVERT: 4 141 ASP cc_start: 0.8492 (m-30) cc_final: 0.8259 (m-30) REVERT: 4 157 ASP cc_start: 0.8797 (m-30) cc_final: 0.8342 (m-30) REVERT: 4 164 LYS cc_start: 0.8619 (mtpp) cc_final: 0.7925 (ttmm) REVERT: 4 189 TYR cc_start: 0.9094 (m-80) cc_final: 0.8664 (m-10) REVERT: 4 205 ASN cc_start: 0.8808 (m-40) cc_final: 0.8359 (m110) REVERT: 4 216 ASP cc_start: 0.7506 (t70) cc_final: 0.7182 (t0) REVERT: 4 256 ARG cc_start: 0.8084 (ptt90) cc_final: 0.7883 (ttp-110) REVERT: 4 286 LYS cc_start: 0.9017 (ttpt) cc_final: 0.8696 (tttt) REVERT: 4 314 ASN cc_start: 0.8030 (p0) cc_final: 0.7501 (p0) REVERT: 4 367 ASP cc_start: 0.8316 (m-30) cc_final: 0.8110 (m-30) REVERT: 5 21 ASP cc_start: 0.7688 (t0) cc_final: 0.7469 (t0) REVERT: 5 80 ILE cc_start: 0.9287 (mm) cc_final: 0.8977 (tp) REVERT: 6 15 GLN cc_start: 0.8999 (mm110) cc_final: 0.8701 (mm-40) REVERT: 8 7 LYS cc_start: 0.8434 (mtpm) cc_final: 0.8073 (tmtt) REVERT: 8 13 LEU cc_start: 0.9137 (mp) cc_final: 0.8840 (mp) REVERT: 8 81 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8246 (tm-30) REVERT: 8 106 MET cc_start: 0.7556 (ptp) cc_final: 0.7257 (ptp) REVERT: 9 105 TRP cc_start: 0.8902 (p-90) cc_final: 0.8340 (p-90) REVERT: 9 189 THR cc_start: 0.9276 (m) cc_final: 0.8959 (p) REVERT: a 156 TYR cc_start: 0.8587 (m-80) cc_final: 0.8378 (m-80) REVERT: a 244 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9246 (tm) REVERT: a 271 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8397 (ttpp) REVERT: a 273 MET cc_start: 0.8735 (mpt) cc_final: 0.7997 (mmt) REVERT: a 284 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8575 (tp30) REVERT: b 119 ASN cc_start: 0.9093 (m-40) cc_final: 0.8889 (m-40) REVERT: b 159 THR cc_start: 0.8638 (p) cc_final: 0.8264 (m) REVERT: b 216 ASP cc_start: 0.7412 (t70) cc_final: 0.6834 (t0) REVERT: b 242 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6903 (mt-10) REVERT: b 256 ARG cc_start: 0.8110 (ptt90) cc_final: 0.7909 (ttp-110) REVERT: b 314 ASN cc_start: 0.8135 (p0) cc_final: 0.7567 (p0) REVERT: c 1 MET cc_start: 0.7579 (tmm) cc_final: 0.6593 (ttp) REVERT: c 21 ASP cc_start: 0.7884 (t0) cc_final: 0.7590 (t0) REVERT: c 131 ARG cc_start: 0.8058 (ptt-90) cc_final: 0.7371 (ptt90) REVERT: c 133 GLU cc_start: 0.8045 (pt0) cc_final: 0.7728 (pt0) REVERT: c 145 SER cc_start: 0.8897 (p) cc_final: 0.8649 (p) REVERT: e 88 ARG cc_start: 0.8421 (mtm180) cc_final: 0.6398 (mmm160) REVERT: f 77 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8250 (tm-30) REVERT: f 123 GLU cc_start: 0.8072 (tp30) cc_final: 0.7705 (tp30) outliers start: 54 outliers final: 12 residues processed: 2535 average time/residue: 0.6826 time to fit residues: 2841.2342 Evaluate side-chains 1830 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1816 time to evaluate : 5.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain O residue 35 GLU Chi-restraints excluded: chain P residue 244 LEU Chi-restraints excluded: chain U residue 45 GLU Chi-restraints excluded: chain V residue 35 GLU Chi-restraints excluded: chain 1 residue 45 GLU Chi-restraints excluded: chain 2 residue 35 GLU Chi-restraints excluded: chain 8 residue 45 GLU Chi-restraints excluded: chain 9 residue 35 GLU Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain f residue 45 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 744 optimal weight: 9.9990 chunk 668 optimal weight: 0.7980 chunk 370 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 450 optimal weight: 8.9990 chunk 357 optimal weight: 0.8980 chunk 691 optimal weight: 7.9990 chunk 267 optimal weight: 0.7980 chunk 420 optimal weight: 3.9990 chunk 514 optimal weight: 0.6980 chunk 800 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 HIS ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 ASN A 349 GLN A 368 GLN B 204 HIS D 161 GLN I 204 HIS I 257 ASN I 349 GLN I 358 GLN J 204 HIS M 100 HIS O 161 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 204 HIS ** P 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 GLN Q 253 GLN T 100 HIS ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 204 HIS ** W 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 319 ASN W 349 GLN W 368 GLN X 204 HIS Y 22 HIS Y 161 GLN 1 92 GLN 1 102 GLN 3 204 HIS 3 257 ASN 3 349 GLN 3 358 GLN 4 204 HIS 7 100 HIS 9 161 GLN ** a 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 204 HIS ** a 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 257 ASN b 183 HIS b 253 GLN e 100 HIS f 102 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 68412 Z= 0.199 Angle : 0.734 15.509 93048 Z= 0.353 Chirality : 0.047 0.309 10404 Planarity : 0.006 0.066 12192 Dihedral : 5.970 51.984 9748 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.84 % Allowed : 15.45 % Favored : 81.71 % 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: -3.92 (0.08), residues: 8748 helix: -2.41 (0.08), residues: 2844 sheet: -2.33 (0.12), residues: 1548 loop : -2.82 (0.08), residues: 4356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 72 HIS 0.005 0.001 HIS U 116 PHE 0.033 0.002 PHE G 83 TYR 0.016 0.001 TYR 2 162 ARG 0.010 0.001 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2248 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 2061 time to evaluate : 5.662 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: C 39 LEU cc_start: 0.9354 (mt) cc_final: 0.9103 (mp) REVERT: C 44 ARG cc_start: 0.8492 (mmm-85) cc_final: 0.8205 (mtt90) REVERT: C 64 ARG cc_start: 0.8314 (ttm110) cc_final: 0.8069 (ttm170) REVERT: C 126 ILE cc_start: 0.8837 (mt) cc_final: 0.8543 (mt) REVERT: C 189 THR cc_start: 0.9356 (m) cc_final: 0.9076 (p) REVERT: C 193 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8192 (tm) REVERT: A 65 LYS cc_start: 0.8852 (tppp) cc_final: 0.7944 (ttmt) REVERT: A 101 GLN cc_start: 0.8804 (tt0) cc_final: 0.8245 (tt0) REVERT: A 212 LYS cc_start: 0.9049 (tttm) cc_final: 0.8683 (tttp) REVERT: A 368 GLN cc_start: 0.8556 (mt0) cc_final: 0.8315 (mt0) REVERT: B 215 LEU cc_start: 0.9343 (mt) cc_final: 0.9078 (mt) REVERT: B 246 PHE cc_start: 0.8703 (t80) cc_final: 0.8477 (t80) REVERT: B 253 GLN cc_start: 0.9296 (mt0) cc_final: 0.8938 (mt0) REVERT: B 262 MET cc_start: 0.9024 (ttm) cc_final: 0.8807 (ttm) REVERT: B 314 ASN cc_start: 0.7616 (p0) cc_final: 0.6949 (p0) REVERT: B 323 TYR cc_start: 0.8345 (m-80) cc_final: 0.7962 (m-80) REVERT: B 333 ARG cc_start: 0.7991 (ttt90) cc_final: 0.7739 (ttp-110) REVERT: B 365 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8223 (mt-10) REVERT: D 163 TYR cc_start: 0.9118 (t80) cc_final: 0.8601 (t80) REVERT: E 88 ARG cc_start: 0.8411 (mtm180) cc_final: 0.6558 (mmm160) REVERT: G 45 GLU cc_start: 0.8064 (pm20) cc_final: 0.7591 (pm20) REVERT: G 77 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8062 (tm-30) REVERT: G 117 ASN cc_start: 0.9179 (p0) cc_final: 0.8899 (p0) REVERT: G 126 MET cc_start: 0.7580 (mtp) cc_final: 0.7194 (mtp) REVERT: H 126 ILE cc_start: 0.8808 (mt) cc_final: 0.8509 (mt) REVERT: H 149 VAL cc_start: 0.9119 (t) cc_final: 0.8901 (t) REVERT: H 189 THR cc_start: 0.9360 (m) cc_final: 0.9083 (p) REVERT: I 65 LYS cc_start: 0.9040 (tppt) cc_final: 0.8293 (tppt) REVERT: I 163 ARG cc_start: 0.7230 (mmm-85) cc_final: 0.6830 (mmt90) REVERT: I 215 LEU cc_start: 0.9408 (mt) cc_final: 0.9177 (mt) REVERT: I 249 GLU cc_start: 0.8383 (tt0) cc_final: 0.8126 (tt0) REVERT: I 271 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8367 (ttpp) REVERT: I 304 ILE cc_start: 0.9094 (tt) cc_final: 0.8869 (pt) REVERT: I 383 GLU cc_start: 0.7433 (tp30) cc_final: 0.7223 (tp30) REVERT: J 157 ASP cc_start: 0.8334 (m-30) cc_final: 0.7514 (m-30) REVERT: J 164 LYS cc_start: 0.8570 (mtpp) cc_final: 0.7580 (mtpp) REVERT: J 189 TYR cc_start: 0.9026 (m-80) cc_final: 0.8791 (m-80) REVERT: J 216 ASP cc_start: 0.7441 (t70) cc_final: 0.7197 (t0) REVERT: J 286 LYS cc_start: 0.8972 (ttpt) cc_final: 0.8573 (tttt) REVERT: J 314 ASN cc_start: 0.7690 (p0) cc_final: 0.6876 (p0) REVERT: K 80 ILE cc_start: 0.9008 (mm) cc_final: 0.8715 (tp) REVERT: K 119 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6816 (mp) REVERT: K 131 ARG cc_start: 0.8068 (ptt90) cc_final: 0.7497 (ptt90) REVERT: K 157 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9215 (mt) REVERT: L 15 GLN cc_start: 0.8869 (mm110) cc_final: 0.8619 (mm-40) REVERT: M 14 GLU cc_start: 0.8282 (tt0) cc_final: 0.7819 (tt0) REVERT: M 47 ARG cc_start: 0.8462 (ttp80) cc_final: 0.7794 (ptt90) REVERT: M 88 ARG cc_start: 0.8269 (mtm180) cc_final: 0.6391 (mmm160) REVERT: N 7 LYS cc_start: 0.8475 (mtpm) cc_final: 0.8096 (tmtt) REVERT: N 43 SER cc_start: 0.8023 (p) cc_final: 0.7773 (m) REVERT: N 77 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7877 (tm-30) REVERT: N 123 GLU cc_start: 0.7811 (tp30) cc_final: 0.7323 (tp30) REVERT: O 105 TRP cc_start: 0.9047 (p-90) cc_final: 0.8352 (p-90) REVERT: O 126 ILE cc_start: 0.8858 (mt) cc_final: 0.8622 (mt) REVERT: O 189 THR cc_start: 0.9264 (m) cc_final: 0.9015 (p) REVERT: P 32 MET cc_start: 0.7250 (ptm) cc_final: 0.6883 (ptp) REVERT: P 150 ASP cc_start: 0.6921 (t0) cc_final: 0.6716 (t0) REVERT: P 163 ARG cc_start: 0.7215 (mmm-85) cc_final: 0.6577 (mmm-85) REVERT: P 164 LYS cc_start: 0.8611 (mtpp) cc_final: 0.8171 (ttmm) REVERT: P 169 MET cc_start: 0.8556 (mmm) cc_final: 0.8345 (mmm) REVERT: P 205 ASN cc_start: 0.9332 (m-40) cc_final: 0.8542 (m-40) REVERT: P 271 LYS cc_start: 0.8987 (ttpt) cc_final: 0.8762 (ttpt) REVERT: Q 105 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8069 (mt-10) REVERT: Q 164 LYS cc_start: 0.8332 (mtpp) cc_final: 0.7820 (mtpp) REVERT: Q 189 TYR cc_start: 0.9024 (m-80) cc_final: 0.8815 (m-80) REVERT: Q 216 ASP cc_start: 0.7403 (t70) cc_final: 0.6943 (t0) REVERT: Q 271 LYS cc_start: 0.8567 (tttt) cc_final: 0.8365 (tttt) REVERT: Q 314 ASN cc_start: 0.7873 (p0) cc_final: 0.7026 (p0) REVERT: R 123 LEU cc_start: 0.9006 (mt) cc_final: 0.8479 (tp) REVERT: S 122 MET cc_start: 0.8239 (mmm) cc_final: 0.7873 (mmm) REVERT: T 47 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8014 (ptt90) REVERT: T 88 ARG cc_start: 0.8237 (mtm180) cc_final: 0.6519 (mmm160) REVERT: U 43 SER cc_start: 0.8521 (p) cc_final: 0.8041 (p) REVERT: U 45 GLU cc_start: 0.7582 (pm20) cc_final: 0.7355 (pm20) REVERT: U 61 SER cc_start: 0.8483 (t) cc_final: 0.8230 (t) REVERT: U 77 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7942 (tm-30) REVERT: U 81 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8527 (tm-30) REVERT: U 106 MET cc_start: 0.6857 (ptp) cc_final: 0.6524 (ptm) REVERT: U 116 HIS cc_start: 0.8553 (p-80) cc_final: 0.7953 (p-80) REVERT: U 126 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7665 (mtp) REVERT: V 44 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.8221 (mtt90) REVERT: V 126 ILE cc_start: 0.8841 (mt) cc_final: 0.8548 (mt) REVERT: V 189 THR cc_start: 0.9347 (m) cc_final: 0.9071 (p) REVERT: V 193 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8198 (tm) REVERT: W 101 GLN cc_start: 0.8775 (tt0) cc_final: 0.8346 (tt0) REVERT: W 164 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8551 (mtpp) REVERT: W 212 LYS cc_start: 0.9043 (tttm) cc_final: 0.8671 (tttp) REVERT: W 368 GLN cc_start: 0.8556 (mt0) cc_final: 0.8318 (mt0) REVERT: X 101 GLN cc_start: 0.8387 (tp-100) cc_final: 0.8078 (tt0) REVERT: X 166 ARG cc_start: 0.8665 (tpp80) cc_final: 0.8364 (tpp80) REVERT: X 215 LEU cc_start: 0.9336 (mt) cc_final: 0.9084 (mt) REVERT: X 253 GLN cc_start: 0.9293 (mt0) cc_final: 0.8895 (mt0) REVERT: X 262 MET cc_start: 0.9039 (ttm) cc_final: 0.8808 (ttm) REVERT: X 314 ASN cc_start: 0.7594 (p0) cc_final: 0.6916 (p0) REVERT: X 323 TYR cc_start: 0.8359 (m-80) cc_final: 0.7959 (m-80) REVERT: X 333 ARG cc_start: 0.7955 (ttt90) cc_final: 0.7753 (ttp-110) REVERT: X 357 ASP cc_start: 0.8973 (t70) cc_final: 0.8566 (t0) REVERT: X 365 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8240 (mt-10) REVERT: Y 131 ARG cc_start: 0.8240 (ptt90) cc_final: 0.6413 (ptt90) REVERT: Y 133 GLU cc_start: 0.7482 (pt0) cc_final: 0.6516 (pt0) REVERT: Y 163 TYR cc_start: 0.9125 (t80) cc_final: 0.8588 (t80) REVERT: 0 88 ARG cc_start: 0.8456 (mtm180) cc_final: 0.6564 (mmm160) REVERT: 1 45 GLU cc_start: 0.8071 (pm20) cc_final: 0.7650 (pm20) REVERT: 1 51 ARG cc_start: 0.8340 (ttp80) cc_final: 0.8132 (ttp80) REVERT: 1 81 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8355 (tm-30) REVERT: 1 91 PHE cc_start: 0.8281 (m-80) cc_final: 0.7975 (m-80) REVERT: 1 117 ASN cc_start: 0.9166 (p0) cc_final: 0.8870 (p0) REVERT: 1 126 MET cc_start: 0.7570 (mtp) cc_final: 0.7161 (mtp) REVERT: 2 90 ARG cc_start: 0.7847 (mtm110) cc_final: 0.7244 (ptt90) REVERT: 2 126 ILE cc_start: 0.8821 (mt) cc_final: 0.8514 (mt) REVERT: 2 149 VAL cc_start: 0.9108 (t) cc_final: 0.8893 (t) REVERT: 2 189 THR cc_start: 0.9342 (m) cc_final: 0.9062 (p) REVERT: 3 32 MET cc_start: 0.7242 (ptm) cc_final: 0.6565 (ptp) REVERT: 3 47 VAL cc_start: 0.8610 (p) cc_final: 0.8309 (m) REVERT: 3 65 LYS cc_start: 0.9036 (tppt) cc_final: 0.8505 (tppt) REVERT: 3 101 GLN cc_start: 0.8735 (tp-100) cc_final: 0.8488 (tt0) REVERT: 3 163 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.5973 (mmm-85) REVERT: 3 164 LYS cc_start: 0.8638 (mtpp) cc_final: 0.8430 (mtpp) REVERT: 3 215 LEU cc_start: 0.9421 (mt) cc_final: 0.9184 (mt) REVERT: 3 249 GLU cc_start: 0.8335 (tt0) cc_final: 0.8071 (tt0) REVERT: 3 271 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8389 (ttpp) REVERT: 3 304 ILE cc_start: 0.9096 (tt) cc_final: 0.8871 (pt) REVERT: 3 383 GLU cc_start: 0.7430 (tp30) cc_final: 0.7209 (tp30) REVERT: 4 91 LEU cc_start: 0.8909 (pt) cc_final: 0.8696 (mp) REVERT: 4 101 GLN cc_start: 0.8260 (tp-100) cc_final: 0.8048 (tt0) REVERT: 4 105 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8038 (mt-10) REVERT: 4 157 ASP cc_start: 0.8352 (m-30) cc_final: 0.8095 (m-30) REVERT: 4 189 TYR cc_start: 0.9026 (m-80) cc_final: 0.8767 (m-80) REVERT: 4 216 ASP cc_start: 0.7471 (t70) cc_final: 0.7213 (t0) REVERT: 4 286 LYS cc_start: 0.8973 (ttpt) cc_final: 0.8562 (tttt) REVERT: 4 314 ASN cc_start: 0.7694 (p0) cc_final: 0.6903 (p0) REVERT: 5 80 ILE cc_start: 0.9020 (mm) cc_final: 0.8718 (tp) REVERT: 5 131 ARG cc_start: 0.8011 (ptt90) cc_final: 0.7374 (ptt90) REVERT: 5 133 GLU cc_start: 0.7973 (pt0) cc_final: 0.7513 (pt0) REVERT: 5 157 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9230 (mt) REVERT: 6 15 GLN cc_start: 0.8861 (mm110) cc_final: 0.8592 (mm-40) REVERT: 7 14 GLU cc_start: 0.8285 (tt0) cc_final: 0.7808 (tt0) REVERT: 8 7 LYS cc_start: 0.8477 (mtpm) cc_final: 0.8115 (tmtt) REVERT: 8 22 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7367 (mt-10) REVERT: 8 43 SER cc_start: 0.8048 (p) cc_final: 0.7772 (m) REVERT: 8 77 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7813 (tp30) REVERT: 8 115 SER cc_start: 0.8921 (p) cc_final: 0.8716 (p) REVERT: 9 105 TRP cc_start: 0.9048 (p-90) cc_final: 0.8371 (p-90) REVERT: 9 126 ILE cc_start: 0.8859 (mt) cc_final: 0.8624 (mt) REVERT: 9 189 THR cc_start: 0.9232 (m) cc_final: 0.8989 (p) REVERT: a 169 MET cc_start: 0.8661 (mmm) cc_final: 0.8461 (mmm) REVERT: a 205 ASN cc_start: 0.9319 (m-40) cc_final: 0.8556 (m-40) REVERT: b 189 TYR cc_start: 0.9021 (m-80) cc_final: 0.8818 (m-80) REVERT: b 205 ASN cc_start: 0.8974 (m-40) cc_final: 0.8636 (m110) REVERT: b 216 ASP cc_start: 0.7407 (t70) cc_final: 0.6980 (t0) REVERT: b 314 ASN cc_start: 0.7865 (p0) cc_final: 0.7005 (p0) REVERT: c 90 ARG cc_start: 0.8172 (ptp90) cc_final: 0.7542 (ptp90) REVERT: c 125 MET cc_start: 0.8622 (mmp) cc_final: 0.8216 (mmm) REVERT: d 122 MET cc_start: 0.8258 (mmm) cc_final: 0.7891 (mmm) REVERT: e 47 ARG cc_start: 0.8362 (ttp80) cc_final: 0.7923 (ptt90) REVERT: e 88 ARG cc_start: 0.8247 (mtm180) cc_final: 0.6477 (mmm160) REVERT: f 43 SER cc_start: 0.8505 (p) cc_final: 0.7806 (p) REVERT: f 45 GLU cc_start: 0.7535 (pm20) cc_final: 0.7275 (pm20) REVERT: f 77 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7974 (tm-30) REVERT: f 78 ARG cc_start: 0.7700 (tpt-90) cc_final: 0.7420 (tpp-160) REVERT: f 81 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8435 (tm-30) REVERT: f 91 PHE cc_start: 0.8378 (m-80) cc_final: 0.7995 (m-80) REVERT: f 106 MET cc_start: 0.6837 (ptp) cc_final: 0.6475 (ptm) REVERT: f 116 HIS cc_start: 0.8549 (p-80) cc_final: 0.7949 (p-80) REVERT: f 123 GLU cc_start: 0.7865 (tp30) cc_final: 0.7474 (tp30) REVERT: f 126 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7562 (mtp) outliers start: 187 outliers final: 102 residues processed: 2147 average time/residue: 0.6412 time to fit residues: 2314.5393 Evaluate side-chains 1863 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1753 time to evaluate : 5.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 231 ASP Chi-restraints excluded: chain I residue 239 GLU Chi-restraints excluded: chain I residue 306 ILE Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 239 GLU Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 326 THR Chi-restraints excluded: chain J residue 356 LEU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 143 SER Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain O residue 157 LEU Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 306 ILE Chi-restraints excluded: chain P residue 356 LEU Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 170 THR Chi-restraints excluded: chain Q residue 278 SER Chi-restraints excluded: chain Q residue 306 ILE Chi-restraints excluded: chain Q residue 331 LEU Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 126 MET Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 128 THR Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 231 ASP Chi-restraints excluded: chain W residue 356 LEU Chi-restraints excluded: chain W residue 373 ILE Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 278 SER Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain X residue 367 ASP Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 30 THR Chi-restraints excluded: chain 1 residue 93 VAL Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 126 CYS Chi-restraints excluded: chain 3 residue 160 VAL Chi-restraints excluded: chain 3 residue 163 ARG Chi-restraints excluded: chain 3 residue 225 ILE Chi-restraints excluded: chain 3 residue 231 ASP Chi-restraints excluded: chain 3 residue 239 GLU Chi-restraints excluded: chain 3 residue 306 ILE Chi-restraints excluded: chain 3 residue 326 THR Chi-restraints excluded: chain 3 residue 356 LEU Chi-restraints excluded: chain 4 residue 125 VAL Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 4 residue 239 GLU Chi-restraints excluded: chain 4 residue 278 SER Chi-restraints excluded: chain 4 residue 306 ILE Chi-restraints excluded: chain 4 residue 356 LEU Chi-restraints excluded: chain 5 residue 119 LEU Chi-restraints excluded: chain 5 residue 157 LEU Chi-restraints excluded: chain 7 residue 27 LEU Chi-restraints excluded: chain 7 residue 53 THR Chi-restraints excluded: chain 8 residue 9 LEU Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 9 residue 128 THR Chi-restraints excluded: chain 9 residue 157 LEU Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 306 ILE Chi-restraints excluded: chain a residue 356 LEU Chi-restraints excluded: chain b residue 160 VAL Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain b residue 278 SER Chi-restraints excluded: chain b residue 306 ILE Chi-restraints excluded: chain b residue 331 LEU Chi-restraints excluded: chain b residue 356 LEU Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain e residue 27 LEU Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 24 ILE Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 100 ILE Chi-restraints excluded: chain f residue 126 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 445 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 666 optimal weight: 1.9990 chunk 545 optimal weight: 8.9990 chunk 220 optimal weight: 0.7980 chunk 802 optimal weight: 5.9990 chunk 866 optimal weight: 6.9990 chunk 714 optimal weight: 4.9990 chunk 795 optimal weight: 20.0000 chunk 273 optimal weight: 2.9990 chunk 643 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 GLN A 349 GLN B 253 GLN D 76 GLN E 100 HIS ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 GLN I 257 ASN I 319 ASN I 349 GLN N 116 HIS ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 349 GLN Q 204 HIS ** Q 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 GLN ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 240 GLN W 349 GLN X 253 GLN Y 76 GLN ** 3 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 240 GLN 3 257 ASN 3 319 ASN 3 349 GLN 8 116 HIS ** 9 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 204 HIS ** b 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 76 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 68412 Z= 0.310 Angle : 0.730 17.205 93048 Z= 0.347 Chirality : 0.047 0.327 10404 Planarity : 0.005 0.062 12192 Dihedral : 5.360 22.103 9708 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 4.87 % Allowed : 17.24 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.08), residues: 8748 helix: -1.30 (0.09), residues: 2808 sheet: -1.96 (0.12), residues: 1608 loop : -2.59 (0.09), residues: 4332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP O 72 HIS 0.004 0.001 HIS U 116 PHE 0.030 0.002 PHE 1 83 TYR 0.019 0.001 TYR 7 101 ARG 0.008 0.001 ARG V 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2161 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 1840 time to evaluate : 5.634 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: C 126 ILE cc_start: 0.8803 (mt) cc_final: 0.8491 (mt) REVERT: C 189 THR cc_start: 0.9406 (m) cc_final: 0.9139 (p) REVERT: A 65 LYS cc_start: 0.8820 (tppp) cc_final: 0.8463 (ttmt) REVERT: A 101 GLN cc_start: 0.8846 (tt0) cc_final: 0.8467 (tt0) REVERT: A 116 LEU cc_start: 0.8898 (mm) cc_final: 0.8654 (mp) REVERT: A 143 MET cc_start: 0.8444 (tpp) cc_final: 0.8023 (ttm) REVERT: B 216 ASP cc_start: 0.7526 (t0) cc_final: 0.7055 (t0) REVERT: B 262 MET cc_start: 0.9098 (ttm) cc_final: 0.8880 (ttm) REVERT: B 314 ASN cc_start: 0.7540 (p0) cc_final: 0.6932 (p0) REVERT: B 379 LEU cc_start: 0.8115 (pp) cc_final: 0.7746 (pp) REVERT: F 14 TYR cc_start: 0.8757 (t80) cc_final: 0.8390 (t80) REVERT: G 45 GLU cc_start: 0.7892 (pm20) cc_final: 0.7482 (pm20) REVERT: G 60 ARG cc_start: 0.8289 (ptp-110) cc_final: 0.7936 (ptp90) REVERT: G 77 GLU cc_start: 0.8269 (tm-30) cc_final: 0.8059 (tm-30) REVERT: G 81 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8381 (tm-30) REVERT: G 117 ASN cc_start: 0.9185 (p0) cc_final: 0.8960 (p0) REVERT: G 126 MET cc_start: 0.7524 (mtp) cc_final: 0.7009 (mtp) REVERT: H 70 TRP cc_start: 0.8787 (m100) cc_final: 0.8548 (m100) REVERT: H 126 ILE cc_start: 0.8810 (mt) cc_final: 0.8580 (mt) REVERT: I 65 LYS cc_start: 0.8875 (tppt) cc_final: 0.8359 (ttmt) REVERT: I 105 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8250 (mt-10) REVERT: I 121 TYR cc_start: 0.8959 (m-80) cc_final: 0.8640 (m-80) REVERT: I 134 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7470 (mm-30) REVERT: I 143 MET cc_start: 0.8796 (tpp) cc_final: 0.8538 (ttm) REVERT: I 164 LYS cc_start: 0.8486 (mtpp) cc_final: 0.8267 (mtpp) REVERT: I 271 LYS cc_start: 0.8807 (ttpt) cc_final: 0.8363 (ttpp) REVERT: I 383 GLU cc_start: 0.7591 (tp30) cc_final: 0.7307 (tp30) REVERT: J 101 GLN cc_start: 0.8645 (tt0) cc_final: 0.8203 (tt0) REVERT: J 157 ASP cc_start: 0.8179 (m-30) cc_final: 0.7590 (m-30) REVERT: J 164 LYS cc_start: 0.8454 (mtpp) cc_final: 0.7603 (mtpp) REVERT: J 189 TYR cc_start: 0.9074 (m-80) cc_final: 0.8626 (m-10) REVERT: J 216 ASP cc_start: 0.7338 (t70) cc_final: 0.6946 (t0) REVERT: J 271 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8328 (tttt) REVERT: J 286 LYS cc_start: 0.9009 (ttpt) cc_final: 0.8558 (tttt) REVERT: J 314 ASN cc_start: 0.7876 (p0) cc_final: 0.7172 (p0) REVERT: J 349 GLN cc_start: 0.8163 (tt0) cc_final: 0.7866 (tt0) REVERT: J 355 ASP cc_start: 0.8228 (m-30) cc_final: 0.7530 (t0) REVERT: K 106 ARG cc_start: 0.8877 (ttp80) cc_final: 0.8339 (ptm160) REVERT: M 14 GLU cc_start: 0.8284 (tt0) cc_final: 0.7840 (tt0) REVERT: N 7 LYS cc_start: 0.8522 (mtpm) cc_final: 0.8093 (tmtt) REVERT: N 22 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7495 (mt-10) REVERT: N 77 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7733 (tm-30) REVERT: N 81 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8435 (tm-30) REVERT: N 123 GLU cc_start: 0.7840 (tp30) cc_final: 0.7593 (tp30) REVERT: O 105 TRP cc_start: 0.9112 (p-90) cc_final: 0.8398 (p-90) REVERT: O 126 ILE cc_start: 0.8735 (mt) cc_final: 0.8479 (mt) REVERT: P 69 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8190 (mt-10) REVERT: P 101 GLN cc_start: 0.8815 (tt0) cc_final: 0.8484 (tt0) REVERT: P 163 ARG cc_start: 0.7323 (mmm-85) cc_final: 0.6464 (mmt90) REVERT: P 164 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8145 (ttmm) REVERT: P 205 ASN cc_start: 0.9220 (m-40) cc_final: 0.8588 (m-40) REVERT: P 244 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9064 (tp) REVERT: P 383 GLU cc_start: 0.7735 (tp30) cc_final: 0.7454 (tp30) REVERT: Q 216 ASP cc_start: 0.7309 (t70) cc_final: 0.6772 (t0) REVERT: Q 314 ASN cc_start: 0.7935 (p0) cc_final: 0.7008 (p0) REVERT: Q 349 GLN cc_start: 0.8234 (tt0) cc_final: 0.8026 (tt0) REVERT: R 76 GLN cc_start: 0.8164 (tp-100) cc_final: 0.7900 (tp-100) REVERT: R 131 ARG cc_start: 0.7919 (ptt90) cc_final: 0.7406 (ptt90) REVERT: S 122 MET cc_start: 0.8361 (mmm) cc_final: 0.7974 (mmm) REVERT: U 52 GLU cc_start: 0.7166 (mp0) cc_final: 0.6185 (mp0) REVERT: U 77 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7903 (tm-30) REVERT: U 81 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8317 (tm-30) REVERT: U 90 GLU cc_start: 0.8800 (tp30) cc_final: 0.8440 (mm-30) REVERT: U 91 PHE cc_start: 0.8194 (m-80) cc_final: 0.7973 (m-80) REVERT: U 116 HIS cc_start: 0.8559 (p-80) cc_final: 0.8041 (p-80) REVERT: U 123 GLU cc_start: 0.7849 (tp30) cc_final: 0.7532 (tp30) REVERT: U 126 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7684 (mtp) REVERT: V 126 ILE cc_start: 0.8751 (mt) cc_final: 0.8445 (mt) REVERT: V 189 THR cc_start: 0.9403 (m) cc_final: 0.9133 (p) REVERT: W 101 GLN cc_start: 0.8808 (tt0) cc_final: 0.8434 (tt0) REVERT: W 116 LEU cc_start: 0.8890 (mm) cc_final: 0.8659 (mp) REVERT: W 164 LYS cc_start: 0.8750 (mtpp) cc_final: 0.8526 (mtpp) REVERT: X 51 ARG cc_start: 0.7849 (ptp90) cc_final: 0.7628 (ptp90) REVERT: X 101 GLN cc_start: 0.8444 (tp-100) cc_final: 0.8186 (tt0) REVERT: X 105 GLU cc_start: 0.8230 (mt-10) cc_final: 0.8012 (mt-10) REVERT: X 216 ASP cc_start: 0.7528 (t0) cc_final: 0.7044 (t0) REVERT: X 262 MET cc_start: 0.9159 (ttm) cc_final: 0.8937 (ttm) REVERT: X 314 ASN cc_start: 0.7518 (p0) cc_final: 0.6904 (p0) REVERT: X 379 LEU cc_start: 0.8120 (pp) cc_final: 0.7765 (pp) REVERT: Y 131 ARG cc_start: 0.8215 (ptt90) cc_final: 0.7930 (ptm-80) REVERT: Z 14 TYR cc_start: 0.8745 (t80) cc_final: 0.8387 (t80) REVERT: 1 45 GLU cc_start: 0.7894 (pm20) cc_final: 0.7609 (pm20) REVERT: 1 60 ARG cc_start: 0.8306 (ptp-110) cc_final: 0.7962 (ptp90) REVERT: 1 81 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8256 (tm-30) REVERT: 1 117 ASN cc_start: 0.9201 (p0) cc_final: 0.8962 (p0) REVERT: 1 126 MET cc_start: 0.7600 (mtp) cc_final: 0.7255 (mtp) REVERT: 2 70 TRP cc_start: 0.8781 (m100) cc_final: 0.8540 (m100) REVERT: 2 126 ILE cc_start: 0.8820 (mt) cc_final: 0.8598 (mt) REVERT: 2 131 ARG cc_start: 0.8679 (ptt90) cc_final: 0.8321 (ppt170) REVERT: 3 65 LYS cc_start: 0.8927 (tppt) cc_final: 0.8503 (tppt) REVERT: 3 101 GLN cc_start: 0.8743 (tp-100) cc_final: 0.8406 (tt0) REVERT: 3 121 TYR cc_start: 0.8959 (m-80) cc_final: 0.8629 (m-80) REVERT: 3 143 MET cc_start: 0.8857 (tpp) cc_final: 0.8485 (ttm) REVERT: 3 164 LYS cc_start: 0.8615 (mtpp) cc_final: 0.8353 (mtpp) REVERT: 3 383 GLU cc_start: 0.7574 (tp30) cc_final: 0.7287 (tp30) REVERT: 4 105 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8117 (mt-10) REVERT: 4 189 TYR cc_start: 0.9068 (m-80) cc_final: 0.8635 (m-10) REVERT: 4 216 ASP cc_start: 0.7357 (t70) cc_final: 0.6933 (t0) REVERT: 4 271 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8305 (tttt) REVERT: 4 286 LYS cc_start: 0.8924 (ttpt) cc_final: 0.8535 (tttt) REVERT: 4 314 ASN cc_start: 0.7879 (p0) cc_final: 0.7195 (p0) REVERT: 4 349 GLN cc_start: 0.8182 (tt0) cc_final: 0.7856 (tt0) REVERT: 4 355 ASP cc_start: 0.8212 (m-30) cc_final: 0.7517 (t0) REVERT: 5 131 ARG cc_start: 0.7885 (ptt90) cc_final: 0.7681 (ptt90) REVERT: 7 14 GLU cc_start: 0.8289 (tt0) cc_final: 0.7827 (tt0) REVERT: 8 7 LYS cc_start: 0.8525 (mtpm) cc_final: 0.8107 (tmtt) REVERT: 8 77 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7678 (tp30) REVERT: 9 105 TRP cc_start: 0.9114 (p-90) cc_final: 0.8412 (p-90) REVERT: 9 126 ILE cc_start: 0.8748 (mt) cc_final: 0.8487 (mt) REVERT: 9 189 THR cc_start: 0.9286 (m) cc_final: 0.9084 (p) REVERT: a 69 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8176 (mt-10) REVERT: a 101 GLN cc_start: 0.8815 (tt0) cc_final: 0.8312 (tt0) REVERT: a 164 LYS cc_start: 0.8663 (mtpt) cc_final: 0.8412 (mtpt) REVERT: a 205 ASN cc_start: 0.9217 (m-40) cc_final: 0.8600 (m-40) REVERT: a 244 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9039 (tp) REVERT: a 271 LYS cc_start: 0.9037 (ttpt) cc_final: 0.8744 (ttpt) REVERT: a 383 GLU cc_start: 0.7699 (tp30) cc_final: 0.7441 (tp30) REVERT: b 189 TYR cc_start: 0.8999 (m-80) cc_final: 0.8792 (m-10) REVERT: b 216 ASP cc_start: 0.7310 (t70) cc_final: 0.6779 (t0) REVERT: b 314 ASN cc_start: 0.7917 (p0) cc_final: 0.6997 (p0) REVERT: b 349 GLN cc_start: 0.8237 (tt0) cc_final: 0.8032 (tt0) REVERT: b 358 GLN cc_start: 0.8825 (pp30) cc_final: 0.8620 (pm20) REVERT: c 76 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7897 (tp-100) REVERT: d 122 MET cc_start: 0.8400 (mmm) cc_final: 0.7987 (mmm) REVERT: e 88 ARG cc_start: 0.8337 (mtm180) cc_final: 0.6592 (mmm160) REVERT: e 95 ARG cc_start: 0.8619 (ttm-80) cc_final: 0.8091 (ttm-80) REVERT: f 51 ARG cc_start: 0.8270 (ttp80) cc_final: 0.7994 (ttp80) REVERT: f 61 SER cc_start: 0.8425 (t) cc_final: 0.8059 (t) REVERT: f 77 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7940 (tm-30) REVERT: f 81 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8243 (tm-30) REVERT: f 90 GLU cc_start: 0.8789 (tp30) cc_final: 0.8480 (mm-30) REVERT: f 91 PHE cc_start: 0.8446 (m-80) cc_final: 0.8203 (m-80) REVERT: f 106 MET cc_start: 0.6878 (ptp) cc_final: 0.6474 (ptm) REVERT: f 116 HIS cc_start: 0.8560 (p-80) cc_final: 0.8042 (p-80) REVERT: f 123 GLU cc_start: 0.7880 (tp30) cc_final: 0.7552 (tp30) REVERT: f 126 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7656 (mtp) outliers start: 321 outliers final: 229 residues processed: 2003 average time/residue: 0.6563 time to fit residues: 2228.7430 Evaluate side-chains 1940 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1707 time to evaluate : 5.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 222 SER Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 231 ASP Chi-restraints excluded: chain I residue 278 SER Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 278 SER Chi-restraints excluded: chain J residue 304 ILE Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 326 THR Chi-restraints excluded: chain J residue 356 LEU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain O residue 4 ASN Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain O residue 157 LEU Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 231 ASP Chi-restraints excluded: chain P residue 244 LEU Chi-restraints excluded: chain P residue 278 SER Chi-restraints excluded: chain P residue 285 THR Chi-restraints excluded: chain P residue 306 ILE Chi-restraints excluded: chain P residue 356 LEU Chi-restraints excluded: chain Q residue 32 MET Chi-restraints excluded: chain Q residue 98 ASN Chi-restraints excluded: chain Q residue 117 SER Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 126 CYS Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 170 THR Chi-restraints excluded: chain Q residue 208 SER Chi-restraints excluded: chain Q residue 222 SER Chi-restraints excluded: chain Q residue 225 ILE Chi-restraints excluded: chain Q residue 278 SER Chi-restraints excluded: chain Q residue 306 ILE Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 331 LEU Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 161 GLN Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 77 GLU Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 44 LEU Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 109 SER Chi-restraints excluded: chain U residue 126 MET Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 128 THR Chi-restraints excluded: chain W residue 122 LEU Chi-restraints excluded: chain W residue 126 CYS Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 177 CYS Chi-restraints excluded: chain W residue 187 ASP Chi-restraints excluded: chain W residue 222 SER Chi-restraints excluded: chain W residue 231 ASP Chi-restraints excluded: chain W residue 245 ILE Chi-restraints excluded: chain W residue 278 SER Chi-restraints excluded: chain W residue 306 ILE Chi-restraints excluded: chain W residue 331 LEU Chi-restraints excluded: chain W residue 356 LEU Chi-restraints excluded: chain X residue 50 MET Chi-restraints excluded: chain X residue 98 ASN Chi-restraints excluded: chain X residue 117 SER Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain X residue 126 CYS Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 177 CYS Chi-restraints excluded: chain X residue 225 ILE Chi-restraints excluded: chain X residue 231 ASP Chi-restraints excluded: chain X residue 278 SER Chi-restraints excluded: chain X residue 306 ILE Chi-restraints excluded: chain X residue 311 THR Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 30 THR Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 1 residue 61 SER Chi-restraints excluded: chain 1 residue 63 SER Chi-restraints excluded: chain 1 residue 65 SER Chi-restraints excluded: chain 1 residue 93 VAL Chi-restraints excluded: chain 1 residue 121 SER Chi-restraints excluded: chain 1 residue 133 SER Chi-restraints excluded: chain 2 residue 4 ASN Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 147 LEU Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 126 CYS Chi-restraints excluded: chain 3 residue 160 VAL Chi-restraints excluded: chain 3 residue 177 CYS Chi-restraints excluded: chain 3 residue 222 SER Chi-restraints excluded: chain 3 residue 231 ASP Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 326 THR Chi-restraints excluded: chain 3 residue 356 LEU Chi-restraints excluded: chain 4 residue 125 VAL Chi-restraints excluded: chain 4 residue 141 ASP Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 4 residue 225 ILE Chi-restraints excluded: chain 4 residue 278 SER Chi-restraints excluded: chain 4 residue 304 ILE Chi-restraints excluded: chain 4 residue 306 ILE Chi-restraints excluded: chain 4 residue 311 THR Chi-restraints excluded: chain 4 residue 356 LEU Chi-restraints excluded: chain 5 residue 119 LEU Chi-restraints excluded: chain 5 residue 133 GLU Chi-restraints excluded: chain 5 residue 143 SER Chi-restraints excluded: chain 6 residue 66 ASP Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 7 residue 27 LEU Chi-restraints excluded: chain 7 residue 53 THR Chi-restraints excluded: chain 7 residue 77 GLU Chi-restraints excluded: chain 8 residue 9 LEU Chi-restraints excluded: chain 8 residue 24 ILE Chi-restraints excluded: chain 8 residue 30 THR Chi-restraints excluded: chain 8 residue 85 ASP Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 9 residue 4 ASN Chi-restraints excluded: chain 9 residue 128 THR Chi-restraints excluded: chain 9 residue 157 LEU Chi-restraints excluded: chain a residue 117 SER Chi-restraints excluded: chain a residue 126 CYS Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 222 SER Chi-restraints excluded: chain a residue 231 ASP Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 278 SER Chi-restraints excluded: chain a residue 285 THR Chi-restraints excluded: chain a residue 306 ILE Chi-restraints excluded: chain a residue 356 LEU Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 98 ASN Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 125 VAL Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 160 VAL Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain b residue 177 CYS Chi-restraints excluded: chain b residue 208 SER Chi-restraints excluded: chain b residue 222 SER Chi-restraints excluded: chain b residue 278 SER Chi-restraints excluded: chain b residue 306 ILE Chi-restraints excluded: chain b residue 311 THR Chi-restraints excluded: chain b residue 331 LEU Chi-restraints excluded: chain b residue 356 LEU Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 161 GLN Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 73 THR Chi-restraints excluded: chain e residue 27 LEU Chi-restraints excluded: chain e residue 77 GLU Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 44 LEU Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 100 ILE Chi-restraints excluded: chain f residue 126 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 792 optimal weight: 4.9990 chunk 603 optimal weight: 0.9980 chunk 416 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 382 optimal weight: 5.9990 chunk 538 optimal weight: 3.9990 chunk 805 optimal weight: 2.9990 chunk 852 optimal weight: 8.9990 chunk 420 optimal weight: 7.9990 chunk 763 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN G 20 GLN ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 257 ASN ** J 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 319 ASN Q 251 HIS ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 368 GLN 0 100 HIS ** 3 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 257 ASN ** 4 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 319 ASN ** a 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 205 ASN b 251 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 68412 Z= 0.337 Angle : 0.739 18.344 93048 Z= 0.350 Chirality : 0.047 0.360 10404 Planarity : 0.005 0.060 12192 Dihedral : 5.287 22.095 9708 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 6.32 % Allowed : 17.24 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.08), residues: 8748 helix: -0.81 (0.09), residues: 2904 sheet: -1.67 (0.13), residues: 1524 loop : -2.48 (0.09), residues: 4320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 9 72 HIS 0.004 0.001 HIS B 283 PHE 0.032 0.002 PHE U 83 TYR 0.016 0.002 TYR 3 315 ARG 0.008 0.001 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2202 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 417 poor density : 1785 time to evaluate : 5.930 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: C 189 THR cc_start: 0.9418 (m) cc_final: 0.9172 (p) REVERT: A 95 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7762 (ttm-80) REVERT: A 101 GLN cc_start: 0.8876 (tt0) cc_final: 0.8554 (tt0) REVERT: A 133 ARG cc_start: 0.7897 (ptp90) cc_final: 0.7672 (ptp90) REVERT: A 164 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8376 (mtpt) REVERT: A 192 SER cc_start: 0.8575 (t) cc_final: 0.8288 (p) REVERT: B 91 LEU cc_start: 0.9283 (mp) cc_final: 0.9012 (mt) REVERT: B 216 ASP cc_start: 0.7658 (t0) cc_final: 0.7201 (t0) REVERT: B 262 MET cc_start: 0.9127 (ttm) cc_final: 0.8847 (ttm) REVERT: B 314 ASN cc_start: 0.7661 (p0) cc_final: 0.7199 (p0) REVERT: B 379 LEU cc_start: 0.8142 (pp) cc_final: 0.7816 (pp) REVERT: F 14 TYR cc_start: 0.8838 (t80) cc_final: 0.8505 (t80) REVERT: G 12 LYS cc_start: 0.8172 (mtpp) cc_final: 0.7878 (mtpm) REVERT: G 22 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7717 (mt-10) REVERT: G 81 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8440 (tm-30) REVERT: G 126 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7350 (mtp) REVERT: H 126 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8696 (mt) REVERT: I 105 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8260 (mt-10) REVERT: I 121 TYR cc_start: 0.8923 (m-80) cc_final: 0.8681 (m-80) REVERT: I 142 ARG cc_start: 0.8506 (mtm180) cc_final: 0.7768 (mtm180) REVERT: I 143 MET cc_start: 0.8845 (tpp) cc_final: 0.8522 (ttm) REVERT: I 271 LYS cc_start: 0.8809 (ttpt) cc_final: 0.8356 (ttpp) REVERT: I 319 ASN cc_start: 0.9010 (t0) cc_final: 0.8630 (t0) REVERT: J 101 GLN cc_start: 0.8809 (tt0) cc_final: 0.8423 (tt0) REVERT: J 157 ASP cc_start: 0.8121 (m-30) cc_final: 0.7859 (m-30) REVERT: J 164 LYS cc_start: 0.8487 (mtpp) cc_final: 0.8081 (mtpp) REVERT: J 189 TYR cc_start: 0.9084 (m-80) cc_final: 0.8649 (m-10) REVERT: J 216 ASP cc_start: 0.7444 (t70) cc_final: 0.7064 (t0) REVERT: J 244 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9094 (tp) REVERT: J 271 LYS cc_start: 0.8679 (ttpt) cc_final: 0.8456 (ttpt) REVERT: J 286 LYS cc_start: 0.9044 (ttpt) cc_final: 0.8525 (tttt) REVERT: J 314 ASN cc_start: 0.7884 (p0) cc_final: 0.7152 (p0) REVERT: J 349 GLN cc_start: 0.8180 (tt0) cc_final: 0.7850 (tt0) REVERT: J 355 ASP cc_start: 0.8003 (m-30) cc_final: 0.7669 (t0) REVERT: K 106 ARG cc_start: 0.8865 (ttp80) cc_final: 0.8418 (ptm160) REVERT: L 15 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8580 (mm-40) REVERT: L 72 ILE cc_start: 0.9126 (mm) cc_final: 0.8895 (mm) REVERT: M 14 GLU cc_start: 0.8225 (tt0) cc_final: 0.7775 (tt0) REVERT: M 50 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7269 (mm-30) REVERT: N 7 LYS cc_start: 0.8622 (mtpm) cc_final: 0.8188 (tmtt) REVERT: N 77 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7772 (tm-30) REVERT: N 81 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8478 (tm-30) REVERT: O 105 TRP cc_start: 0.9204 (p-90) cc_final: 0.8486 (p-90) REVERT: O 126 ILE cc_start: 0.8774 (mt) cc_final: 0.8542 (mt) REVERT: P 32 MET cc_start: 0.7075 (ptt) cc_final: 0.6531 (ptt) REVERT: P 101 GLN cc_start: 0.8861 (tt0) cc_final: 0.8546 (tt0) REVERT: P 163 ARG cc_start: 0.7580 (mmm-85) cc_final: 0.6880 (mmt90) REVERT: P 192 SER cc_start: 0.8597 (t) cc_final: 0.8343 (p) REVERT: P 205 ASN cc_start: 0.9206 (m-40) cc_final: 0.8583 (m-40) REVERT: Q 201 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9053 (mm) REVERT: Q 216 ASP cc_start: 0.7378 (t70) cc_final: 0.6750 (t0) REVERT: R 76 GLN cc_start: 0.8290 (tp-100) cc_final: 0.8036 (tp40) REVERT: R 131 ARG cc_start: 0.7872 (ptt90) cc_final: 0.7450 (ptt90) REVERT: S 122 MET cc_start: 0.8419 (mmm) cc_final: 0.8190 (mmm) REVERT: T 95 ARG cc_start: 0.8588 (ttm-80) cc_final: 0.7934 (ttm-80) REVERT: U 77 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7962 (tm-30) REVERT: U 81 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8271 (tm-30) REVERT: U 90 GLU cc_start: 0.8780 (tp30) cc_final: 0.8381 (mm-30) REVERT: U 91 PHE cc_start: 0.8432 (m-80) cc_final: 0.7975 (m-10) REVERT: U 106 MET cc_start: 0.6895 (ptp) cc_final: 0.6589 (ptm) REVERT: U 123 GLU cc_start: 0.7857 (tp30) cc_final: 0.7549 (tp30) REVERT: U 126 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7596 (mtp) REVERT: V 189 THR cc_start: 0.9418 (m) cc_final: 0.9158 (p) REVERT: W 101 GLN cc_start: 0.8824 (tt0) cc_final: 0.8497 (tt0) REVERT: W 164 LYS cc_start: 0.8801 (mtpp) cc_final: 0.8361 (ttmm) REVERT: W 192 SER cc_start: 0.8574 (t) cc_final: 0.8271 (p) REVERT: X 51 ARG cc_start: 0.7876 (ptp90) cc_final: 0.7647 (ptp90) REVERT: X 105 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8075 (mt-10) REVERT: X 163 ARG cc_start: 0.7547 (mpp80) cc_final: 0.7194 (mtm180) REVERT: X 216 ASP cc_start: 0.7658 (t0) cc_final: 0.7188 (t0) REVERT: X 271 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8345 (ttpt) REVERT: X 314 ASN cc_start: 0.7642 (p0) cc_final: 0.7178 (p0) REVERT: X 379 LEU cc_start: 0.8176 (pp) cc_final: 0.7884 (pp) REVERT: Y 131 ARG cc_start: 0.8160 (ptt90) cc_final: 0.7885 (ptm-80) REVERT: Z 14 TYR cc_start: 0.8836 (t80) cc_final: 0.8511 (t80) REVERT: 1 81 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8352 (tm-30) REVERT: 1 112 TYR cc_start: 0.8624 (m-80) cc_final: 0.8333 (m-80) REVERT: 1 117 ASN cc_start: 0.9162 (p0) cc_final: 0.8940 (p0) REVERT: 1 126 MET cc_start: 0.7516 (mtp) cc_final: 0.7255 (mtp) REVERT: 2 76 GLN cc_start: 0.8782 (tp-100) cc_final: 0.8532 (tp-100) REVERT: 2 131 ARG cc_start: 0.8796 (ptt90) cc_final: 0.8503 (ppt170) REVERT: 3 65 LYS cc_start: 0.8931 (tppt) cc_final: 0.8275 (tppt) REVERT: 3 69 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8133 (mt-10) REVERT: 3 101 GLN cc_start: 0.8765 (tp-100) cc_final: 0.8471 (tt0) REVERT: 3 105 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8217 (mt-10) REVERT: 3 121 TYR cc_start: 0.8889 (m-80) cc_final: 0.8630 (m-80) REVERT: 3 134 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7499 (mm-30) REVERT: 3 142 ARG cc_start: 0.8543 (mtm180) cc_final: 0.8085 (mtm180) REVERT: 3 143 MET cc_start: 0.8859 (tpp) cc_final: 0.8527 (ttm) REVERT: 3 164 LYS cc_start: 0.8659 (mtpp) cc_final: 0.8393 (mtpp) REVERT: 3 192 SER cc_start: 0.8596 (t) cc_final: 0.8142 (p) REVERT: 3 319 ASN cc_start: 0.9002 (t0) cc_final: 0.8631 (t0) REVERT: 4 101 GLN cc_start: 0.8574 (tt0) cc_final: 0.8234 (tt0) REVERT: 4 189 TYR cc_start: 0.9067 (m-80) cc_final: 0.8646 (m-10) REVERT: 4 216 ASP cc_start: 0.7467 (t70) cc_final: 0.7046 (t0) REVERT: 4 244 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9075 (tp) REVERT: 4 271 LYS cc_start: 0.8668 (ttpt) cc_final: 0.8435 (ttpt) REVERT: 4 286 LYS cc_start: 0.8892 (ttpt) cc_final: 0.8540 (tttt) REVERT: 4 314 ASN cc_start: 0.7928 (p0) cc_final: 0.7212 (p0) REVERT: 4 349 GLN cc_start: 0.8203 (tt0) cc_final: 0.7851 (tt0) REVERT: 4 355 ASP cc_start: 0.7985 (m-30) cc_final: 0.7727 (t0) REVERT: 5 131 ARG cc_start: 0.7916 (ptt90) cc_final: 0.7644 (ptt90) REVERT: 5 193 LEU cc_start: 0.9016 (tp) cc_final: 0.8638 (tp) REVERT: 6 15 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8570 (mm-40) REVERT: 6 72 ILE cc_start: 0.9117 (mm) cc_final: 0.8899 (mm) REVERT: 6 90 ASP cc_start: 0.7822 (m-30) cc_final: 0.7591 (m-30) REVERT: 7 14 GLU cc_start: 0.8262 (tt0) cc_final: 0.7783 (tt0) REVERT: 8 7 LYS cc_start: 0.8628 (mtpm) cc_final: 0.8344 (tmtt) REVERT: 8 22 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7531 (mt-10) REVERT: 8 77 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7664 (tp30) REVERT: 9 105 TRP cc_start: 0.9191 (p-90) cc_final: 0.8486 (p-90) REVERT: a 101 GLN cc_start: 0.8849 (tt0) cc_final: 0.8385 (tt0) REVERT: a 164 LYS cc_start: 0.8677 (mtpt) cc_final: 0.8424 (mtpt) REVERT: a 192 SER cc_start: 0.8583 (t) cc_final: 0.8309 (p) REVERT: a 205 ASN cc_start: 0.9206 (m-40) cc_final: 0.8593 (m-40) REVERT: a 244 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9013 (tp) REVERT: b 189 TYR cc_start: 0.9020 (m-80) cc_final: 0.8725 (m-10) REVERT: b 201 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9100 (mm) REVERT: b 216 ASP cc_start: 0.7378 (t70) cc_final: 0.6750 (t0) REVERT: b 257 ASN cc_start: 0.8812 (m-40) cc_final: 0.8566 (m110) REVERT: b 271 LYS cc_start: 0.8875 (tttt) cc_final: 0.8607 (tttt) REVERT: b 358 GLN cc_start: 0.8963 (pp30) cc_final: 0.8661 (pm20) REVERT: c 125 MET cc_start: 0.8576 (mmp) cc_final: 0.8224 (mmm) REVERT: c 131 ARG cc_start: 0.7976 (ptt90) cc_final: 0.6568 (ptt90) REVERT: c 133 GLU cc_start: 0.7800 (pt0) cc_final: 0.7214 (pt0) REVERT: d 122 MET cc_start: 0.8455 (mmm) cc_final: 0.8204 (mmm) REVERT: e 95 ARG cc_start: 0.8570 (ttm-80) cc_final: 0.7948 (ttm-80) REVERT: f 51 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7989 (ttp80) REVERT: f 77 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7807 (tm-30) REVERT: f 81 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8256 (tm-30) REVERT: f 90 GLU cc_start: 0.8807 (tp30) cc_final: 0.8534 (mm-30) REVERT: f 91 PHE cc_start: 0.8418 (m-80) cc_final: 0.8135 (m-80) REVERT: f 123 GLU cc_start: 0.7875 (tp30) cc_final: 0.7529 (tp30) REVERT: f 126 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7428 (mtp) outliers start: 417 outliers final: 272 residues processed: 2018 average time/residue: 0.6483 time to fit residues: 2212.1364 Evaluate side-chains 1971 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 1689 time to evaluate : 5.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 177 CYS Chi-restraints excluded: chain I residue 222 SER Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 231 ASP Chi-restraints excluded: chain I residue 239 GLU Chi-restraints excluded: chain I residue 245 ILE Chi-restraints excluded: chain I residue 278 SER Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 306 ILE Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 177 CYS Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 278 SER Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 326 THR Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 356 LEU Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain N residue 133 SER Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 222 SER Chi-restraints excluded: chain P residue 231 ASP Chi-restraints excluded: chain P residue 278 SER Chi-restraints excluded: chain P residue 285 THR Chi-restraints excluded: chain P residue 306 ILE Chi-restraints excluded: chain P residue 356 LEU Chi-restraints excluded: chain Q residue 117 SER Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 126 CYS Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 168 ASP Chi-restraints excluded: chain Q residue 170 THR Chi-restraints excluded: chain Q residue 177 CYS Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 208 SER Chi-restraints excluded: chain Q residue 222 SER Chi-restraints excluded: chain Q residue 225 ILE Chi-restraints excluded: chain Q residue 278 SER Chi-restraints excluded: chain Q residue 306 ILE Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 331 LEU Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain R residue 133 GLU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 161 GLN Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 45 SER Chi-restraints excluded: chain T residue 77 GLU Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 44 LEU Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain U residue 126 MET Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 128 THR Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 122 LEU Chi-restraints excluded: chain W residue 126 CYS Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 177 CYS Chi-restraints excluded: chain W residue 187 ASP Chi-restraints excluded: chain W residue 222 SER Chi-restraints excluded: chain W residue 231 ASP Chi-restraints excluded: chain W residue 245 ILE Chi-restraints excluded: chain W residue 278 SER Chi-restraints excluded: chain W residue 331 LEU Chi-restraints excluded: chain W residue 356 LEU Chi-restraints excluded: chain W residue 373 ILE Chi-restraints excluded: chain X residue 50 MET Chi-restraints excluded: chain X residue 98 ASN Chi-restraints excluded: chain X residue 117 SER Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain X residue 126 CYS Chi-restraints excluded: chain X residue 133 ARG Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 177 CYS Chi-restraints excluded: chain X residue 231 ASP Chi-restraints excluded: chain X residue 278 SER Chi-restraints excluded: chain X residue 311 THR Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain X residue 367 ASP Chi-restraints excluded: chain Y residue 107 LEU Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 45 SER Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 30 THR Chi-restraints excluded: chain 1 residue 61 SER Chi-restraints excluded: chain 1 residue 63 SER Chi-restraints excluded: chain 1 residue 65 SER Chi-restraints excluded: chain 1 residue 85 ASP Chi-restraints excluded: chain 1 residue 93 VAL Chi-restraints excluded: chain 1 residue 121 SER Chi-restraints excluded: chain 1 residue 133 SER Chi-restraints excluded: chain 2 residue 4 ASN Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 54 THR Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 147 LEU Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 3 residue 46 THR Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 122 LEU Chi-restraints excluded: chain 3 residue 160 VAL Chi-restraints excluded: chain 3 residue 177 CYS Chi-restraints excluded: chain 3 residue 222 SER Chi-restraints excluded: chain 3 residue 231 ASP Chi-restraints excluded: chain 3 residue 245 ILE Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 303 LEU Chi-restraints excluded: chain 3 residue 304 ILE Chi-restraints excluded: chain 3 residue 306 ILE Chi-restraints excluded: chain 3 residue 326 THR Chi-restraints excluded: chain 3 residue 356 LEU Chi-restraints excluded: chain 4 residue 125 VAL Chi-restraints excluded: chain 4 residue 141 ASP Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 4 residue 177 CYS Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 4 residue 278 SER Chi-restraints excluded: chain 4 residue 306 ILE Chi-restraints excluded: chain 4 residue 311 THR Chi-restraints excluded: chain 4 residue 356 LEU Chi-restraints excluded: chain 5 residue 133 GLU Chi-restraints excluded: chain 5 residue 143 SER Chi-restraints excluded: chain 6 residue 66 ASP Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 97 LEU Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 7 residue 27 LEU Chi-restraints excluded: chain 7 residue 53 THR Chi-restraints excluded: chain 7 residue 77 GLU Chi-restraints excluded: chain 8 residue 9 LEU Chi-restraints excluded: chain 8 residue 24 ILE Chi-restraints excluded: chain 8 residue 30 THR Chi-restraints excluded: chain 8 residue 44 LEU Chi-restraints excluded: chain 8 residue 85 ASP Chi-restraints excluded: chain 8 residue 133 SER Chi-restraints excluded: chain 9 residue 4 ASN Chi-restraints excluded: chain 9 residue 12 THR Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 54 THR Chi-restraints excluded: chain 9 residue 128 THR Chi-restraints excluded: chain 9 residue 193 LEU Chi-restraints excluded: chain a residue 117 SER Chi-restraints excluded: chain a residue 126 CYS Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 222 SER Chi-restraints excluded: chain a residue 231 ASP Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 278 SER Chi-restraints excluded: chain a residue 285 THR Chi-restraints excluded: chain a residue 306 ILE Chi-restraints excluded: chain a residue 356 LEU Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 125 VAL Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 160 VAL Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain b residue 177 CYS Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain b residue 208 SER Chi-restraints excluded: chain b residue 222 SER Chi-restraints excluded: chain b residue 263 LEU Chi-restraints excluded: chain b residue 278 SER Chi-restraints excluded: chain b residue 306 ILE Chi-restraints excluded: chain b residue 311 THR Chi-restraints excluded: chain b residue 331 LEU Chi-restraints excluded: chain b residue 356 LEU Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 161 GLN Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 73 THR Chi-restraints excluded: chain e residue 27 LEU Chi-restraints excluded: chain e residue 45 SER Chi-restraints excluded: chain e residue 53 THR Chi-restraints excluded: chain e residue 77 GLU Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 44 LEU Chi-restraints excluded: chain f residue 85 ASP Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 100 ILE Chi-restraints excluded: chain f residue 121 SER Chi-restraints excluded: chain f residue 126 MET Chi-restraints excluded: chain f residue 133 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 710 optimal weight: 5.9990 chunk 483 optimal weight: 0.0670 chunk 12 optimal weight: 10.0000 chunk 634 optimal weight: 0.2980 chunk 351 optimal weight: 0.9990 chunk 727 optimal weight: 3.9990 chunk 589 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 435 optimal weight: 6.9990 chunk 765 optimal weight: 0.9980 chunk 215 optimal weight: 7.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 ASN B 257 ASN G 116 HIS ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 257 ASN ** J 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 ASN K 76 GLN ** P 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 240 GLN R 4 ASN R 76 GLN U 117 ASN ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 319 ASN X 257 ASN Y 4 ASN ** 3 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 257 ASN 3 349 GLN ** 4 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 319 ASN 5 76 GLN ** a 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 240 GLN ** a 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 76 GLN f 117 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 68412 Z= 0.193 Angle : 0.668 15.689 93048 Z= 0.313 Chirality : 0.045 0.384 10404 Planarity : 0.005 0.069 12192 Dihedral : 4.914 20.662 9708 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 5.17 % Allowed : 19.76 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.09), residues: 8748 helix: -0.25 (0.10), residues: 2916 sheet: -1.69 (0.13), residues: 1608 loop : -2.41 (0.09), residues: 4224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 9 72 HIS 0.005 0.001 HIS U 116 PHE 0.031 0.002 PHE G 83 TYR 0.018 0.001 TYR b 315 ARG 0.007 0.000 ARG Q 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2178 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 1837 time to evaluate : 5.587 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: C 131 ARG cc_start: 0.8473 (ptt90) cc_final: 0.7993 (ppt170) REVERT: C 189 THR cc_start: 0.9415 (m) cc_final: 0.9149 (p) REVERT: A 65 LYS cc_start: 0.8847 (tppp) cc_final: 0.8539 (tptm) REVERT: A 133 ARG cc_start: 0.7906 (ptp90) cc_final: 0.7674 (ptp90) REVERT: A 164 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8334 (mtpt) REVERT: A 192 SER cc_start: 0.8544 (t) cc_final: 0.8180 (p) REVERT: B 163 ARG cc_start: 0.7357 (mpt-90) cc_final: 0.6987 (mpp80) REVERT: B 164 LYS cc_start: 0.8040 (mtmm) cc_final: 0.7761 (ttmm) REVERT: B 215 LEU cc_start: 0.9323 (mt) cc_final: 0.9041 (mt) REVERT: B 216 ASP cc_start: 0.7620 (t0) cc_final: 0.7182 (t0) REVERT: B 257 ASN cc_start: 0.8848 (m-40) cc_final: 0.8646 (m110) REVERT: B 262 MET cc_start: 0.8929 (ttm) cc_final: 0.8708 (ttm) REVERT: B 314 ASN cc_start: 0.7437 (p0) cc_final: 0.6583 (p0) REVERT: B 379 LEU cc_start: 0.8080 (pp) cc_final: 0.7806 (pp) REVERT: F 14 TYR cc_start: 0.8819 (t80) cc_final: 0.8493 (t80) REVERT: F 122 MET cc_start: 0.8460 (mmm) cc_final: 0.8159 (mtp) REVERT: G 22 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7625 (mt-10) REVERT: G 81 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8390 (tm-30) REVERT: G 126 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7062 (mtp) REVERT: H 149 VAL cc_start: 0.9105 (t) cc_final: 0.8871 (t) REVERT: I 105 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8321 (mt-10) REVERT: I 121 TYR cc_start: 0.8841 (m-80) cc_final: 0.8621 (m-80) REVERT: I 142 ARG cc_start: 0.8451 (mtm180) cc_final: 0.7703 (mtm180) REVERT: I 143 MET cc_start: 0.8824 (tpp) cc_final: 0.8496 (ttm) REVERT: I 192 SER cc_start: 0.8444 (t) cc_final: 0.7967 (p) REVERT: I 271 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8311 (ttpp) REVERT: I 319 ASN cc_start: 0.9007 (t0) cc_final: 0.8639 (t0) REVERT: J 101 GLN cc_start: 0.8765 (tt0) cc_final: 0.8372 (tt0) REVERT: J 157 ASP cc_start: 0.8107 (m-30) cc_final: 0.7844 (m-30) REVERT: J 164 LYS cc_start: 0.8499 (mtpp) cc_final: 0.8074 (mtpp) REVERT: J 189 TYR cc_start: 0.9079 (m-80) cc_final: 0.8622 (m-10) REVERT: J 216 ASP cc_start: 0.7381 (t70) cc_final: 0.6914 (t0) REVERT: J 286 LYS cc_start: 0.9008 (ttpt) cc_final: 0.8475 (tttt) REVERT: J 314 ASN cc_start: 0.7804 (p0) cc_final: 0.7110 (p0) REVERT: J 349 GLN cc_start: 0.8211 (tt0) cc_final: 0.7871 (tt0) REVERT: J 355 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7371 (t0) REVERT: K 106 ARG cc_start: 0.8865 (ttp80) cc_final: 0.8359 (ptm160) REVERT: K 193 LEU cc_start: 0.9026 (tp) cc_final: 0.8630 (tp) REVERT: L 15 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8242 (mm-40) REVERT: L 72 ILE cc_start: 0.9093 (mm) cc_final: 0.8869 (mm) REVERT: M 47 ARG cc_start: 0.8422 (ttp80) cc_final: 0.7901 (ptt90) REVERT: N 7 LYS cc_start: 0.8625 (mtpm) cc_final: 0.8185 (tmtt) REVERT: N 22 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7557 (mt-10) REVERT: N 77 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7683 (tm-30) REVERT: N 81 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8439 (tm-30) REVERT: N 91 PHE cc_start: 0.7823 (m-80) cc_final: 0.7599 (m-10) REVERT: N 106 MET cc_start: 0.7055 (ptm) cc_final: 0.6803 (ptm) REVERT: O 105 TRP cc_start: 0.9143 (p-90) cc_final: 0.8533 (p-90) REVERT: O 110 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8101 (t70) REVERT: O 126 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8502 (mt) REVERT: P 32 MET cc_start: 0.7171 (ptt) cc_final: 0.6362 (ptt) REVERT: P 101 GLN cc_start: 0.8807 (tt0) cc_final: 0.8534 (tt0) REVERT: P 163 ARG cc_start: 0.7587 (mmm-85) cc_final: 0.6966 (mmt90) REVERT: P 192 SER cc_start: 0.8525 (t) cc_final: 0.8225 (p) REVERT: P 205 ASN cc_start: 0.9151 (m-40) cc_final: 0.8757 (m-40) REVERT: P 244 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9037 (tp) REVERT: P 271 LYS cc_start: 0.9100 (ttpt) cc_final: 0.8845 (ttpt) REVERT: Q 136 HIS cc_start: 0.8478 (m-70) cc_final: 0.8171 (m-70) REVERT: Q 216 ASP cc_start: 0.7345 (t70) cc_final: 0.6705 (t0) REVERT: Q 271 LYS cc_start: 0.8836 (tttt) cc_final: 0.8571 (tttt) REVERT: Q 314 ASN cc_start: 0.7931 (p0) cc_final: 0.6984 (p0) REVERT: R 89 LEU cc_start: 0.8983 (tt) cc_final: 0.8745 (tt) REVERT: R 131 ARG cc_start: 0.7811 (ptt90) cc_final: 0.7469 (ptt90) REVERT: S 97 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7320 (pp) REVERT: T 47 ARG cc_start: 0.8180 (ttp80) cc_final: 0.7819 (ptt90) REVERT: U 51 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7962 (ttp80) REVERT: U 52 GLU cc_start: 0.7172 (mp0) cc_final: 0.6050 (mp0) REVERT: U 60 ARG cc_start: 0.8429 (ptp-110) cc_final: 0.7840 (ptp90) REVERT: U 81 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8422 (tm-30) REVERT: U 90 GLU cc_start: 0.8746 (tp30) cc_final: 0.8358 (mm-30) REVERT: U 91 PHE cc_start: 0.8409 (m-80) cc_final: 0.8055 (m-10) REVERT: U 106 MET cc_start: 0.6648 (ptp) cc_final: 0.6368 (ptm) REVERT: U 107 ILE cc_start: 0.8292 (tp) cc_final: 0.7992 (tp) REVERT: U 123 GLU cc_start: 0.7770 (tp30) cc_final: 0.7425 (tp30) REVERT: U 126 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7285 (mtp) REVERT: V 167 HIS cc_start: 0.7743 (p-80) cc_final: 0.7524 (p-80) REVERT: V 189 THR cc_start: 0.9406 (m) cc_final: 0.9143 (p) REVERT: W 65 LYS cc_start: 0.8761 (tptm) cc_final: 0.8368 (tppp) REVERT: W 164 LYS cc_start: 0.8769 (mtpp) cc_final: 0.8263 (ttmm) REVERT: W 192 SER cc_start: 0.8516 (t) cc_final: 0.8164 (p) REVERT: X 51 ARG cc_start: 0.7827 (ptp90) cc_final: 0.7592 (ptp90) REVERT: X 105 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8012 (mt-10) REVERT: X 215 LEU cc_start: 0.9331 (mt) cc_final: 0.9045 (mt) REVERT: X 216 ASP cc_start: 0.7619 (t0) cc_final: 0.7159 (t0) REVERT: X 253 GLN cc_start: 0.9165 (mt0) cc_final: 0.8879 (mt0) REVERT: X 262 MET cc_start: 0.8978 (ttm) cc_final: 0.8728 (ttm) REVERT: X 271 LYS cc_start: 0.8486 (ttpt) cc_final: 0.8278 (ttpt) REVERT: X 314 ASN cc_start: 0.7417 (p0) cc_final: 0.6564 (p0) REVERT: X 357 ASP cc_start: 0.9021 (t70) cc_final: 0.8749 (t0) REVERT: Y 131 ARG cc_start: 0.8162 (ptt90) cc_final: 0.7941 (ptm-80) REVERT: Z 14 TYR cc_start: 0.8794 (t80) cc_final: 0.8482 (t80) REVERT: 0 94 GLU cc_start: 0.7528 (tt0) cc_final: 0.7315 (tm-30) REVERT: 1 14 ASP cc_start: 0.7709 (p0) cc_final: 0.7502 (p0) REVERT: 1 112 TYR cc_start: 0.8557 (m-80) cc_final: 0.8157 (m-80) REVERT: 1 117 ASN cc_start: 0.9117 (p0) cc_final: 0.8879 (p0) REVERT: 1 126 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.6961 (mtp) REVERT: 2 131 ARG cc_start: 0.8763 (ptt90) cc_final: 0.8479 (ppt170) REVERT: 2 149 VAL cc_start: 0.9090 (t) cc_final: 0.8869 (t) REVERT: 3 65 LYS cc_start: 0.8888 (tppt) cc_final: 0.8449 (tppt) REVERT: 3 69 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8062 (mt-10) REVERT: 3 105 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8269 (mt-10) REVERT: 3 121 TYR cc_start: 0.8807 (m-80) cc_final: 0.8592 (m-80) REVERT: 3 142 ARG cc_start: 0.8488 (mtm180) cc_final: 0.7988 (mtm180) REVERT: 3 143 MET cc_start: 0.8820 (tpp) cc_final: 0.8504 (ttm) REVERT: 3 164 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8166 (ttmm) REVERT: 3 192 SER cc_start: 0.8472 (t) cc_final: 0.7982 (p) REVERT: 3 319 ASN cc_start: 0.8976 (t0) cc_final: 0.8537 (t0) REVERT: 4 101 GLN cc_start: 0.8650 (tt0) cc_final: 0.8222 (tt0) REVERT: 4 189 TYR cc_start: 0.9062 (m-80) cc_final: 0.8548 (m-10) REVERT: 4 216 ASP cc_start: 0.7408 (t70) cc_final: 0.6939 (t0) REVERT: 4 286 LYS cc_start: 0.8900 (ttpt) cc_final: 0.8436 (tttt) REVERT: 4 314 ASN cc_start: 0.7822 (p0) cc_final: 0.7252 (p0) REVERT: 4 349 GLN cc_start: 0.8228 (tt0) cc_final: 0.7857 (tt0) REVERT: 4 355 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7350 (t0) REVERT: 5 106 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8332 (ptm160) REVERT: 5 193 LEU cc_start: 0.8942 (tp) cc_final: 0.8544 (tp) REVERT: 6 15 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8229 (mm-40) REVERT: 6 72 ILE cc_start: 0.9077 (mm) cc_final: 0.8848 (mm) REVERT: 6 90 ASP cc_start: 0.7849 (m-30) cc_final: 0.7599 (m-30) REVERT: 8 7 LYS cc_start: 0.8600 (mtpm) cc_final: 0.8199 (tmtt) REVERT: 8 22 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7480 (mt-10) REVERT: 8 106 MET cc_start: 0.6859 (ptm) cc_final: 0.6655 (ptm) REVERT: 9 2 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7154 (tpt) REVERT: 9 105 TRP cc_start: 0.9139 (p-90) cc_final: 0.8558 (p-90) REVERT: 9 110 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8130 (t70) REVERT: 9 131 ARG cc_start: 0.8514 (ptt90) cc_final: 0.8173 (ppt170) REVERT: a 101 GLN cc_start: 0.8815 (tt0) cc_final: 0.8394 (tt0) REVERT: a 164 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8411 (mtpt) REVERT: a 192 SER cc_start: 0.8445 (t) cc_final: 0.8167 (p) REVERT: a 205 ASN cc_start: 0.9145 (m-40) cc_final: 0.8764 (m-40) REVERT: a 244 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9026 (tp) REVERT: a 271 LYS cc_start: 0.9054 (ttpt) cc_final: 0.8705 (ttpt) REVERT: b 51 ARG cc_start: 0.8035 (ptp90) cc_final: 0.7704 (ptp90) REVERT: b 189 TYR cc_start: 0.8989 (m-80) cc_final: 0.8770 (m-10) REVERT: b 201 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8953 (mm) REVERT: b 216 ASP cc_start: 0.7355 (t70) cc_final: 0.6717 (t0) REVERT: b 271 LYS cc_start: 0.8859 (tttt) cc_final: 0.8530 (tttt) REVERT: b 355 ASP cc_start: 0.7656 (t0) cc_final: 0.7412 (t0) REVERT: b 358 GLN cc_start: 0.8885 (pp30) cc_final: 0.8642 (pm20) REVERT: d 97 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7348 (pp) REVERT: f 51 ARG cc_start: 0.8274 (ttp80) cc_final: 0.8052 (ttp80) REVERT: f 81 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8391 (tm-30) REVERT: f 90 GLU cc_start: 0.8808 (tp30) cc_final: 0.8511 (mm-30) REVERT: f 123 GLU cc_start: 0.7815 (tp30) cc_final: 0.7479 (tp30) outliers start: 341 outliers final: 227 residues processed: 2020 average time/residue: 0.6364 time to fit residues: 2165.9548 Evaluate side-chains 1953 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1712 time to evaluate : 5.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 222 SER Chi-restraints excluded: chain I residue 231 ASP Chi-restraints excluded: chain I residue 245 ILE Chi-restraints excluded: chain I residue 278 SER Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain I residue 373 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 278 SER Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 355 ASP Chi-restraints excluded: chain J residue 356 LEU Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 110 ASP Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 187 ASP Chi-restraints excluded: chain P residue 222 SER Chi-restraints excluded: chain P residue 231 ASP Chi-restraints excluded: chain P residue 244 LEU Chi-restraints excluded: chain P residue 278 SER Chi-restraints excluded: chain P residue 306 ILE Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 356 LEU Chi-restraints excluded: chain Q residue 32 MET Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 126 CYS Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 170 THR Chi-restraints excluded: chain Q residue 231 ASP Chi-restraints excluded: chain Q residue 278 SER Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain R residue 161 GLN Chi-restraints excluded: chain S residue 2 SER Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 77 GLU Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 117 ASN Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain U residue 126 MET Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 29 PHE Chi-restraints excluded: chain V residue 123 LEU Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 122 LEU Chi-restraints excluded: chain W residue 126 CYS Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 187 ASP Chi-restraints excluded: chain W residue 222 SER Chi-restraints excluded: chain W residue 231 ASP Chi-restraints excluded: chain W residue 245 ILE Chi-restraints excluded: chain W residue 278 SER Chi-restraints excluded: chain W residue 319 ASN Chi-restraints excluded: chain W residue 331 LEU Chi-restraints excluded: chain W residue 356 LEU Chi-restraints excluded: chain W residue 373 ILE Chi-restraints excluded: chain X residue 98 ASN Chi-restraints excluded: chain X residue 117 SER Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain X residue 126 CYS Chi-restraints excluded: chain X residue 133 ARG Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 231 ASP Chi-restraints excluded: chain X residue 235 VAL Chi-restraints excluded: chain X residue 278 SER Chi-restraints excluded: chain X residue 306 ILE Chi-restraints excluded: chain X residue 311 THR Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 38 GLU Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 1 residue 30 THR Chi-restraints excluded: chain 1 residue 61 SER Chi-restraints excluded: chain 1 residue 63 SER Chi-restraints excluded: chain 1 residue 65 SER Chi-restraints excluded: chain 1 residue 85 ASP Chi-restraints excluded: chain 1 residue 93 VAL Chi-restraints excluded: chain 1 residue 126 MET Chi-restraints excluded: chain 1 residue 132 LEU Chi-restraints excluded: chain 2 residue 147 LEU Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 3 residue 122 LEU Chi-restraints excluded: chain 3 residue 126 CYS Chi-restraints excluded: chain 3 residue 160 VAL Chi-restraints excluded: chain 3 residue 222 SER Chi-restraints excluded: chain 3 residue 225 ILE Chi-restraints excluded: chain 3 residue 231 ASP Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 309 ASP Chi-restraints excluded: chain 3 residue 326 THR Chi-restraints excluded: chain 3 residue 356 LEU Chi-restraints excluded: chain 4 residue 125 VAL Chi-restraints excluded: chain 4 residue 133 ARG Chi-restraints excluded: chain 4 residue 141 ASP Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 4 residue 201 LEU Chi-restraints excluded: chain 4 residue 278 SER Chi-restraints excluded: chain 4 residue 306 ILE Chi-restraints excluded: chain 4 residue 311 THR Chi-restraints excluded: chain 4 residue 355 ASP Chi-restraints excluded: chain 4 residue 356 LEU Chi-restraints excluded: chain 4 residue 379 LEU Chi-restraints excluded: chain 5 residue 133 GLU Chi-restraints excluded: chain 5 residue 143 SER Chi-restraints excluded: chain 6 residue 66 ASP Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 97 LEU Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 7 residue 27 LEU Chi-restraints excluded: chain 7 residue 77 GLU Chi-restraints excluded: chain 8 residue 9 LEU Chi-restraints excluded: chain 8 residue 24 ILE Chi-restraints excluded: chain 8 residue 30 THR Chi-restraints excluded: chain 8 residue 54 LEU Chi-restraints excluded: chain 8 residue 85 ASP Chi-restraints excluded: chain 8 residue 100 ILE Chi-restraints excluded: chain 9 residue 2 MET Chi-restraints excluded: chain 9 residue 4 ASN Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 54 THR Chi-restraints excluded: chain 9 residue 110 ASP Chi-restraints excluded: chain 9 residue 193 LEU Chi-restraints excluded: chain a residue 117 SER Chi-restraints excluded: chain a residue 126 CYS Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 187 ASP Chi-restraints excluded: chain a residue 231 ASP Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 278 SER Chi-restraints excluded: chain a residue 306 ILE Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain a residue 356 LEU Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 125 VAL Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 160 VAL Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain b residue 235 VAL Chi-restraints excluded: chain b residue 263 LEU Chi-restraints excluded: chain b residue 278 SER Chi-restraints excluded: chain b residue 311 THR Chi-restraints excluded: chain b residue 331 LEU Chi-restraints excluded: chain b residue 356 LEU Chi-restraints excluded: chain c residue 161 GLN Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 73 THR Chi-restraints excluded: chain d residue 97 LEU Chi-restraints excluded: chain e residue 27 LEU Chi-restraints excluded: chain e residue 77 GLU Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 85 ASP Chi-restraints excluded: chain f residue 100 ILE Chi-restraints excluded: chain f residue 117 ASN Chi-restraints excluded: chain f residue 121 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 286 optimal weight: 0.0870 chunk 767 optimal weight: 0.0870 chunk 168 optimal weight: 4.9990 chunk 500 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 853 optimal weight: 0.9990 chunk 708 optimal weight: 0.7980 chunk 395 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 282 optimal weight: 7.9990 chunk 448 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS B 319 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 GLN ** P 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 319 ASN R 22 HIS R 76 GLN ** U 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 319 ASN 0 100 HIS 1 20 GLN ** 3 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 349 GLN ** 4 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 319 ASN ** a 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 205 ASN b 257 ASN b 319 ASN c 22 HIS c 76 GLN ** f 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 68412 Z= 0.173 Angle : 0.655 14.712 93048 Z= 0.306 Chirality : 0.044 0.394 10404 Planarity : 0.005 0.072 12192 Dihedral : 4.666 19.566 9708 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 5.58 % Allowed : 20.08 % Favored : 74.34 % 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: -1.91 (0.09), residues: 8748 helix: 0.11 (0.10), residues: 2988 sheet: -1.48 (0.13), residues: 1512 loop : -2.23 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP 2 72 HIS 0.004 0.001 HIS b 165 PHE 0.034 0.002 PHE 1 83 TYR 0.030 0.001 TYR X 315 ARG 0.010 0.000 ARG O 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2165 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 1797 time to evaluate : 5.646 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: C 131 ARG cc_start: 0.8464 (ptt90) cc_final: 0.8157 (ppt170) REVERT: C 176 MET cc_start: 0.7711 (ttt) cc_final: 0.7476 (mtp) REVERT: C 189 THR cc_start: 0.9424 (m) cc_final: 0.9158 (p) REVERT: A 95 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7724 (ttm-80) REVERT: A 164 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8307 (mtpt) REVERT: A 192 SER cc_start: 0.8451 (t) cc_final: 0.8122 (p) REVERT: A 253 GLN cc_start: 0.8638 (mt0) cc_final: 0.8351 (mt0) REVERT: A 271 LYS cc_start: 0.8830 (tttt) cc_final: 0.8586 (ptmm) REVERT: B 101 GLN cc_start: 0.8462 (tp40) cc_final: 0.8169 (tt0) REVERT: B 163 ARG cc_start: 0.7232 (mpt-90) cc_final: 0.6892 (mpp80) REVERT: B 215 LEU cc_start: 0.9251 (mt) cc_final: 0.8983 (mt) REVERT: B 216 ASP cc_start: 0.7633 (t0) cc_final: 0.7169 (t0) REVERT: B 262 MET cc_start: 0.8963 (ttm) cc_final: 0.8692 (ttm) REVERT: B 314 ASN cc_start: 0.7418 (p0) cc_final: 0.6586 (p0) REVERT: D 90 ARG cc_start: 0.7931 (ptp90) cc_final: 0.7191 (ptp90) REVERT: D 133 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6979 (pt0) REVERT: F 14 TYR cc_start: 0.8789 (t80) cc_final: 0.8451 (t80) REVERT: F 122 MET cc_start: 0.8439 (mmm) cc_final: 0.8143 (mtp) REVERT: G 14 ASP cc_start: 0.7879 (p0) cc_final: 0.7632 (p0) REVERT: G 126 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7343 (mtp) REVERT: I 32 MET cc_start: 0.6069 (ptt) cc_final: 0.5679 (ptt) REVERT: I 105 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8363 (mt-10) REVERT: I 142 ARG cc_start: 0.8428 (mtm180) cc_final: 0.7796 (mtm180) REVERT: I 143 MET cc_start: 0.8857 (tpp) cc_final: 0.8331 (ttm) REVERT: I 164 LYS cc_start: 0.8402 (mtpp) cc_final: 0.7931 (mtpp) REVERT: I 192 SER cc_start: 0.8433 (t) cc_final: 0.8004 (p) REVERT: I 271 LYS cc_start: 0.8710 (ttpt) cc_final: 0.8281 (ttpp) REVERT: I 319 ASN cc_start: 0.8849 (t0) cc_final: 0.8553 (t0) REVERT: J 101 GLN cc_start: 0.8709 (tt0) cc_final: 0.8287 (tt0) REVERT: J 157 ASP cc_start: 0.8151 (m-30) cc_final: 0.7800 (m-30) REVERT: J 164 LYS cc_start: 0.8595 (mtpp) cc_final: 0.8164 (mtpp) REVERT: J 189 TYR cc_start: 0.9078 (m-80) cc_final: 0.8587 (m-10) REVERT: J 216 ASP cc_start: 0.7558 (t70) cc_final: 0.7197 (t0) REVERT: J 271 LYS cc_start: 0.8806 (tttt) cc_final: 0.8605 (pttt) REVERT: J 314 ASN cc_start: 0.7767 (p0) cc_final: 0.7100 (p0) REVERT: J 349 GLN cc_start: 0.8234 (tt0) cc_final: 0.7878 (tt0) REVERT: J 355 ASP cc_start: 0.7242 (OUTLIER) cc_final: 0.6999 (t0) REVERT: J 357 ASP cc_start: 0.8799 (t70) cc_final: 0.8270 (t0) REVERT: K 106 ARG cc_start: 0.8873 (ttp80) cc_final: 0.8455 (ptm160) REVERT: K 193 LEU cc_start: 0.8952 (tp) cc_final: 0.8566 (tp) REVERT: L 15 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8414 (mm-40) REVERT: L 72 ILE cc_start: 0.9056 (mm) cc_final: 0.8796 (mm) REVERT: M 58 PRO cc_start: 0.8556 (Cg_exo) cc_final: 0.8065 (Cg_endo) REVERT: N 7 LYS cc_start: 0.8598 (mtpm) cc_final: 0.8200 (tmtt) REVERT: N 116 HIS cc_start: 0.8453 (p90) cc_final: 0.8203 (p-80) REVERT: O 105 TRP cc_start: 0.9117 (p-90) cc_final: 0.8513 (p-90) REVERT: O 110 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8030 (t70) REVERT: P 32 MET cc_start: 0.7330 (ptt) cc_final: 0.6904 (ptt) REVERT: P 69 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8160 (mt-10) REVERT: P 101 GLN cc_start: 0.8792 (tt0) cc_final: 0.8538 (tt0) REVERT: P 163 ARG cc_start: 0.7538 (mmm-85) cc_final: 0.6923 (mmt90) REVERT: P 192 SER cc_start: 0.8578 (t) cc_final: 0.8243 (p) REVERT: P 205 ASN cc_start: 0.9314 (m-40) cc_final: 0.8749 (m-40) REVERT: P 244 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9042 (tp) REVERT: P 271 LYS cc_start: 0.9045 (ttpt) cc_final: 0.8815 (ttpt) REVERT: Q 216 ASP cc_start: 0.7419 (t70) cc_final: 0.6860 (t0) REVERT: Q 271 LYS cc_start: 0.8809 (tttt) cc_final: 0.8541 (tttt) REVERT: Q 314 ASN cc_start: 0.7948 (p0) cc_final: 0.7013 (p0) REVERT: Q 349 GLN cc_start: 0.8394 (tt0) cc_final: 0.8155 (tt0) REVERT: R 76 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7805 (tp-100) REVERT: R 89 LEU cc_start: 0.9005 (tt) cc_final: 0.8781 (tt) REVERT: R 131 ARG cc_start: 0.7786 (ptt90) cc_final: 0.7571 (ptt90) REVERT: S 97 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7271 (pp) REVERT: U 7 LYS cc_start: 0.8691 (ttpp) cc_final: 0.7913 (tmtt) REVERT: U 51 ARG cc_start: 0.8227 (ttp80) cc_final: 0.7984 (ttp80) REVERT: U 52 GLU cc_start: 0.7206 (mp0) cc_final: 0.6051 (mp0) REVERT: U 60 ARG cc_start: 0.8461 (ptp-110) cc_final: 0.8029 (ptp90) REVERT: U 81 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8268 (tm-30) REVERT: U 90 GLU cc_start: 0.8713 (tp30) cc_final: 0.8376 (mm-30) REVERT: U 91 PHE cc_start: 0.8185 (m-80) cc_final: 0.7895 (m-10) REVERT: U 106 MET cc_start: 0.6678 (ptp) cc_final: 0.6436 (ptm) REVERT: U 123 GLU cc_start: 0.7744 (tp30) cc_final: 0.7359 (tp30) REVERT: U 126 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7260 (mtp) REVERT: V 2 MET cc_start: 0.7598 (tpt) cc_final: 0.7028 (tpt) REVERT: V 131 ARG cc_start: 0.8512 (ptt90) cc_final: 0.8141 (ppt170) REVERT: V 176 MET cc_start: 0.7695 (ttt) cc_final: 0.7447 (mtp) REVERT: V 189 THR cc_start: 0.9419 (m) cc_final: 0.9167 (p) REVERT: W 65 LYS cc_start: 0.8555 (tptm) cc_final: 0.8284 (ttmt) REVERT: W 164 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8238 (ttmm) REVERT: W 192 SER cc_start: 0.8421 (t) cc_final: 0.8091 (p) REVERT: W 271 LYS cc_start: 0.8851 (tttt) cc_final: 0.8614 (ptmm) REVERT: X 51 ARG cc_start: 0.7821 (ptp90) cc_final: 0.7582 (ptp90) REVERT: X 101 GLN cc_start: 0.8229 (tt0) cc_final: 0.7851 (tt0) REVERT: X 215 LEU cc_start: 0.9272 (mt) cc_final: 0.8997 (mt) REVERT: X 216 ASP cc_start: 0.7628 (t0) cc_final: 0.7158 (t0) REVERT: X 253 GLN cc_start: 0.9148 (mt0) cc_final: 0.8795 (mt0) REVERT: X 262 MET cc_start: 0.8915 (ttm) cc_final: 0.8596 (ttm) REVERT: X 271 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8228 (ttpt) REVERT: X 314 ASN cc_start: 0.7429 (p0) cc_final: 0.6596 (p0) REVERT: Z 14 TYR cc_start: 0.8769 (t80) cc_final: 0.8448 (t80) REVERT: Z 122 MET cc_start: 0.8462 (mmm) cc_final: 0.8180 (mtp) REVERT: 0 94 GLU cc_start: 0.7488 (tt0) cc_final: 0.7225 (tm-30) REVERT: 1 81 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8348 (tm-30) REVERT: 1 117 ASN cc_start: 0.9100 (p0) cc_final: 0.8871 (p0) REVERT: 1 126 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6885 (mtp) REVERT: 2 131 ARG cc_start: 0.8708 (ptt90) cc_final: 0.7988 (ppt170) REVERT: 3 69 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8016 (mt-10) REVERT: 3 105 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8304 (mt-10) REVERT: 3 142 ARG cc_start: 0.8381 (mtm180) cc_final: 0.7878 (mtm180) REVERT: 3 143 MET cc_start: 0.8856 (tpp) cc_final: 0.8282 (ttm) REVERT: 3 164 LYS cc_start: 0.8586 (mtpp) cc_final: 0.8155 (ttmm) REVERT: 3 192 SER cc_start: 0.8418 (t) cc_final: 0.8011 (p) REVERT: 3 319 ASN cc_start: 0.8840 (t0) cc_final: 0.8509 (t0) REVERT: 4 101 GLN cc_start: 0.8658 (tt0) cc_final: 0.8229 (tt0) REVERT: 4 183 HIS cc_start: 0.8745 (t-90) cc_final: 0.8516 (t-170) REVERT: 4 189 TYR cc_start: 0.9056 (m-80) cc_final: 0.8602 (m-10) REVERT: 4 216 ASP cc_start: 0.7577 (t70) cc_final: 0.7212 (t0) REVERT: 4 314 ASN cc_start: 0.7794 (p0) cc_final: 0.7127 (p0) REVERT: 4 349 GLN cc_start: 0.8249 (tt0) cc_final: 0.7866 (tt0) REVERT: 5 106 ARG cc_start: 0.8882 (ttp80) cc_final: 0.8430 (ptm160) REVERT: 5 193 LEU cc_start: 0.8928 (tp) cc_final: 0.8529 (tp) REVERT: 6 15 GLN cc_start: 0.8925 (mm-40) cc_final: 0.8401 (mm-40) REVERT: 6 72 ILE cc_start: 0.9038 (mm) cc_final: 0.8774 (mm) REVERT: 7 58 PRO cc_start: 0.8599 (Cg_exo) cc_final: 0.8102 (Cg_endo) REVERT: 8 7 LYS cc_start: 0.8596 (mtpm) cc_final: 0.8253 (tmtt) REVERT: 8 22 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7476 (mt-10) REVERT: 9 2 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7062 (tpt) REVERT: 9 105 TRP cc_start: 0.9113 (p-90) cc_final: 0.8544 (p-90) REVERT: a 69 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: a 101 GLN cc_start: 0.8797 (tt0) cc_final: 0.8486 (tt0) REVERT: a 192 SER cc_start: 0.8565 (t) cc_final: 0.8280 (p) REVERT: a 205 ASN cc_start: 0.9291 (m-40) cc_final: 0.8772 (m-40) REVERT: a 244 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9055 (tp) REVERT: a 328 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8849 (mm) REVERT: b 51 ARG cc_start: 0.8069 (ptp90) cc_final: 0.7818 (ptp90) REVERT: b 189 TYR cc_start: 0.8947 (m-80) cc_final: 0.8734 (m-10) REVERT: b 216 ASP cc_start: 0.7407 (t70) cc_final: 0.6749 (t0) REVERT: b 314 ASN cc_start: 0.7954 (p0) cc_final: 0.7015 (p0) REVERT: b 355 ASP cc_start: 0.7634 (t0) cc_final: 0.7340 (t0) REVERT: b 358 GLN cc_start: 0.8850 (pp30) cc_final: 0.8561 (pm20) REVERT: c 76 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7695 (tp-100) REVERT: c 193 LEU cc_start: 0.8706 (tp) cc_final: 0.8410 (tp) REVERT: d 97 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7318 (pp) REVERT: f 7 LYS cc_start: 0.8677 (ttpp) cc_final: 0.7894 (tmtt) REVERT: f 51 ARG cc_start: 0.8247 (ttp80) cc_final: 0.8025 (ttp80) REVERT: f 75 THR cc_start: 0.7676 (OUTLIER) cc_final: 0.7443 (t) REVERT: f 81 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8353 (tm-30) REVERT: f 90 GLU cc_start: 0.8762 (tp30) cc_final: 0.8501 (mm-30) REVERT: f 123 GLU cc_start: 0.7730 (tp30) cc_final: 0.7374 (tp30) outliers start: 368 outliers final: 245 residues processed: 2012 average time/residue: 0.6314 time to fit residues: 2139.8757 Evaluate side-chains 1965 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1704 time to evaluate : 5.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 222 SER Chi-restraints excluded: chain I residue 231 ASP Chi-restraints excluded: chain I residue 245 ILE Chi-restraints excluded: chain I residue 278 SER Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 306 ILE Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain I residue 373 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain J residue 355 ASP Chi-restraints excluded: chain J residue 356 LEU Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 161 GLN Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 110 ASP Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 187 ASP Chi-restraints excluded: chain P residue 231 ASP Chi-restraints excluded: chain P residue 244 LEU Chi-restraints excluded: chain P residue 278 SER Chi-restraints excluded: chain P residue 306 ILE Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 356 LEU Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 126 CYS Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 170 THR Chi-restraints excluded: chain Q residue 231 ASP Chi-restraints excluded: chain Q residue 235 VAL Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 77 GLU Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 44 LEU Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 110 ILE Chi-restraints excluded: chain U residue 117 ASN Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain U residue 126 MET Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 29 PHE Chi-restraints excluded: chain V residue 50 ILE Chi-restraints excluded: chain V residue 143 SER Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 122 LEU Chi-restraints excluded: chain W residue 126 CYS Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 187 ASP Chi-restraints excluded: chain W residue 222 SER Chi-restraints excluded: chain W residue 231 ASP Chi-restraints excluded: chain W residue 245 ILE Chi-restraints excluded: chain W residue 278 SER Chi-restraints excluded: chain W residue 306 ILE Chi-restraints excluded: chain W residue 331 LEU Chi-restraints excluded: chain W residue 356 LEU Chi-restraints excluded: chain W residue 373 ILE Chi-restraints excluded: chain X residue 98 ASN Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain X residue 126 CYS Chi-restraints excluded: chain X residue 133 ARG Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 231 ASP Chi-restraints excluded: chain X residue 235 VAL Chi-restraints excluded: chain X residue 278 SER Chi-restraints excluded: chain X residue 306 ILE Chi-restraints excluded: chain X residue 311 THR Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 38 GLU Chi-restraints excluded: chain 0 residue 53 THR Chi-restraints excluded: chain 0 residue 110 VAL Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 30 THR Chi-restraints excluded: chain 1 residue 43 SER Chi-restraints excluded: chain 1 residue 61 SER Chi-restraints excluded: chain 1 residue 63 SER Chi-restraints excluded: chain 1 residue 65 SER Chi-restraints excluded: chain 1 residue 85 ASP Chi-restraints excluded: chain 1 residue 93 VAL Chi-restraints excluded: chain 1 residue 121 SER Chi-restraints excluded: chain 1 residue 126 MET Chi-restraints excluded: chain 1 residue 133 SER Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 29 PHE Chi-restraints excluded: chain 2 residue 147 LEU Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 3 residue 122 LEU Chi-restraints excluded: chain 3 residue 126 CYS Chi-restraints excluded: chain 3 residue 160 VAL Chi-restraints excluded: chain 3 residue 177 CYS Chi-restraints excluded: chain 3 residue 187 ASP Chi-restraints excluded: chain 3 residue 222 SER Chi-restraints excluded: chain 3 residue 225 ILE Chi-restraints excluded: chain 3 residue 231 ASP Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 304 ILE Chi-restraints excluded: chain 3 residue 306 ILE Chi-restraints excluded: chain 3 residue 326 THR Chi-restraints excluded: chain 3 residue 356 LEU Chi-restraints excluded: chain 3 residue 373 ILE Chi-restraints excluded: chain 4 residue 125 VAL Chi-restraints excluded: chain 4 residue 141 ASP Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 306 ILE Chi-restraints excluded: chain 4 residue 311 THR Chi-restraints excluded: chain 4 residue 328 LEU Chi-restraints excluded: chain 4 residue 356 LEU Chi-restraints excluded: chain 4 residue 379 LEU Chi-restraints excluded: chain 5 residue 143 SER Chi-restraints excluded: chain 5 residue 161 GLN Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 97 LEU Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 7 residue 27 LEU Chi-restraints excluded: chain 7 residue 38 GLU Chi-restraints excluded: chain 7 residue 53 THR Chi-restraints excluded: chain 7 residue 77 GLU Chi-restraints excluded: chain 8 residue 9 LEU Chi-restraints excluded: chain 8 residue 24 ILE Chi-restraints excluded: chain 8 residue 30 THR Chi-restraints excluded: chain 8 residue 54 LEU Chi-restraints excluded: chain 8 residue 85 ASP Chi-restraints excluded: chain 8 residue 100 ILE Chi-restraints excluded: chain 8 residue 126 MET Chi-restraints excluded: chain 9 residue 2 MET Chi-restraints excluded: chain 9 residue 12 THR Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 54 THR Chi-restraints excluded: chain 9 residue 193 LEU Chi-restraints excluded: chain a residue 69 GLU Chi-restraints excluded: chain a residue 117 SER Chi-restraints excluded: chain a residue 126 CYS Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain a residue 187 ASP Chi-restraints excluded: chain a residue 231 ASP Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 278 SER Chi-restraints excluded: chain a residue 306 ILE Chi-restraints excluded: chain a residue 328 LEU Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain a residue 356 LEU Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 125 VAL Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 160 VAL Chi-restraints excluded: chain b residue 187 ASP Chi-restraints excluded: chain b residue 231 ASP Chi-restraints excluded: chain b residue 235 VAL Chi-restraints excluded: chain b residue 311 THR Chi-restraints excluded: chain b residue 356 LEU Chi-restraints excluded: chain c residue 161 GLN Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 73 THR Chi-restraints excluded: chain d residue 97 LEU Chi-restraints excluded: chain e residue 27 LEU Chi-restraints excluded: chain e residue 77 GLU Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 44 LEU Chi-restraints excluded: chain f residue 75 THR Chi-restraints excluded: chain f residue 85 ASP Chi-restraints excluded: chain f residue 100 ILE Chi-restraints excluded: chain f residue 121 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 822 optimal weight: 0.0060 chunk 96 optimal weight: 1.9990 chunk 486 optimal weight: 1.9990 chunk 623 optimal weight: 0.9990 chunk 482 optimal weight: 2.9990 chunk 718 optimal weight: 8.9990 chunk 476 optimal weight: 6.9990 chunk 850 optimal weight: 10.0000 chunk 532 optimal weight: 9.9990 chunk 518 optimal weight: 3.9990 chunk 392 optimal weight: 4.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 ASN G 20 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 319 ASN R 161 GLN ** W 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 319 ASN Y 76 GLN 1 20 GLN ** 2 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 319 ASN ** a 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 319 ASN f 117 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 68412 Z= 0.230 Angle : 0.681 15.815 93048 Z= 0.317 Chirality : 0.045 0.263 10404 Planarity : 0.005 0.080 12192 Dihedral : 4.665 19.396 9708 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 5.43 % Allowed : 20.84 % Favored : 73.73 % 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: -1.82 (0.09), residues: 8748 helix: 0.22 (0.10), residues: 3012 sheet: -1.45 (0.13), residues: 1512 loop : -2.21 (0.09), residues: 4224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP 2 72 HIS 0.005 0.001 HIS f 116 PHE 0.034 0.002 PHE 1 83 TYR 0.032 0.001 TYR Q 315 ARG 0.009 0.000 ARG Q 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2099 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 358 poor density : 1741 time to evaluate : 5.662 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: C 2 MET cc_start: 0.7527 (tpt) cc_final: 0.6976 (tpt) REVERT: C 131 ARG cc_start: 0.8448 (ptt90) cc_final: 0.8158 (ppt170) REVERT: C 189 THR cc_start: 0.9434 (m) cc_final: 0.9193 (p) REVERT: A 65 LYS cc_start: 0.8724 (tppp) cc_final: 0.8471 (tppp) REVERT: A 95 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7687 (ttm-80) REVERT: A 192 SER cc_start: 0.8580 (t) cc_final: 0.8207 (p) REVERT: A 253 GLN cc_start: 0.8778 (mt0) cc_final: 0.8507 (mt0) REVERT: A 271 LYS cc_start: 0.8863 (tttt) cc_final: 0.8582 (ptmm) REVERT: A 315 TYR cc_start: 0.8470 (t80) cc_final: 0.8218 (t80) REVERT: B 101 GLN cc_start: 0.8488 (tp40) cc_final: 0.8174 (tt0) REVERT: B 163 ARG cc_start: 0.7250 (mpt-90) cc_final: 0.7006 (mpp80) REVERT: B 215 LEU cc_start: 0.9266 (mt) cc_final: 0.9027 (mt) REVERT: B 257 ASN cc_start: 0.8727 (m-40) cc_final: 0.8454 (m110) REVERT: B 271 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8356 (tttm) REVERT: B 314 ASN cc_start: 0.7509 (p0) cc_final: 0.6638 (p0) REVERT: D 131 ARG cc_start: 0.8003 (ptm-80) cc_final: 0.7527 (ptt-90) REVERT: D 157 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9209 (mm) REVERT: F 14 TYR cc_start: 0.8806 (t80) cc_final: 0.8481 (t80) REVERT: F 122 MET cc_start: 0.8481 (mmm) cc_final: 0.8137 (mtp) REVERT: G 22 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7598 (mt-10) REVERT: G 81 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8424 (tm-30) REVERT: I 32 MET cc_start: 0.6091 (ptt) cc_final: 0.5731 (ptt) REVERT: I 69 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: I 105 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8344 (mt-10) REVERT: I 164 LYS cc_start: 0.8428 (mtpp) cc_final: 0.7933 (mtpp) REVERT: I 192 SER cc_start: 0.8473 (t) cc_final: 0.8010 (p) REVERT: I 271 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8350 (ttpp) REVERT: I 319 ASN cc_start: 0.8925 (t0) cc_final: 0.8510 (t0) REVERT: J 65 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8721 (ttmt) REVERT: J 101 GLN cc_start: 0.8761 (tt0) cc_final: 0.8341 (tt0) REVERT: J 157 ASP cc_start: 0.8277 (m-30) cc_final: 0.7617 (m-30) REVERT: J 164 LYS cc_start: 0.8597 (mtpp) cc_final: 0.8207 (mtpp) REVERT: J 189 TYR cc_start: 0.9081 (m-80) cc_final: 0.8598 (m-10) REVERT: J 216 ASP cc_start: 0.7738 (t70) cc_final: 0.7434 (t0) REVERT: J 286 LYS cc_start: 0.9046 (ttpt) cc_final: 0.8495 (tttt) REVERT: J 314 ASN cc_start: 0.7739 (p0) cc_final: 0.7157 (p0) REVERT: J 349 GLN cc_start: 0.8207 (tt0) cc_final: 0.7863 (tt0) REVERT: J 357 ASP cc_start: 0.8819 (t70) cc_final: 0.8276 (t0) REVERT: J 358 GLN cc_start: 0.8461 (pm20) cc_final: 0.8168 (pm20) REVERT: K 106 ARG cc_start: 0.8901 (ttp80) cc_final: 0.8477 (ptm160) REVERT: K 193 LEU cc_start: 0.9036 (tp) cc_final: 0.8666 (tp) REVERT: L 15 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8338 (mm-40) REVERT: L 72 ILE cc_start: 0.9102 (mm) cc_final: 0.8796 (mm) REVERT: M 50 GLU cc_start: 0.7248 (mm-30) cc_final: 0.7045 (mm-30) REVERT: N 7 LYS cc_start: 0.8615 (mtpm) cc_final: 0.8199 (tmtt) REVERT: N 81 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8396 (tm-30) REVERT: N 116 HIS cc_start: 0.8476 (p90) cc_final: 0.8186 (p-80) REVERT: O 105 TRP cc_start: 0.9129 (p-90) cc_final: 0.8528 (p-90) REVERT: P 32 MET cc_start: 0.7507 (ptt) cc_final: 0.6881 (ptp) REVERT: P 69 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: P 101 GLN cc_start: 0.8832 (tt0) cc_final: 0.8582 (tt0) REVERT: P 163 ARG cc_start: 0.7600 (mmm-85) cc_final: 0.6926 (mmt90) REVERT: P 192 SER cc_start: 0.8606 (t) cc_final: 0.8289 (p) REVERT: P 205 ASN cc_start: 0.9298 (m-40) cc_final: 0.8778 (m-40) REVERT: P 244 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9039 (tp) REVERT: P 271 LYS cc_start: 0.9094 (ttpt) cc_final: 0.8843 (ttpt) REVERT: Q 216 ASP cc_start: 0.7627 (t70) cc_final: 0.7045 (t0) REVERT: Q 271 LYS cc_start: 0.8838 (tttt) cc_final: 0.8574 (tttt) REVERT: Q 314 ASN cc_start: 0.7963 (p0) cc_final: 0.6969 (p0) REVERT: Q 349 GLN cc_start: 0.8397 (tt0) cc_final: 0.8187 (tt0) REVERT: R 89 LEU cc_start: 0.9026 (tt) cc_final: 0.8795 (tt) REVERT: R 133 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7195 (pt0) REVERT: R 193 LEU cc_start: 0.8777 (tp) cc_final: 0.8476 (tp) REVERT: S 50 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7067 (pm20) REVERT: S 97 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7265 (pp) REVERT: T 47 ARG cc_start: 0.8160 (ttp80) cc_final: 0.7880 (ptt90) REVERT: U 12 LYS cc_start: 0.8136 (mttm) cc_final: 0.7826 (mttm) REVERT: U 51 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7942 (ttp80) REVERT: U 60 ARG cc_start: 0.8433 (ptp-110) cc_final: 0.8002 (ptp90) REVERT: U 81 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8297 (tm-30) REVERT: U 90 GLU cc_start: 0.8767 (tp30) cc_final: 0.8309 (mm-30) REVERT: U 123 GLU cc_start: 0.7740 (tp30) cc_final: 0.7352 (tp30) REVERT: V 2 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.6979 (tpt) REVERT: V 189 THR cc_start: 0.9419 (m) cc_final: 0.9178 (p) REVERT: W 65 LYS cc_start: 0.8578 (tptm) cc_final: 0.8124 (tppp) REVERT: W 192 SER cc_start: 0.8542 (t) cc_final: 0.8173 (p) REVERT: W 271 LYS cc_start: 0.8919 (tttt) cc_final: 0.8623 (ptmm) REVERT: X 51 ARG cc_start: 0.7852 (ptp90) cc_final: 0.7623 (ptp90) REVERT: X 101 GLN cc_start: 0.8316 (tt0) cc_final: 0.7993 (tt0) REVERT: X 167 PHE cc_start: 0.8779 (m-10) cc_final: 0.8561 (m-80) REVERT: X 215 LEU cc_start: 0.9277 (mt) cc_final: 0.9039 (mt) REVERT: X 257 ASN cc_start: 0.8709 (m-40) cc_final: 0.8440 (m110) REVERT: X 271 LYS cc_start: 0.8505 (ttpt) cc_final: 0.8209 (ttpt) REVERT: X 314 ASN cc_start: 0.7505 (p0) cc_final: 0.6653 (p0) REVERT: Y 117 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7827 (mt-10) REVERT: Y 133 GLU cc_start: 0.7323 (pt0) cc_final: 0.7012 (pt0) REVERT: Y 157 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9222 (mm) REVERT: Z 14 TYR cc_start: 0.8786 (t80) cc_final: 0.8464 (t80) REVERT: 0 14 GLU cc_start: 0.8023 (tt0) cc_final: 0.7660 (tt0) REVERT: 0 94 GLU cc_start: 0.7562 (tt0) cc_final: 0.7293 (tm-30) REVERT: 1 52 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7117 (mt-10) REVERT: 1 81 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8202 (tm-30) REVERT: 1 117 ASN cc_start: 0.9115 (p0) cc_final: 0.8902 (p0) REVERT: 1 126 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7428 (mtp) REVERT: 3 65 LYS cc_start: 0.8882 (tppt) cc_final: 0.8558 (tppt) REVERT: 3 105 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8301 (mt-10) REVERT: 3 142 ARG cc_start: 0.8497 (mtm180) cc_final: 0.7981 (mtm180) REVERT: 3 143 MET cc_start: 0.8909 (tpp) cc_final: 0.8297 (ttm) REVERT: 3 164 LYS cc_start: 0.8618 (mtpp) cc_final: 0.8170 (ttmm) REVERT: 3 192 SER cc_start: 0.8570 (t) cc_final: 0.8070 (p) REVERT: 3 319 ASN cc_start: 0.8869 (t0) cc_final: 0.8447 (t0) REVERT: 4 101 GLN cc_start: 0.8704 (tt0) cc_final: 0.8296 (tt0) REVERT: 4 183 HIS cc_start: 0.8821 (t-90) cc_final: 0.8574 (t-170) REVERT: 4 189 TYR cc_start: 0.9070 (m-80) cc_final: 0.8628 (m-10) REVERT: 4 216 ASP cc_start: 0.7714 (t70) cc_final: 0.7297 (t0) REVERT: 4 244 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9054 (tp) REVERT: 4 286 LYS cc_start: 0.8963 (ttpt) cc_final: 0.8475 (tttt) REVERT: 4 314 ASN cc_start: 0.7785 (p0) cc_final: 0.7232 (p0) REVERT: 4 328 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8545 (mp) REVERT: 4 349 GLN cc_start: 0.8239 (tt0) cc_final: 0.7856 (tt0) REVERT: 4 355 ASP cc_start: 0.7547 (t0) cc_final: 0.7072 (t0) REVERT: 5 106 ARG cc_start: 0.8910 (ttp80) cc_final: 0.8442 (ptm160) REVERT: 5 193 LEU cc_start: 0.9003 (tp) cc_final: 0.8648 (tp) REVERT: 6 15 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8324 (mm-40) REVERT: 6 72 ILE cc_start: 0.9088 (mm) cc_final: 0.8807 (mm) REVERT: 7 58 PRO cc_start: 0.8621 (Cg_exo) cc_final: 0.8144 (Cg_endo) REVERT: 8 7 LYS cc_start: 0.8646 (mtpm) cc_final: 0.8246 (tmtt) REVERT: 8 22 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7538 (mt-10) REVERT: 9 2 MET cc_start: 0.7574 (tpt) cc_final: 0.7025 (tpt) REVERT: 9 105 TRP cc_start: 0.9129 (p-90) cc_final: 0.8552 (p-90) REVERT: 9 110 ASP cc_start: 0.8453 (t0) cc_final: 0.7861 (m-30) REVERT: 9 131 ARG cc_start: 0.8396 (ptt90) cc_final: 0.8168 (ppt170) REVERT: a 69 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: a 101 GLN cc_start: 0.8801 (tt0) cc_final: 0.8468 (tt0) REVERT: a 164 LYS cc_start: 0.8459 (mtpt) cc_final: 0.8185 (mtpt) REVERT: a 192 SER cc_start: 0.8623 (t) cc_final: 0.8284 (p) REVERT: a 205 ASN cc_start: 0.9300 (m-40) cc_final: 0.8785 (m-40) REVERT: a 244 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9014 (tp) REVERT: b 51 ARG cc_start: 0.8075 (ptp90) cc_final: 0.7855 (ptp90) REVERT: b 189 TYR cc_start: 0.8954 (m-80) cc_final: 0.8744 (m-10) REVERT: b 216 ASP cc_start: 0.7610 (t70) cc_final: 0.7026 (t0) REVERT: b 314 ASN cc_start: 0.7972 (p0) cc_final: 0.6960 (p0) REVERT: b 358 GLN cc_start: 0.8931 (pp30) cc_final: 0.8511 (pm20) REVERT: c 76 GLN cc_start: 0.8305 (tp-100) cc_final: 0.8089 (tp-100) REVERT: c 193 LEU cc_start: 0.8781 (tp) cc_final: 0.8492 (tp) REVERT: d 50 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7122 (pm20) REVERT: d 97 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7217 (pp) REVERT: f 51 ARG cc_start: 0.8286 (ttp80) cc_final: 0.8017 (ttp80) REVERT: f 60 ARG cc_start: 0.8438 (ptp-110) cc_final: 0.7915 (ptp90) REVERT: f 75 THR cc_start: 0.7693 (OUTLIER) cc_final: 0.7466 (t) REVERT: f 81 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8381 (tm-30) REVERT: f 90 GLU cc_start: 0.8826 (tp30) cc_final: 0.8487 (mm-30) REVERT: f 91 PHE cc_start: 0.8198 (m-80) cc_final: 0.7934 (m-10) REVERT: f 123 GLU cc_start: 0.7722 (tp30) cc_final: 0.7364 (tp30) outliers start: 358 outliers final: 277 residues processed: 1932 average time/residue: 0.6506 time to fit residues: 2106.1172 Evaluate side-chains 1950 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 1655 time to evaluate : 5.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 222 SER Chi-restraints excluded: chain I residue 231 ASP Chi-restraints excluded: chain I residue 239 GLU Chi-restraints excluded: chain I residue 245 ILE Chi-restraints excluded: chain I residue 278 SER Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 306 ILE Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain I residue 373 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 278 SER Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain J residue 356 LEU Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 161 GLN Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 187 ASP Chi-restraints excluded: chain P residue 222 SER Chi-restraints excluded: chain P residue 231 ASP Chi-restraints excluded: chain P residue 244 LEU Chi-restraints excluded: chain P residue 278 SER Chi-restraints excluded: chain P residue 306 ILE Chi-restraints excluded: chain P residue 319 ASN Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 356 LEU Chi-restraints excluded: chain P residue 386 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 126 CYS Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 170 THR Chi-restraints excluded: chain Q residue 222 SER Chi-restraints excluded: chain Q residue 231 ASP Chi-restraints excluded: chain Q residue 235 VAL Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 133 GLU Chi-restraints excluded: chain S residue 50 GLU Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 77 GLU Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain V residue 2 MET Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 29 PHE Chi-restraints excluded: chain V residue 143 SER Chi-restraints excluded: chain V residue 149 VAL Chi-restraints excluded: chain V residue 165 LEU Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 122 LEU Chi-restraints excluded: chain W residue 126 CYS Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 187 ASP Chi-restraints excluded: chain W residue 222 SER Chi-restraints excluded: chain W residue 231 ASP Chi-restraints excluded: chain W residue 245 ILE Chi-restraints excluded: chain W residue 278 SER Chi-restraints excluded: chain W residue 306 ILE Chi-restraints excluded: chain W residue 331 LEU Chi-restraints excluded: chain W residue 356 LEU Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 98 ASN Chi-restraints excluded: chain X residue 117 SER Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain X residue 126 CYS Chi-restraints excluded: chain X residue 133 ARG Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 177 CYS Chi-restraints excluded: chain X residue 235 VAL Chi-restraints excluded: chain X residue 278 SER Chi-restraints excluded: chain X residue 311 THR Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Y residue 157 LEU Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 38 GLU Chi-restraints excluded: chain 0 residue 53 THR Chi-restraints excluded: chain 0 residue 77 GLU Chi-restraints excluded: chain 0 residue 110 VAL Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 1 residue 30 THR Chi-restraints excluded: chain 1 residue 43 SER Chi-restraints excluded: chain 1 residue 61 SER Chi-restraints excluded: chain 1 residue 63 SER Chi-restraints excluded: chain 1 residue 65 SER Chi-restraints excluded: chain 1 residue 85 ASP Chi-restraints excluded: chain 1 residue 93 VAL Chi-restraints excluded: chain 1 residue 121 SER Chi-restraints excluded: chain 1 residue 126 MET Chi-restraints excluded: chain 1 residue 132 LEU Chi-restraints excluded: chain 1 residue 133 SER Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 29 PHE Chi-restraints excluded: chain 2 residue 147 LEU Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 3 residue 122 LEU Chi-restraints excluded: chain 3 residue 126 CYS Chi-restraints excluded: chain 3 residue 160 VAL Chi-restraints excluded: chain 3 residue 177 CYS Chi-restraints excluded: chain 3 residue 187 ASP Chi-restraints excluded: chain 3 residue 222 SER Chi-restraints excluded: chain 3 residue 225 ILE Chi-restraints excluded: chain 3 residue 231 ASP Chi-restraints excluded: chain 3 residue 245 ILE Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 304 ILE Chi-restraints excluded: chain 3 residue 306 ILE Chi-restraints excluded: chain 3 residue 309 ASP Chi-restraints excluded: chain 3 residue 326 THR Chi-restraints excluded: chain 3 residue 356 LEU Chi-restraints excluded: chain 3 residue 373 ILE Chi-restraints excluded: chain 4 residue 125 VAL Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 4 residue 225 ILE Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 4 residue 306 ILE Chi-restraints excluded: chain 4 residue 311 THR Chi-restraints excluded: chain 4 residue 328 LEU Chi-restraints excluded: chain 4 residue 356 LEU Chi-restraints excluded: chain 4 residue 379 LEU Chi-restraints excluded: chain 5 residue 59 ILE Chi-restraints excluded: chain 5 residue 143 SER Chi-restraints excluded: chain 5 residue 145 SER Chi-restraints excluded: chain 5 residue 161 GLN Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 97 LEU Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 7 residue 27 LEU Chi-restraints excluded: chain 7 residue 38 GLU Chi-restraints excluded: chain 7 residue 53 THR Chi-restraints excluded: chain 7 residue 77 GLU Chi-restraints excluded: chain 8 residue 9 LEU Chi-restraints excluded: chain 8 residue 24 ILE Chi-restraints excluded: chain 8 residue 30 THR Chi-restraints excluded: chain 8 residue 54 LEU Chi-restraints excluded: chain 8 residue 85 ASP Chi-restraints excluded: chain 8 residue 100 ILE Chi-restraints excluded: chain 8 residue 126 MET Chi-restraints excluded: chain 9 residue 4 ASN Chi-restraints excluded: chain 9 residue 12 THR Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 54 THR Chi-restraints excluded: chain 9 residue 193 LEU Chi-restraints excluded: chain a residue 69 GLU Chi-restraints excluded: chain a residue 117 SER Chi-restraints excluded: chain a residue 126 CYS Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain a residue 187 ASP Chi-restraints excluded: chain a residue 222 SER Chi-restraints excluded: chain a residue 231 ASP Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 278 SER Chi-restraints excluded: chain a residue 306 ILE Chi-restraints excluded: chain a residue 319 ASN Chi-restraints excluded: chain a residue 328 LEU Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain a residue 356 LEU Chi-restraints excluded: chain b residue 125 VAL Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 160 VAL Chi-restraints excluded: chain b residue 187 ASP Chi-restraints excluded: chain b residue 222 SER Chi-restraints excluded: chain b residue 231 ASP Chi-restraints excluded: chain b residue 235 VAL Chi-restraints excluded: chain b residue 311 THR Chi-restraints excluded: chain b residue 356 LEU Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain c residue 161 GLN Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 73 THR Chi-restraints excluded: chain d residue 97 LEU Chi-restraints excluded: chain e residue 27 LEU Chi-restraints excluded: chain e residue 77 GLU Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 63 SER Chi-restraints excluded: chain f residue 75 THR Chi-restraints excluded: chain f residue 85 ASP Chi-restraints excluded: chain f residue 100 ILE Chi-restraints excluded: chain f residue 117 ASN Chi-restraints excluded: chain f residue 121 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 525 optimal weight: 0.8980 chunk 339 optimal weight: 2.9990 chunk 507 optimal weight: 10.0000 chunk 256 optimal weight: 0.4980 chunk 167 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 chunk 540 optimal weight: 4.9990 chunk 579 optimal weight: 10.0000 chunk 420 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 668 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN B 217 ASN F 65 HIS ** G 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 217 ASN K 161 GLN ** P 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 319 ASN Q 205 ASN U 117 ASN ** W 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 217 ASN Z 65 HIS 1 20 GLN ** 3 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 217 ASN ** 3 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 161 GLN ** a 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 319 ASN ** a 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 117 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 68412 Z= 0.233 Angle : 0.686 15.622 93048 Z= 0.320 Chirality : 0.045 0.327 10404 Planarity : 0.005 0.070 12192 Dihedral : 4.680 19.256 9708 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 5.43 % Allowed : 21.78 % Favored : 72.79 % 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: -1.71 (0.09), residues: 8748 helix: 0.31 (0.10), residues: 3012 sheet: -1.40 (0.13), residues: 1506 loop : -2.14 (0.09), residues: 4230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP O 72 HIS 0.005 0.001 HIS U 116 PHE 0.035 0.002 PHE 1 83 TYR 0.036 0.001 TYR Q 315 ARG 0.012 0.000 ARG 9 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2051 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 358 poor density : 1693 time to evaluate : 5.730 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: C 2 MET cc_start: 0.7623 (tpt) cc_final: 0.7053 (tpt) REVERT: C 131 ARG cc_start: 0.8426 (ptt90) cc_final: 0.8170 (ppt170) REVERT: C 189 THR cc_start: 0.9438 (m) cc_final: 0.9214 (p) REVERT: A 65 LYS cc_start: 0.8733 (tppp) cc_final: 0.8506 (tppp) REVERT: A 95 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7684 (ttm-80) REVERT: A 192 SER cc_start: 0.8599 (t) cc_final: 0.8215 (p) REVERT: A 253 GLN cc_start: 0.8775 (mt0) cc_final: 0.8515 (mt0) REVERT: A 271 LYS cc_start: 0.8889 (tttt) cc_final: 0.8625 (ptmm) REVERT: B 163 ARG cc_start: 0.7307 (mpt-90) cc_final: 0.7015 (mpp80) REVERT: B 164 LYS cc_start: 0.8031 (mtmm) cc_final: 0.7740 (ttmm) REVERT: B 215 LEU cc_start: 0.9304 (mt) cc_final: 0.9054 (mt) REVERT: B 217 ASN cc_start: 0.9135 (p0) cc_final: 0.8922 (p0) REVERT: B 257 ASN cc_start: 0.8693 (m-40) cc_final: 0.8388 (m110) REVERT: B 271 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8336 (tttm) REVERT: B 314 ASN cc_start: 0.7535 (p0) cc_final: 0.6652 (p0) REVERT: D 74 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7879 (p0) REVERT: D 119 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6573 (mt) REVERT: D 131 ARG cc_start: 0.7948 (ptm-80) cc_final: 0.7734 (ptt-90) REVERT: D 157 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9209 (mm) REVERT: F 14 TYR cc_start: 0.8798 (t80) cc_final: 0.8489 (t80) REVERT: F 122 MET cc_start: 0.8477 (mmm) cc_final: 0.8186 (mtp) REVERT: G 106 MET cc_start: 0.7332 (ptp) cc_final: 0.7107 (ptm) REVERT: I 32 MET cc_start: 0.6132 (ptt) cc_final: 0.5812 (ptt) REVERT: I 69 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8026 (mt-10) REVERT: I 105 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8351 (mt-10) REVERT: I 143 MET cc_start: 0.8931 (ttm) cc_final: 0.8670 (ttm) REVERT: I 164 LYS cc_start: 0.8413 (mtpp) cc_final: 0.7930 (mtpp) REVERT: I 192 SER cc_start: 0.8506 (t) cc_final: 0.8061 (p) REVERT: I 271 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8332 (ttpp) REVERT: I 351 GLU cc_start: 0.8012 (pt0) cc_final: 0.7090 (pm20) REVERT: J 101 GLN cc_start: 0.8750 (tt0) cc_final: 0.8335 (tt0) REVERT: J 157 ASP cc_start: 0.8035 (m-30) cc_final: 0.7799 (m-30) REVERT: J 164 LYS cc_start: 0.8621 (mtpp) cc_final: 0.8181 (mtpp) REVERT: J 189 TYR cc_start: 0.9075 (m-80) cc_final: 0.8593 (m-10) REVERT: J 216 ASP cc_start: 0.7789 (t70) cc_final: 0.7332 (t0) REVERT: J 271 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8338 (tttm) REVERT: J 286 LYS cc_start: 0.9041 (ttpt) cc_final: 0.8499 (tttt) REVERT: J 314 ASN cc_start: 0.7843 (p0) cc_final: 0.7299 (p0) REVERT: J 349 GLN cc_start: 0.8209 (tt0) cc_final: 0.7873 (tt0) REVERT: K 106 ARG cc_start: 0.8916 (ttp80) cc_final: 0.8498 (ptm160) REVERT: K 193 LEU cc_start: 0.9069 (tp) cc_final: 0.8718 (tp) REVERT: L 15 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8289 (mm-40) REVERT: L 72 ILE cc_start: 0.9068 (mm) cc_final: 0.8793 (mm) REVERT: N 7 LYS cc_start: 0.8604 (mtpm) cc_final: 0.8186 (tmtt) REVERT: N 76 ASP cc_start: 0.8272 (t0) cc_final: 0.7955 (t0) REVERT: N 81 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8275 (tm-30) REVERT: N 116 HIS cc_start: 0.8489 (p90) cc_final: 0.8209 (p-80) REVERT: O 105 TRP cc_start: 0.9178 (p-90) cc_final: 0.8592 (p-90) REVERT: O 110 ASP cc_start: 0.8499 (t0) cc_final: 0.7906 (m-30) REVERT: P 32 MET cc_start: 0.7452 (ptt) cc_final: 0.6907 (ptp) REVERT: P 69 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8194 (mt-10) REVERT: P 101 GLN cc_start: 0.8834 (tt0) cc_final: 0.8596 (tt0) REVERT: P 163 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.6924 (mmt90) REVERT: P 192 SER cc_start: 0.8596 (t) cc_final: 0.8305 (p) REVERT: P 205 ASN cc_start: 0.9304 (m-40) cc_final: 0.8754 (m-40) REVERT: P 244 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9033 (tp) REVERT: Q 216 ASP cc_start: 0.7684 (t70) cc_final: 0.7091 (t0) REVERT: Q 314 ASN cc_start: 0.7991 (p0) cc_final: 0.6967 (p0) REVERT: Q 349 GLN cc_start: 0.8419 (tt0) cc_final: 0.8206 (tt0) REVERT: R 193 LEU cc_start: 0.8771 (tp) cc_final: 0.8478 (tp) REVERT: S 50 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7093 (pm20) REVERT: S 97 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7264 (pp) REVERT: T 47 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7877 (ptt90) REVERT: U 12 LYS cc_start: 0.8139 (mttm) cc_final: 0.7830 (mttm) REVERT: U 51 ARG cc_start: 0.8211 (ttp80) cc_final: 0.7940 (ttp80) REVERT: U 60 ARG cc_start: 0.8379 (ptp-110) cc_final: 0.7994 (ptp90) REVERT: U 81 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8425 (tm-30) REVERT: U 123 GLU cc_start: 0.7704 (tp30) cc_final: 0.7309 (tp30) REVERT: V 189 THR cc_start: 0.9412 (m) cc_final: 0.9203 (p) REVERT: X 101 GLN cc_start: 0.8239 (tt0) cc_final: 0.7890 (tt0) REVERT: X 215 LEU cc_start: 0.9310 (mt) cc_final: 0.9067 (mt) REVERT: X 257 ASN cc_start: 0.8682 (m-40) cc_final: 0.8371 (m110) REVERT: X 271 LYS cc_start: 0.8506 (ttpt) cc_final: 0.8223 (ttpt) REVERT: X 314 ASN cc_start: 0.7517 (p0) cc_final: 0.6631 (p0) REVERT: Y 133 GLU cc_start: 0.7207 (pt0) cc_final: 0.6902 (pt0) REVERT: Y 157 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9211 (mm) REVERT: Z 14 TYR cc_start: 0.8792 (t80) cc_final: 0.8487 (t80) REVERT: 0 94 GLU cc_start: 0.7558 (tt0) cc_final: 0.7299 (tm-30) REVERT: 1 7 LYS cc_start: 0.8779 (ttpp) cc_final: 0.7864 (tptp) REVERT: 1 52 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7139 (mt-10) REVERT: 1 81 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8249 (tm-30) REVERT: 1 126 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7219 (mtp) REVERT: 3 65 LYS cc_start: 0.8903 (tppt) cc_final: 0.8235 (tppt) REVERT: 3 69 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8135 (mt-10) REVERT: 3 164 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8163 (ttmm) REVERT: 3 192 SER cc_start: 0.8561 (t) cc_final: 0.8081 (p) REVERT: 4 101 GLN cc_start: 0.8720 (tt0) cc_final: 0.8312 (tt0) REVERT: 4 189 TYR cc_start: 0.9041 (m-80) cc_final: 0.8615 (m-10) REVERT: 4 216 ASP cc_start: 0.7777 (t70) cc_final: 0.7348 (t0) REVERT: 4 244 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9052 (tp) REVERT: 4 286 LYS cc_start: 0.8929 (ttpt) cc_final: 0.8457 (tttt) REVERT: 4 314 ASN cc_start: 0.7684 (p0) cc_final: 0.7155 (p0) REVERT: 4 349 GLN cc_start: 0.8251 (tt0) cc_final: 0.7871 (tt0) REVERT: 4 355 ASP cc_start: 0.7722 (t0) cc_final: 0.7154 (t0) REVERT: 5 106 ARG cc_start: 0.8893 (ttp80) cc_final: 0.8380 (ptm160) REVERT: 5 193 LEU cc_start: 0.9024 (tp) cc_final: 0.8687 (tp) REVERT: 6 15 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8341 (mm-40) REVERT: 6 72 ILE cc_start: 0.9054 (mm) cc_final: 0.8776 (mm) REVERT: 7 50 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7103 (mm-30) REVERT: 7 58 PRO cc_start: 0.8613 (Cg_exo) cc_final: 0.8129 (Cg_endo) REVERT: 8 7 LYS cc_start: 0.8633 (mtpm) cc_final: 0.8366 (tmtt) REVERT: 8 22 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7460 (mt-10) REVERT: 8 76 ASP cc_start: 0.8244 (t0) cc_final: 0.7935 (t0) REVERT: 9 2 MET cc_start: 0.7716 (tpt) cc_final: 0.7094 (tpt) REVERT: 9 105 TRP cc_start: 0.9159 (p-90) cc_final: 0.8603 (p-90) REVERT: 9 110 ASP cc_start: 0.8551 (t0) cc_final: 0.7961 (m-30) REVERT: a 69 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8246 (mt-10) REVERT: a 101 GLN cc_start: 0.8788 (tt0) cc_final: 0.8485 (tt0) REVERT: a 164 LYS cc_start: 0.8545 (mtpt) cc_final: 0.8332 (mtpt) REVERT: a 192 SER cc_start: 0.8591 (t) cc_final: 0.8285 (p) REVERT: a 205 ASN cc_start: 0.9300 (m-40) cc_final: 0.8754 (m-40) REVERT: a 244 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9020 (tp) REVERT: b 51 ARG cc_start: 0.8080 (ptp90) cc_final: 0.7812 (ptp90) REVERT: b 189 TYR cc_start: 0.8997 (m-80) cc_final: 0.8785 (m-10) REVERT: b 216 ASP cc_start: 0.7668 (t70) cc_final: 0.7082 (t0) REVERT: b 271 LYS cc_start: 0.8855 (tttt) cc_final: 0.8486 (pttt) REVERT: b 314 ASN cc_start: 0.8008 (p0) cc_final: 0.6959 (p0) REVERT: b 358 GLN cc_start: 0.8940 (pp30) cc_final: 0.8504 (pm20) REVERT: c 193 LEU cc_start: 0.8788 (tp) cc_final: 0.8513 (tp) REVERT: d 50 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7135 (pm20) REVERT: d 97 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7210 (pp) REVERT: f 12 LYS cc_start: 0.8189 (mttm) cc_final: 0.7842 (mttm) REVERT: f 60 ARG cc_start: 0.8415 (ptp-110) cc_final: 0.7937 (ptp90) REVERT: f 76 ASP cc_start: 0.8058 (t0) cc_final: 0.7843 (t0) REVERT: f 81 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8367 (tm-30) REVERT: f 90 GLU cc_start: 0.8795 (tp30) cc_final: 0.8586 (mm-30) REVERT: f 91 PHE cc_start: 0.8175 (m-80) cc_final: 0.7847 (m-10) REVERT: f 123 GLU cc_start: 0.7626 (tp30) cc_final: 0.7240 (tp30) outliers start: 358 outliers final: 284 residues processed: 1882 average time/residue: 0.6436 time to fit residues: 2039.6231 Evaluate side-chains 1929 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1628 time to evaluate : 5.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 222 SER Chi-restraints excluded: chain I residue 231 ASP Chi-restraints excluded: chain I residue 239 GLU Chi-restraints excluded: chain I residue 245 ILE Chi-restraints excluded: chain I residue 278 SER Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 306 ILE Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain I residue 373 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 271 LYS Chi-restraints excluded: chain J residue 278 SER Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 356 LEU Chi-restraints excluded: chain J residue 368 GLN Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 145 SER Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 133 SER Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 187 ASP Chi-restraints excluded: chain P residue 222 SER Chi-restraints excluded: chain P residue 231 ASP Chi-restraints excluded: chain P residue 244 LEU Chi-restraints excluded: chain P residue 278 SER Chi-restraints excluded: chain P residue 306 ILE Chi-restraints excluded: chain P residue 319 ASN Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 356 LEU Chi-restraints excluded: chain P residue 386 VAL Chi-restraints excluded: chain Q residue 32 MET Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 126 CYS Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 199 VAL Chi-restraints excluded: chain Q residue 222 SER Chi-restraints excluded: chain Q residue 231 ASP Chi-restraints excluded: chain Q residue 235 VAL Chi-restraints excluded: chain Q residue 278 SER Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain S residue 50 GLU Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 77 GLU Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 117 ASN Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 29 PHE Chi-restraints excluded: chain V residue 143 SER Chi-restraints excluded: chain V residue 149 VAL Chi-restraints excluded: chain V residue 165 LEU Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain W residue 122 LEU Chi-restraints excluded: chain W residue 126 CYS Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 187 ASP Chi-restraints excluded: chain W residue 222 SER Chi-restraints excluded: chain W residue 231 ASP Chi-restraints excluded: chain W residue 245 ILE Chi-restraints excluded: chain W residue 249 GLU Chi-restraints excluded: chain W residue 278 SER Chi-restraints excluded: chain W residue 306 ILE Chi-restraints excluded: chain W residue 331 LEU Chi-restraints excluded: chain W residue 356 LEU Chi-restraints excluded: chain W residue 373 ILE Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 98 ASN Chi-restraints excluded: chain X residue 117 SER Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain X residue 126 CYS Chi-restraints excluded: chain X residue 133 ARG Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 177 CYS Chi-restraints excluded: chain X residue 235 VAL Chi-restraints excluded: chain X residue 278 SER Chi-restraints excluded: chain X residue 311 THR Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Y residue 157 LEU Chi-restraints excluded: chain Y residue 164 GLU Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 38 GLU Chi-restraints excluded: chain 0 residue 53 THR Chi-restraints excluded: chain 0 residue 77 GLU Chi-restraints excluded: chain 0 residue 110 VAL Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 1 residue 30 THR Chi-restraints excluded: chain 1 residue 43 SER Chi-restraints excluded: chain 1 residue 61 SER Chi-restraints excluded: chain 1 residue 63 SER Chi-restraints excluded: chain 1 residue 65 SER Chi-restraints excluded: chain 1 residue 85 ASP Chi-restraints excluded: chain 1 residue 93 VAL Chi-restraints excluded: chain 1 residue 121 SER Chi-restraints excluded: chain 1 residue 126 MET Chi-restraints excluded: chain 1 residue 132 LEU Chi-restraints excluded: chain 1 residue 133 SER Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 29 PHE Chi-restraints excluded: chain 2 residue 147 LEU Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 3 residue 122 LEU Chi-restraints excluded: chain 3 residue 160 VAL Chi-restraints excluded: chain 3 residue 177 CYS Chi-restraints excluded: chain 3 residue 187 ASP Chi-restraints excluded: chain 3 residue 222 SER Chi-restraints excluded: chain 3 residue 225 ILE Chi-restraints excluded: chain 3 residue 231 ASP Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 304 ILE Chi-restraints excluded: chain 3 residue 309 ASP Chi-restraints excluded: chain 3 residue 326 THR Chi-restraints excluded: chain 3 residue 328 LEU Chi-restraints excluded: chain 3 residue 356 LEU Chi-restraints excluded: chain 4 residue 125 VAL Chi-restraints excluded: chain 4 residue 133 ARG Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 4 residue 278 SER Chi-restraints excluded: chain 4 residue 306 ILE Chi-restraints excluded: chain 4 residue 311 THR Chi-restraints excluded: chain 4 residue 356 LEU Chi-restraints excluded: chain 4 residue 379 LEU Chi-restraints excluded: chain 5 residue 143 SER Chi-restraints excluded: chain 5 residue 145 SER Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 97 LEU Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 7 residue 27 LEU Chi-restraints excluded: chain 7 residue 38 GLU Chi-restraints excluded: chain 7 residue 53 THR Chi-restraints excluded: chain 7 residue 77 GLU Chi-restraints excluded: chain 8 residue 9 LEU Chi-restraints excluded: chain 8 residue 24 ILE Chi-restraints excluded: chain 8 residue 30 THR Chi-restraints excluded: chain 8 residue 54 LEU Chi-restraints excluded: chain 8 residue 85 ASP Chi-restraints excluded: chain 8 residue 100 ILE Chi-restraints excluded: chain 8 residue 126 MET Chi-restraints excluded: chain 9 residue 12 THR Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 54 THR Chi-restraints excluded: chain 9 residue 126 ILE Chi-restraints excluded: chain 9 residue 193 LEU Chi-restraints excluded: chain a residue 69 GLU Chi-restraints excluded: chain a residue 117 SER Chi-restraints excluded: chain a residue 126 CYS Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 187 ASP Chi-restraints excluded: chain a residue 222 SER Chi-restraints excluded: chain a residue 231 ASP Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 278 SER Chi-restraints excluded: chain a residue 306 ILE Chi-restraints excluded: chain a residue 319 ASN Chi-restraints excluded: chain a residue 328 LEU Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain a residue 356 LEU Chi-restraints excluded: chain b residue 125 VAL Chi-restraints excluded: chain b residue 126 CYS Chi-restraints excluded: chain b residue 160 VAL Chi-restraints excluded: chain b residue 187 ASP Chi-restraints excluded: chain b residue 222 SER Chi-restraints excluded: chain b residue 231 ASP Chi-restraints excluded: chain b residue 235 VAL Chi-restraints excluded: chain b residue 278 SER Chi-restraints excluded: chain b residue 311 THR Chi-restraints excluded: chain b residue 356 LEU Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 161 GLN Chi-restraints excluded: chain c residue 164 GLU Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 73 THR Chi-restraints excluded: chain d residue 97 LEU Chi-restraints excluded: chain e residue 27 LEU Chi-restraints excluded: chain e residue 45 SER Chi-restraints excluded: chain e residue 77 GLU Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 63 SER Chi-restraints excluded: chain f residue 85 ASP Chi-restraints excluded: chain f residue 100 ILE Chi-restraints excluded: chain f residue 121 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 773 optimal weight: 0.0470 chunk 814 optimal weight: 4.9990 chunk 743 optimal weight: 0.4980 chunk 792 optimal weight: 2.9990 chunk 476 optimal weight: 1.9990 chunk 345 optimal weight: 7.9990 chunk 622 optimal weight: 0.7980 chunk 243 optimal weight: 0.8980 chunk 715 optimal weight: 9.9990 chunk 749 optimal weight: 2.9990 chunk 789 optimal weight: 2.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 217 ASN ** I 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 240 GLN ** K 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 319 ASN P 381 ASN V 4 ASN ** W 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 217 ASN Y 76 GLN 1 20 GLN 1 116 HIS ** 3 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 217 ASN ** 3 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 319 ASN ** a 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 68412 Z= 0.175 Angle : 0.668 13.965 93048 Z= 0.311 Chirality : 0.044 0.344 10404 Planarity : 0.005 0.070 12192 Dihedral : 4.538 18.454 9708 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.58 % Allowed : 22.93 % Favored : 72.49 % 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: -1.57 (0.09), residues: 8748 helix: 0.49 (0.10), residues: 3012 sheet: -1.51 (0.13), residues: 1584 loop : -2.04 (0.10), residues: 4152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP 2 72 HIS 0.005 0.001 HIS f 116 PHE 0.037 0.001 PHE 1 83 TYR 0.037 0.001 TYR Q 315 ARG 0.012 0.000 ARG 9 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2033 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 1731 time to evaluate : 5.748 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: C 2 MET cc_start: 0.7658 (tpt) cc_final: 0.6537 (tpt) REVERT: C 131 ARG cc_start: 0.8363 (ptt90) cc_final: 0.8142 (ppt170) REVERT: A 65 LYS cc_start: 0.8719 (tppp) cc_final: 0.8512 (tppp) REVERT: A 95 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7723 (ttm-80) REVERT: A 164 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8318 (mtpt) REVERT: A 192 SER cc_start: 0.8547 (t) cc_final: 0.8156 (p) REVERT: A 216 ASP cc_start: 0.8304 (m-30) cc_final: 0.7943 (m-30) REVERT: A 271 LYS cc_start: 0.8795 (tttt) cc_final: 0.8586 (ptmm) REVERT: B 101 GLN cc_start: 0.8364 (tp40) cc_final: 0.8051 (tt0) REVERT: B 163 ARG cc_start: 0.7280 (mpt-90) cc_final: 0.7001 (mpp80) REVERT: B 215 LEU cc_start: 0.9284 (mt) cc_final: 0.9035 (mt) REVERT: B 253 GLN cc_start: 0.9147 (mt0) cc_final: 0.8830 (mt0) REVERT: B 262 MET cc_start: 0.8908 (ttm) cc_final: 0.8568 (ttm) REVERT: B 271 LYS cc_start: 0.8562 (ttpt) cc_final: 0.8226 (tttm) REVERT: B 314 ASN cc_start: 0.7415 (p0) cc_final: 0.6584 (p0) REVERT: D 74 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7778 (p0) REVERT: D 119 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6574 (mt) REVERT: D 157 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9159 (mm) REVERT: F 14 TYR cc_start: 0.8779 (t80) cc_final: 0.8478 (t80) REVERT: F 122 MET cc_start: 0.8458 (mmm) cc_final: 0.8186 (mtp) REVERT: G 7 LYS cc_start: 0.8684 (ttpp) cc_final: 0.7774 (tptp) REVERT: G 81 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8491 (tm-30) REVERT: G 106 MET cc_start: 0.7357 (ptp) cc_final: 0.7075 (ptm) REVERT: I 32 MET cc_start: 0.6178 (ptt) cc_final: 0.5767 (ptt) REVERT: I 69 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7927 (mt-10) REVERT: I 105 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8370 (mt-10) REVERT: I 134 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7773 (mt-10) REVERT: I 143 MET cc_start: 0.8900 (ttm) cc_final: 0.8610 (ttm) REVERT: I 164 LYS cc_start: 0.8376 (mtpp) cc_final: 0.7880 (mtpp) REVERT: I 192 SER cc_start: 0.8432 (t) cc_final: 0.8022 (p) REVERT: I 271 LYS cc_start: 0.8721 (ttpt) cc_final: 0.8317 (ttpp) REVERT: J 101 GLN cc_start: 0.8713 (tt0) cc_final: 0.8239 (tt0) REVERT: J 157 ASP cc_start: 0.8055 (m-30) cc_final: 0.7705 (m-30) REVERT: J 164 LYS cc_start: 0.8587 (mtpp) cc_final: 0.8171 (mtpp) REVERT: J 189 TYR cc_start: 0.9062 (m-80) cc_final: 0.8616 (m-10) REVERT: J 216 ASP cc_start: 0.7741 (t70) cc_final: 0.7404 (t0) REVERT: J 314 ASN cc_start: 0.7696 (p0) cc_final: 0.7241 (p0) REVERT: J 349 GLN cc_start: 0.8238 (tt0) cc_final: 0.7888 (tt0) REVERT: J 351 GLU cc_start: 0.6797 (pm20) cc_final: 0.6089 (pm20) REVERT: J 353 LYS cc_start: 0.8736 (ptpp) cc_final: 0.8368 (ptpp) REVERT: K 106 ARG cc_start: 0.8856 (ttp80) cc_final: 0.8425 (ptm160) REVERT: K 193 LEU cc_start: 0.9003 (tp) cc_final: 0.8639 (tp) REVERT: L 15 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8323 (mm-40) REVERT: L 72 ILE cc_start: 0.9041 (mm) cc_final: 0.8772 (mm) REVERT: M 58 PRO cc_start: 0.8512 (Cg_exo) cc_final: 0.8027 (Cg_endo) REVERT: N 7 LYS cc_start: 0.8589 (mtpm) cc_final: 0.8191 (tmtt) REVERT: N 76 ASP cc_start: 0.8202 (t0) cc_final: 0.7943 (t0) REVERT: N 78 ARG cc_start: 0.7667 (tpp-160) cc_final: 0.7463 (tpp80) REVERT: N 81 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8385 (tm-30) REVERT: N 106 MET cc_start: 0.7011 (ptm) cc_final: 0.6735 (ptm) REVERT: O 105 TRP cc_start: 0.9151 (p-90) cc_final: 0.8591 (p-90) REVERT: O 110 ASP cc_start: 0.8507 (t0) cc_final: 0.7987 (m-30) REVERT: P 32 MET cc_start: 0.7476 (ptt) cc_final: 0.6930 (ptp) REVERT: P 69 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8200 (mt-10) REVERT: P 101 GLN cc_start: 0.8814 (tt0) cc_final: 0.8573 (tt0) REVERT: P 163 ARG cc_start: 0.7550 (mmm-85) cc_final: 0.6903 (mmt90) REVERT: P 192 SER cc_start: 0.8546 (t) cc_final: 0.8248 (p) REVERT: P 205 ASN cc_start: 0.9292 (m-40) cc_final: 0.8768 (m-40) REVERT: P 216 ASP cc_start: 0.8197 (m-30) cc_final: 0.7574 (t0) REVERT: P 244 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9030 (tp) REVERT: Q 136 HIS cc_start: 0.8440 (m-70) cc_final: 0.8122 (m-70) REVERT: Q 216 ASP cc_start: 0.7621 (t70) cc_final: 0.7163 (t0) REVERT: Q 271 LYS cc_start: 0.8780 (tttt) cc_final: 0.8480 (tttt) REVERT: Q 314 ASN cc_start: 0.7887 (p0) cc_final: 0.7030 (p0) REVERT: Q 349 GLN cc_start: 0.8415 (tt0) cc_final: 0.8164 (tt0) REVERT: R 193 LEU cc_start: 0.8738 (tp) cc_final: 0.8432 (tp) REVERT: S 50 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7147 (pm20) REVERT: S 97 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7225 (pp) REVERT: T 47 ARG cc_start: 0.8168 (ttp80) cc_final: 0.7922 (ptt90) REVERT: U 12 LYS cc_start: 0.8109 (mttm) cc_final: 0.7676 (mttm) REVERT: U 51 ARG cc_start: 0.8151 (ttp80) cc_final: 0.7899 (ttp80) REVERT: U 60 ARG cc_start: 0.8348 (ptp-110) cc_final: 0.7950 (ptp90) REVERT: U 81 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8353 (tm-30) REVERT: U 123 GLU cc_start: 0.7601 (tp30) cc_final: 0.7215 (tp30) REVERT: V 90 ARG cc_start: 0.7754 (mtm110) cc_final: 0.6843 (ptt90) REVERT: V 131 ARG cc_start: 0.8531 (ptt90) cc_final: 0.8234 (ppt170) REVERT: V 189 THR cc_start: 0.9402 (m) cc_final: 0.9191 (p) REVERT: W 121 TYR cc_start: 0.8723 (m-80) cc_final: 0.8367 (m-80) REVERT: W 143 MET cc_start: 0.8698 (tpp) cc_final: 0.7954 (ttm) REVERT: W 192 SER cc_start: 0.8461 (t) cc_final: 0.8044 (p) REVERT: W 216 ASP cc_start: 0.8329 (m-30) cc_final: 0.7976 (m-30) REVERT: W 271 LYS cc_start: 0.8890 (tttt) cc_final: 0.8653 (ptmm) REVERT: W 379 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8256 (pp) REVERT: X 215 LEU cc_start: 0.9270 (mt) cc_final: 0.9014 (mt) REVERT: X 253 GLN cc_start: 0.9158 (mt0) cc_final: 0.8760 (mt0) REVERT: X 257 ASN cc_start: 0.8571 (m-40) cc_final: 0.8317 (m110) REVERT: X 262 MET cc_start: 0.8951 (ttm) cc_final: 0.8587 (ttm) REVERT: X 271 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8181 (ttpt) REVERT: X 314 ASN cc_start: 0.7389 (p0) cc_final: 0.6634 (p0) REVERT: Y 133 GLU cc_start: 0.7147 (pt0) cc_final: 0.6941 (pt0) REVERT: Y 157 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9161 (mm) REVERT: Z 14 TYR cc_start: 0.8761 (t80) cc_final: 0.8450 (t80) REVERT: 0 14 GLU cc_start: 0.8033 (tt0) cc_final: 0.7807 (tt0) REVERT: 0 94 GLU cc_start: 0.7468 (tt0) cc_final: 0.7185 (tm-30) REVERT: 1 7 LYS cc_start: 0.8738 (ttpp) cc_final: 0.7791 (tptp) REVERT: 1 52 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7155 (mt-10) REVERT: 1 78 ARG cc_start: 0.7526 (tpp80) cc_final: 0.7217 (tpp80) REVERT: 1 81 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8173 (tm-30) REVERT: 1 126 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7323 (mtp) REVERT: 2 176 MET cc_start: 0.7780 (ttt) cc_final: 0.7579 (mtp) REVERT: 3 69 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8054 (mt-10) REVERT: 3 134 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7741 (mt-10) REVERT: 3 142 ARG cc_start: 0.8536 (mtm180) cc_final: 0.7912 (mtm180) REVERT: 3 164 LYS cc_start: 0.8654 (mtpp) cc_final: 0.8194 (ttmm) REVERT: 3 192 SER cc_start: 0.8394 (t) cc_final: 0.7967 (p) REVERT: 4 101 GLN cc_start: 0.8660 (tt0) cc_final: 0.8236 (tt0) REVERT: 4 189 TYR cc_start: 0.9039 (m-80) cc_final: 0.8640 (m-10) REVERT: 4 216 ASP cc_start: 0.7763 (t70) cc_final: 0.7437 (t0) REVERT: 4 244 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9047 (tp) REVERT: 4 314 ASN cc_start: 0.7704 (p0) cc_final: 0.7244 (p0) REVERT: 4 349 GLN cc_start: 0.8269 (tt0) cc_final: 0.7888 (tt0) REVERT: 4 351 GLU cc_start: 0.6935 (pm20) cc_final: 0.6402 (pm20) REVERT: 4 355 ASP cc_start: 0.7725 (t0) cc_final: 0.7178 (t0) REVERT: 5 106 ARG cc_start: 0.8852 (ttp80) cc_final: 0.8341 (ptm160) REVERT: 6 15 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8408 (mm-40) REVERT: 6 72 ILE cc_start: 0.9020 (mm) cc_final: 0.8748 (mm) REVERT: 7 58 PRO cc_start: 0.8565 (Cg_exo) cc_final: 0.8080 (Cg_endo) REVERT: 8 22 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7449 (mt-10) REVERT: 8 76 ASP cc_start: 0.8164 (t0) cc_final: 0.7903 (t0) REVERT: 9 2 MET cc_start: 0.7608 (tpt) cc_final: 0.6863 (tpt) REVERT: 9 105 TRP cc_start: 0.9156 (p-90) cc_final: 0.8613 (p-90) REVERT: 9 110 ASP cc_start: 0.8510 (t0) cc_final: 0.7906 (m-30) REVERT: a 69 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8226 (mt-10) REVERT: a 101 GLN cc_start: 0.8771 (tt0) cc_final: 0.8470 (tt0) REVERT: a 192 SER cc_start: 0.8559 (t) cc_final: 0.8237 (p) REVERT: a 205 ASN cc_start: 0.9285 (m-40) cc_final: 0.8759 (m-40) REVERT: a 216 ASP cc_start: 0.8261 (m-30) cc_final: 0.7722 (t0) REVERT: a 244 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.9000 (tp) REVERT: b 51 ARG cc_start: 0.8031 (ptp90) cc_final: 0.7831 (ptp90) REVERT: b 136 HIS cc_start: 0.8462 (m-70) cc_final: 0.8067 (m-70) REVERT: b 216 ASP cc_start: 0.7611 (t70) cc_final: 0.7043 (t0) REVERT: b 271 LYS cc_start: 0.8813 (tttt) cc_final: 0.8466 (pttt) REVERT: b 314 ASN cc_start: 0.7893 (p0) cc_final: 0.7016 (p0) REVERT: b 358 GLN cc_start: 0.8894 (pp30) cc_final: 0.8471 (pm20) REVERT: c 193 LEU cc_start: 0.8754 (tp) cc_final: 0.8459 (tp) REVERT: d 50 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7065 (pm20) REVERT: e 47 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7907 (ptt90) REVERT: f 60 ARG cc_start: 0.8365 (ptp-110) cc_final: 0.7900 (ptp90) REVERT: f 76 ASP cc_start: 0.8113 (t0) cc_final: 0.7785 (t0) REVERT: f 81 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8412 (tm-30) REVERT: f 91 PHE cc_start: 0.8087 (m-80) cc_final: 0.7779 (m-10) REVERT: f 123 GLU cc_start: 0.7613 (tp30) cc_final: 0.7212 (tp30) outliers start: 302 outliers final: 235 residues processed: 1887 average time/residue: 0.6368 time to fit residues: 2026.7743 Evaluate side-chains 1930 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1679 time to evaluate : 5.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 222 SER Chi-restraints excluded: chain I residue 231 ASP Chi-restraints excluded: chain I residue 245 ILE Chi-restraints excluded: chain I residue 278 SER Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 306 ILE Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain I residue 373 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 278 SER Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 356 LEU Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 133 SER Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 187 ASP Chi-restraints excluded: chain P residue 222 SER Chi-restraints excluded: chain P residue 231 ASP Chi-restraints excluded: chain P residue 244 LEU Chi-restraints excluded: chain P residue 278 SER Chi-restraints excluded: chain P residue 306 ILE Chi-restraints excluded: chain P residue 328 LEU Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 356 LEU Chi-restraints excluded: chain P residue 386 VAL Chi-restraints excluded: chain Q residue 32 MET Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 170 THR Chi-restraints excluded: chain Q residue 231 ASP Chi-restraints excluded: chain Q residue 235 VAL Chi-restraints excluded: chain Q residue 278 SER Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain S residue 50 GLU Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 77 GLU Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain V residue 29 PHE Chi-restraints excluded: chain V residue 149 VAL Chi-restraints excluded: chain V residue 165 LEU Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain W residue 122 LEU Chi-restraints excluded: chain W residue 126 CYS Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 187 ASP Chi-restraints excluded: chain W residue 222 SER Chi-restraints excluded: chain W residue 231 ASP Chi-restraints excluded: chain W residue 245 ILE Chi-restraints excluded: chain W residue 249 GLU Chi-restraints excluded: chain W residue 278 SER Chi-restraints excluded: chain W residue 331 LEU Chi-restraints excluded: chain W residue 356 LEU Chi-restraints excluded: chain W residue 373 ILE Chi-restraints excluded: chain W residue 379 LEU Chi-restraints excluded: chain X residue 78 CYS Chi-restraints excluded: chain X residue 98 ASN Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain X residue 126 CYS Chi-restraints excluded: chain X residue 133 ARG Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 231 ASP Chi-restraints excluded: chain X residue 235 VAL Chi-restraints excluded: chain X residue 278 SER Chi-restraints excluded: chain X residue 306 ILE Chi-restraints excluded: chain X residue 311 THR Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Y residue 157 LEU Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 38 GLU Chi-restraints excluded: chain 0 residue 77 GLU Chi-restraints excluded: chain 0 residue 110 VAL Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 1 residue 30 THR Chi-restraints excluded: chain 1 residue 43 SER Chi-restraints excluded: chain 1 residue 61 SER Chi-restraints excluded: chain 1 residue 65 SER Chi-restraints excluded: chain 1 residue 85 ASP Chi-restraints excluded: chain 1 residue 93 VAL Chi-restraints excluded: chain 1 residue 126 MET Chi-restraints excluded: chain 1 residue 132 LEU Chi-restraints excluded: chain 1 residue 133 SER Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 29 PHE Chi-restraints excluded: chain 2 residue 147 LEU Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 3 residue 122 LEU Chi-restraints excluded: chain 3 residue 160 VAL Chi-restraints excluded: chain 3 residue 177 CYS Chi-restraints excluded: chain 3 residue 187 ASP Chi-restraints excluded: chain 3 residue 222 SER Chi-restraints excluded: chain 3 residue 225 ILE Chi-restraints excluded: chain 3 residue 231 ASP Chi-restraints excluded: chain 3 residue 245 ILE Chi-restraints excluded: chain 3 residue 249 GLU Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 309 ASP Chi-restraints excluded: chain 3 residue 326 THR Chi-restraints excluded: chain 3 residue 356 LEU Chi-restraints excluded: chain 3 residue 373 ILE Chi-restraints excluded: chain 4 residue 133 ARG Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 4 residue 306 ILE Chi-restraints excluded: chain 4 residue 311 THR Chi-restraints excluded: chain 4 residue 356 LEU Chi-restraints excluded: chain 4 residue 379 LEU Chi-restraints excluded: chain 5 residue 143 SER Chi-restraints excluded: chain 5 residue 145 SER Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 97 LEU Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 7 residue 27 LEU Chi-restraints excluded: chain 7 residue 38 GLU Chi-restraints excluded: chain 7 residue 53 THR Chi-restraints excluded: chain 7 residue 77 GLU Chi-restraints excluded: chain 8 residue 9 LEU Chi-restraints excluded: chain 8 residue 24 ILE Chi-restraints excluded: chain 8 residue 30 THR Chi-restraints excluded: chain 8 residue 54 LEU Chi-restraints excluded: chain 8 residue 85 ASP Chi-restraints excluded: chain 8 residue 100 ILE Chi-restraints excluded: chain 8 residue 126 MET Chi-restraints excluded: chain 9 residue 12 THR Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 54 THR Chi-restraints excluded: chain 9 residue 126 ILE Chi-restraints excluded: chain 9 residue 193 LEU Chi-restraints excluded: chain a residue 69 GLU Chi-restraints excluded: chain a residue 117 SER Chi-restraints excluded: chain a residue 126 CYS Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 187 ASP Chi-restraints excluded: chain a residue 222 SER Chi-restraints excluded: chain a residue 231 ASP Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 278 SER Chi-restraints excluded: chain a residue 306 ILE Chi-restraints excluded: chain a residue 328 LEU Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain a residue 356 LEU Chi-restraints excluded: chain b residue 125 VAL Chi-restraints excluded: chain b residue 160 VAL Chi-restraints excluded: chain b residue 187 ASP Chi-restraints excluded: chain b residue 231 ASP Chi-restraints excluded: chain b residue 235 VAL Chi-restraints excluded: chain b residue 278 SER Chi-restraints excluded: chain b residue 311 THR Chi-restraints excluded: chain b residue 356 LEU Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain c residue 161 GLN Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 73 THR Chi-restraints excluded: chain e residue 45 SER Chi-restraints excluded: chain e residue 77 GLU Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 85 ASP Chi-restraints excluded: chain f residue 100 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 520 optimal weight: 0.2980 chunk 837 optimal weight: 5.9990 chunk 511 optimal weight: 8.9990 chunk 397 optimal weight: 1.9990 chunk 582 optimal weight: 1.9990 chunk 878 optimal weight: 5.9990 chunk 808 optimal weight: 0.4980 chunk 699 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 540 optimal weight: 4.9990 chunk 429 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN B 217 ASN ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN I 101 GLN ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 217 ASN ** K 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 240 GLN P 319 ASN U 117 ASN ** W 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 319 ASN X 217 ASN ** Y 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 20 GLN ** 3 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 217 ASN ** 3 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 240 GLN a 319 ASN ** a 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 117 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 68412 Z= 0.212 Angle : 0.682 15.239 93048 Z= 0.318 Chirality : 0.045 0.315 10404 Planarity : 0.005 0.073 12192 Dihedral : 4.552 18.575 9708 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.35 % Allowed : 23.81 % Favored : 71.84 % 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: -1.49 (0.09), residues: 8748 helix: 0.57 (0.10), residues: 3018 sheet: -1.49 (0.13), residues: 1584 loop : -1.99 (0.10), residues: 4146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP H 72 HIS 0.005 0.001 HIS b 165 PHE 0.030 0.002 PHE G 83 TYR 0.036 0.001 TYR Q 315 ARG 0.009 0.000 ARG P 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1989 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1702 time to evaluate : 6.570 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: A 95 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7696 (ttm-80) REVERT: A 164 LYS cc_start: 0.8732 (mtpt) cc_final: 0.8412 (mtpp) REVERT: A 192 SER cc_start: 0.8630 (t) cc_final: 0.8219 (p) REVERT: A 216 ASP cc_start: 0.8295 (m-30) cc_final: 0.7910 (m-30) REVERT: B 101 GLN cc_start: 0.8401 (tp40) cc_final: 0.8104 (tt0) REVERT: B 163 ARG cc_start: 0.7303 (mpt-90) cc_final: 0.6994 (mpp80) REVERT: B 215 LEU cc_start: 0.9255 (mt) cc_final: 0.8996 (mt) REVERT: B 253 GLN cc_start: 0.9222 (mt0) cc_final: 0.8982 (mt0) REVERT: B 262 MET cc_start: 0.8974 (ttm) cc_final: 0.8616 (ttm) REVERT: B 271 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8276 (tttm) REVERT: B 314 ASN cc_start: 0.7433 (p0) cc_final: 0.6580 (p0) REVERT: D 74 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7783 (p0) REVERT: D 119 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6597 (mt) REVERT: F 14 TYR cc_start: 0.8805 (t80) cc_final: 0.8484 (t80) REVERT: F 15 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8532 (mm-40) REVERT: G 7 LYS cc_start: 0.8796 (ttpp) cc_final: 0.7855 (tptp) REVERT: G 81 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8212 (tm-30) REVERT: I 69 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: I 105 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8352 (mt-10) REVERT: I 134 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7792 (mt-10) REVERT: I 143 MET cc_start: 0.8950 (ttm) cc_final: 0.8644 (ttm) REVERT: I 164 LYS cc_start: 0.8414 (mtpp) cc_final: 0.7914 (mtpp) REVERT: I 192 SER cc_start: 0.8522 (t) cc_final: 0.8084 (p) REVERT: I 271 LYS cc_start: 0.8795 (ttpt) cc_final: 0.8364 (ttpp) REVERT: I 323 TYR cc_start: 0.8624 (m-80) cc_final: 0.8330 (m-80) REVERT: I 351 GLU cc_start: 0.7972 (pt0) cc_final: 0.7182 (pm20) REVERT: J 101 GLN cc_start: 0.8775 (tt0) cc_final: 0.8317 (tt0) REVERT: J 157 ASP cc_start: 0.8080 (m-30) cc_final: 0.7708 (m-30) REVERT: J 164 LYS cc_start: 0.8594 (mtpp) cc_final: 0.8200 (mtpp) REVERT: J 189 TYR cc_start: 0.9057 (m-80) cc_final: 0.8608 (m-10) REVERT: J 216 ASP cc_start: 0.7823 (t70) cc_final: 0.7520 (t0) REVERT: J 314 ASN cc_start: 0.7635 (p0) cc_final: 0.7187 (p0) REVERT: J 349 GLN cc_start: 0.8241 (tt0) cc_final: 0.7893 (tt0) REVERT: J 353 LYS cc_start: 0.8735 (ptpp) cc_final: 0.8478 (ptpp) REVERT: K 106 ARG cc_start: 0.8937 (ttp80) cc_final: 0.8508 (ptm160) REVERT: K 193 LEU cc_start: 0.9059 (tp) cc_final: 0.8694 (tp) REVERT: L 15 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8330 (mm-40) REVERT: L 72 ILE cc_start: 0.9061 (mm) cc_final: 0.8782 (mm) REVERT: M 47 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7678 (ptt90) REVERT: N 7 LYS cc_start: 0.8619 (mtpm) cc_final: 0.8352 (tmtt) REVERT: N 76 ASP cc_start: 0.8304 (t0) cc_final: 0.8038 (t0) REVERT: N 81 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8331 (tm-30) REVERT: O 105 TRP cc_start: 0.9187 (p-90) cc_final: 0.8648 (p-90) REVERT: O 110 ASP cc_start: 0.8534 (t0) cc_final: 0.7944 (m-30) REVERT: P 32 MET cc_start: 0.7508 (ptt) cc_final: 0.6932 (ptt) REVERT: P 69 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8216 (mt-10) REVERT: P 101 GLN cc_start: 0.8826 (tt0) cc_final: 0.8595 (tt0) REVERT: P 163 ARG cc_start: 0.7549 (mmm-85) cc_final: 0.6895 (mmt90) REVERT: P 192 SER cc_start: 0.8562 (t) cc_final: 0.8302 (p) REVERT: P 205 ASN cc_start: 0.9296 (m-40) cc_final: 0.8750 (m-40) REVERT: P 216 ASP cc_start: 0.8230 (m-30) cc_final: 0.7617 (t0) REVERT: P 244 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9049 (tp) REVERT: Q 136 HIS cc_start: 0.8467 (m-70) cc_final: 0.8141 (m-70) REVERT: Q 216 ASP cc_start: 0.7704 (t70) cc_final: 0.7155 (t0) REVERT: Q 314 ASN cc_start: 0.7890 (p0) cc_final: 0.7031 (p0) REVERT: R 193 LEU cc_start: 0.8806 (tp) cc_final: 0.8512 (tp) REVERT: S 50 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: S 97 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7241 (pp) REVERT: T 47 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7943 (ptt90) REVERT: U 12 LYS cc_start: 0.8117 (mttm) cc_final: 0.7734 (mttm) REVERT: U 51 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7903 (ttp80) REVERT: U 60 ARG cc_start: 0.8264 (ptp-110) cc_final: 0.7896 (ptp90) REVERT: U 78 ARG cc_start: 0.7670 (tpt90) cc_final: 0.7452 (tpp80) REVERT: U 81 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8402 (tm-30) REVERT: U 123 GLU cc_start: 0.7636 (tp30) cc_final: 0.7237 (tp30) REVERT: V 2 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.6888 (tpt) REVERT: V 90 ARG cc_start: 0.7760 (mtm110) cc_final: 0.6856 (ptt90) REVERT: V 131 ARG cc_start: 0.8534 (ptt90) cc_final: 0.8214 (ppt170) REVERT: V 189 THR cc_start: 0.9403 (m) cc_final: 0.9183 (p) REVERT: W 121 TYR cc_start: 0.8725 (m-80) cc_final: 0.8358 (m-80) REVERT: W 143 MET cc_start: 0.8719 (tpp) cc_final: 0.8011 (ttm) REVERT: W 192 SER cc_start: 0.8528 (t) cc_final: 0.8084 (p) REVERT: W 216 ASP cc_start: 0.8285 (m-30) cc_final: 0.7958 (m-30) REVERT: W 271 LYS cc_start: 0.8969 (tttt) cc_final: 0.8666 (ptmm) REVERT: X 49 LEU cc_start: 0.9018 (mt) cc_final: 0.8754 (tt) REVERT: X 215 LEU cc_start: 0.9285 (mt) cc_final: 0.9032 (mt) REVERT: X 253 GLN cc_start: 0.9214 (mt0) cc_final: 0.8905 (mt0) REVERT: X 257 ASN cc_start: 0.8556 (m-40) cc_final: 0.8327 (m110) REVERT: X 262 MET cc_start: 0.8993 (ttm) cc_final: 0.8635 (ttm) REVERT: X 271 LYS cc_start: 0.8505 (ttpt) cc_final: 0.8224 (ttpt) REVERT: X 314 ASN cc_start: 0.7413 (p0) cc_final: 0.6641 (p0) REVERT: Y 133 GLU cc_start: 0.7170 (pt0) cc_final: 0.6937 (pt0) REVERT: Z 14 TYR cc_start: 0.8781 (t80) cc_final: 0.8455 (t80) REVERT: 0 14 GLU cc_start: 0.8031 (tt0) cc_final: 0.7811 (tt0) REVERT: 0 94 GLU cc_start: 0.7493 (tt0) cc_final: 0.7230 (tm-30) REVERT: 1 7 LYS cc_start: 0.8768 (ttpp) cc_final: 0.7806 (tptp) REVERT: 1 52 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7234 (mt-10) REVERT: 1 81 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8218 (tm-30) REVERT: 1 106 MET cc_start: 0.6981 (ptp) cc_final: 0.6726 (ptm) REVERT: 3 69 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8067 (mt-10) REVERT: 3 134 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7764 (mt-10) REVERT: 3 164 LYS cc_start: 0.8762 (mtpp) cc_final: 0.8373 (ttmm) REVERT: 3 192 SER cc_start: 0.8475 (t) cc_final: 0.8028 (p) REVERT: 3 323 TYR cc_start: 0.8645 (m-80) cc_final: 0.8320 (m-80) REVERT: 3 351 GLU cc_start: 0.7895 (pt0) cc_final: 0.6985 (pm20) REVERT: 4 101 GLN cc_start: 0.8686 (tt0) cc_final: 0.8276 (tt0) REVERT: 4 189 TYR cc_start: 0.9048 (m-80) cc_final: 0.8622 (m-10) REVERT: 4 216 ASP cc_start: 0.7840 (t70) cc_final: 0.7419 (t0) REVERT: 4 244 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9032 (tp) REVERT: 4 286 LYS cc_start: 0.8934 (ttpt) cc_final: 0.8504 (tttt) REVERT: 4 314 ASN cc_start: 0.7581 (p0) cc_final: 0.7106 (p0) REVERT: 4 349 GLN cc_start: 0.8296 (tt0) cc_final: 0.7945 (tt0) REVERT: 5 106 ARG cc_start: 0.8890 (ttp80) cc_final: 0.8386 (ptm160) REVERT: 5 193 LEU cc_start: 0.8991 (tp) cc_final: 0.8519 (tp) REVERT: 6 15 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8312 (mm-40) REVERT: 6 72 ILE cc_start: 0.9036 (mm) cc_final: 0.8761 (mm) REVERT: 7 58 PRO cc_start: 0.8592 (Cg_exo) cc_final: 0.8109 (Cg_endo) REVERT: 8 22 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7457 (mt-10) REVERT: 8 76 ASP cc_start: 0.8243 (t0) cc_final: 0.7923 (t0) REVERT: 9 2 MET cc_start: 0.7607 (tpt) cc_final: 0.6822 (tpt) REVERT: 9 105 TRP cc_start: 0.9172 (p-90) cc_final: 0.8664 (p-90) REVERT: 9 110 ASP cc_start: 0.8531 (t0) cc_final: 0.7785 (m-30) REVERT: a 69 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8231 (mt-10) REVERT: a 101 GLN cc_start: 0.8791 (tt0) cc_final: 0.8504 (tt0) REVERT: a 164 LYS cc_start: 0.8507 (mtpt) cc_final: 0.8254 (mtpt) REVERT: a 192 SER cc_start: 0.8624 (t) cc_final: 0.8292 (p) REVERT: a 205 ASN cc_start: 0.9292 (m-40) cc_final: 0.8769 (m-40) REVERT: a 216 ASP cc_start: 0.8253 (m-30) cc_final: 0.7732 (t0) REVERT: a 244 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9008 (tp) REVERT: b 51 ARG cc_start: 0.8078 (ptp90) cc_final: 0.7811 (ptp90) REVERT: b 216 ASP cc_start: 0.7686 (t70) cc_final: 0.7126 (t0) REVERT: b 271 LYS cc_start: 0.8827 (tttt) cc_final: 0.8469 (pttt) REVERT: b 314 ASN cc_start: 0.7942 (p0) cc_final: 0.7166 (p0) REVERT: c 89 LEU cc_start: 0.8995 (tt) cc_final: 0.8749 (tt) REVERT: c 193 LEU cc_start: 0.8824 (tp) cc_final: 0.8538 (tp) REVERT: d 50 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7080 (pm20) REVERT: f 60 ARG cc_start: 0.8259 (ptp-110) cc_final: 0.7899 (ptp90) REVERT: f 76 ASP cc_start: 0.8238 (t0) cc_final: 0.7934 (t0) REVERT: f 81 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8353 (tm-30) REVERT: f 123 GLU cc_start: 0.7626 (tp30) cc_final: 0.7221 (tp30) outliers start: 287 outliers final: 241 residues processed: 1858 average time/residue: 0.6407 time to fit residues: 2005.8909 Evaluate side-chains 1925 residues out of total 6606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1671 time to evaluate : 5.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 222 SER Chi-restraints excluded: chain I residue 231 ASP Chi-restraints excluded: chain I residue 239 GLU Chi-restraints excluded: chain I residue 245 ILE Chi-restraints excluded: chain I residue 278 SER Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 306 ILE Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 356 LEU Chi-restraints excluded: chain I residue 373 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 222 SER Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 278 SER Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 356 LEU Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 133 SER Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 184 ILE Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 187 ASP Chi-restraints excluded: chain P residue 222 SER Chi-restraints excluded: chain P residue 231 ASP Chi-restraints excluded: chain P residue 244 LEU Chi-restraints excluded: chain P residue 278 SER Chi-restraints excluded: chain P residue 306 ILE Chi-restraints excluded: chain P residue 319 ASN Chi-restraints excluded: chain P residue 328 LEU Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 356 LEU Chi-restraints excluded: chain Q residue 32 MET Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 231 ASP Chi-restraints excluded: chain Q residue 235 VAL Chi-restraints excluded: chain Q residue 278 SER Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain S residue 50 GLU Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain U residue 117 ASN Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain V residue 2 MET Chi-restraints excluded: chain V residue 29 PHE Chi-restraints excluded: chain V residue 143 SER Chi-restraints excluded: chain V residue 149 VAL Chi-restraints excluded: chain V residue 165 LEU Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain W residue 126 CYS Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 187 ASP Chi-restraints excluded: chain W residue 222 SER Chi-restraints excluded: chain W residue 231 ASP Chi-restraints excluded: chain W residue 278 SER Chi-restraints excluded: chain W residue 319 ASN Chi-restraints excluded: chain W residue 328 LEU Chi-restraints excluded: chain W residue 331 LEU Chi-restraints excluded: chain W residue 356 LEU Chi-restraints excluded: chain W residue 373 ILE Chi-restraints excluded: chain X residue 78 CYS Chi-restraints excluded: chain X residue 92 ASP Chi-restraints excluded: chain X residue 98 ASN Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain X residue 126 CYS Chi-restraints excluded: chain X residue 133 ARG Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 177 CYS Chi-restraints excluded: chain X residue 235 VAL Chi-restraints excluded: chain X residue 278 SER Chi-restraints excluded: chain X residue 306 ILE Chi-restraints excluded: chain X residue 311 THR Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain 0 residue 18 VAL Chi-restraints excluded: chain 0 residue 38 GLU Chi-restraints excluded: chain 0 residue 53 THR Chi-restraints excluded: chain 0 residue 110 VAL Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 1 residue 30 THR Chi-restraints excluded: chain 1 residue 43 SER Chi-restraints excluded: chain 1 residue 61 SER Chi-restraints excluded: chain 1 residue 65 SER Chi-restraints excluded: chain 1 residue 85 ASP Chi-restraints excluded: chain 1 residue 93 VAL Chi-restraints excluded: chain 1 residue 132 LEU Chi-restraints excluded: chain 1 residue 133 SER Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 29 PHE Chi-restraints excluded: chain 2 residue 147 LEU Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 3 residue 122 LEU Chi-restraints excluded: chain 3 residue 160 VAL Chi-restraints excluded: chain 3 residue 177 CYS Chi-restraints excluded: chain 3 residue 187 ASP Chi-restraints excluded: chain 3 residue 222 SER Chi-restraints excluded: chain 3 residue 225 ILE Chi-restraints excluded: chain 3 residue 231 ASP Chi-restraints excluded: chain 3 residue 245 ILE Chi-restraints excluded: chain 3 residue 249 GLU Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 309 ASP Chi-restraints excluded: chain 3 residue 326 THR Chi-restraints excluded: chain 3 residue 356 LEU Chi-restraints excluded: chain 3 residue 373 ILE Chi-restraints excluded: chain 4 residue 133 ARG Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 4 residue 225 ILE Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 4 residue 278 SER Chi-restraints excluded: chain 4 residue 306 ILE Chi-restraints excluded: chain 4 residue 311 THR Chi-restraints excluded: chain 4 residue 356 LEU Chi-restraints excluded: chain 4 residue 379 LEU Chi-restraints excluded: chain 5 residue 143 SER Chi-restraints excluded: chain 5 residue 145 SER Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 97 LEU Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 7 residue 27 LEU Chi-restraints excluded: chain 7 residue 38 GLU Chi-restraints excluded: chain 7 residue 53 THR Chi-restraints excluded: chain 7 residue 77 GLU Chi-restraints excluded: chain 8 residue 9 LEU Chi-restraints excluded: chain 8 residue 24 ILE Chi-restraints excluded: chain 8 residue 30 THR Chi-restraints excluded: chain 8 residue 85 ASP Chi-restraints excluded: chain 8 residue 100 ILE Chi-restraints excluded: chain 8 residue 126 MET Chi-restraints excluded: chain 9 residue 12 THR Chi-restraints excluded: chain 9 residue 54 THR Chi-restraints excluded: chain 9 residue 193 LEU Chi-restraints excluded: chain a residue 69 GLU Chi-restraints excluded: chain a residue 117 SER Chi-restraints excluded: chain a residue 126 CYS Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 187 ASP Chi-restraints excluded: chain a residue 222 SER Chi-restraints excluded: chain a residue 231 ASP Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 278 SER Chi-restraints excluded: chain a residue 306 ILE Chi-restraints excluded: chain a residue 319 ASN Chi-restraints excluded: chain a residue 328 LEU Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain a residue 356 LEU Chi-restraints excluded: chain b residue 125 VAL Chi-restraints excluded: chain b residue 160 VAL Chi-restraints excluded: chain b residue 187 ASP Chi-restraints excluded: chain b residue 231 ASP Chi-restraints excluded: chain b residue 235 VAL Chi-restraints excluded: chain b residue 278 SER Chi-restraints excluded: chain b residue 311 THR Chi-restraints excluded: chain b residue 356 LEU Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain c residue 161 GLN Chi-restraints excluded: chain c residue 176 MET Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 73 THR Chi-restraints excluded: chain e residue 77 GLU Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 85 ASP Chi-restraints excluded: chain f residue 100 ILE Chi-restraints excluded: chain f residue 117 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 555 optimal weight: 0.6980 chunk 745 optimal weight: 6.9990 chunk 214 optimal weight: 7.9990 chunk 645 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 194 optimal weight: 5.9990 chunk 700 optimal weight: 0.4980 chunk 293 optimal weight: 1.9990 chunk 719 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 217 ASN ** K 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 319 ASN ** W 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 319 ASN X 101 GLN X 217 ASN X 319 ASN 1 20 GLN ** 1 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 217 ASN ** 3 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 319 ASN ** a 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.124764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.096889 restraints weight = 104682.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.100019 restraints weight = 53794.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.102029 restraints weight = 34723.219| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 68412 Z= 0.226 Angle : 0.689 15.500 93048 Z= 0.321 Chirality : 0.045 0.326 10404 Planarity : 0.005 0.071 12192 Dihedral : 4.584 18.563 9708 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 4.52 % Allowed : 23.89 % Favored : 71.60 % 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: -1.44 (0.09), residues: 8748 helix: 0.62 (0.10), residues: 3018 sheet: -1.49 (0.13), residues: 1596 loop : -1.95 (0.10), residues: 4134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP H 72 HIS 0.005 0.001 HIS 1 116 PHE 0.036 0.002 PHE 1 83 TYR 0.037 0.001 TYR Q 315 ARG 0.008 0.000 ARG P 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26556.19 seconds wall clock time: 391 minutes 7.66 seconds (23467.66 seconds total)