Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 13:11:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j06_5185/08_2023/3j06_5185.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j06_5185/08_2023/3j06_5185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j06_5185/08_2023/3j06_5185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j06_5185/08_2023/3j06_5185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j06_5185/08_2023/3j06_5185.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j06_5185/08_2023/3j06_5185.pdb" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= 0.229 sd= 1.474 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 147 5.49 5 S 49 5.16 5 C 38906 2.51 5 N 11074 2.21 5 O 12740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 112": "NH1" <-> "NH2" Residue "D ASP 116": "OD1" <-> "OD2" Residue "D TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 90": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ASP 116": "OD1" <-> "OD2" Residue "F TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 90": "NH1" <-> "NH2" Residue "H ARG 112": "NH1" <-> "NH2" Residue "H ASP 116": "OD1" <-> "OD2" Residue "H TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 90": "NH1" <-> "NH2" Residue "J ARG 112": "NH1" <-> "NH2" Residue "J ASP 116": "OD1" <-> "OD2" Residue "J TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 90": "NH1" <-> "NH2" Residue "L ARG 112": "NH1" <-> "NH2" Residue "L ASP 116": "OD1" <-> "OD2" Residue "L TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 90": "NH1" <-> "NH2" Residue "N ARG 112": "NH1" <-> "NH2" Residue "N ASP 116": "OD1" <-> "OD2" Residue "N TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 90": "NH1" <-> "NH2" Residue "P ARG 112": "NH1" <-> "NH2" Residue "P ASP 116": "OD1" <-> "OD2" Residue "P TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 90": "NH1" <-> "NH2" Residue "S ARG 112": "NH1" <-> "NH2" Residue "S ASP 116": "OD1" <-> "OD2" Residue "S TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 90": "NH1" <-> "NH2" Residue "U ARG 112": "NH1" <-> "NH2" Residue "U ASP 116": "OD1" <-> "OD2" Residue "U TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 90": "NH1" <-> "NH2" Residue "W ARG 112": "NH1" <-> "NH2" Residue "W ASP 116": "OD1" <-> "OD2" Residue "W TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 90": "NH1" <-> "NH2" Residue "Y ARG 112": "NH1" <-> "NH2" Residue "Y ASP 116": "OD1" <-> "OD2" Residue "Y TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 90": "NH1" <-> "NH2" Residue "0 ARG 112": "NH1" <-> "NH2" Residue "0 ASP 116": "OD1" <-> "OD2" Residue "0 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 90": "NH1" <-> "NH2" Residue "2 ARG 112": "NH1" <-> "NH2" Residue "2 ASP 116": "OD1" <-> "OD2" Residue "2 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 90": "NH1" <-> "NH2" Residue "4 ARG 112": "NH1" <-> "NH2" Residue "4 ASP 116": "OD1" <-> "OD2" Residue "4 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 90": "NH1" <-> "NH2" Residue "6 ARG 112": "NH1" <-> "NH2" Residue "6 ASP 116": "OD1" <-> "OD2" Residue "6 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 90": "NH1" <-> "NH2" Residue "8 ARG 112": "NH1" <-> "NH2" Residue "8 ASP 116": "OD1" <-> "OD2" Residue "8 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 90": "NH1" <-> "NH2" Residue "a ARG 112": "NH1" <-> "NH2" Residue "a ASP 116": "OD1" <-> "OD2" Residue "a TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 90": "NH1" <-> "NH2" Residue "c ARG 112": "NH1" <-> "NH2" Residue "c ASP 116": "OD1" <-> "OD2" Residue "c TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 90": "NH1" <-> "NH2" Residue "e ARG 112": "NH1" <-> "NH2" Residue "e ASP 116": "OD1" <-> "OD2" Residue "e TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 90": "NH1" <-> "NH2" Residue "g ARG 112": "NH1" <-> "NH2" Residue "g ASP 116": "OD1" <-> "OD2" Residue "g TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 90": "NH1" <-> "NH2" Residue "i ARG 112": "NH1" <-> "NH2" Residue "i ASP 116": "OD1" <-> "OD2" Residue "i TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 90": "NH1" <-> "NH2" Residue "k ARG 112": "NH1" <-> "NH2" Residue "k ASP 116": "OD1" <-> "OD2" Residue "k TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 90": "NH1" <-> "NH2" Residue "m ARG 112": "NH1" <-> "NH2" Residue "m ASP 116": "OD1" <-> "OD2" Residue "m TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 90": "NH1" <-> "NH2" Residue "o ARG 112": "NH1" <-> "NH2" Residue "o ASP 116": "OD1" <-> "OD2" Residue "o TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 90": "NH1" <-> "NH2" Residue "q ARG 112": "NH1" <-> "NH2" Residue "q ASP 116": "OD1" <-> "OD2" Residue "q TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 90": "NH1" <-> "NH2" Residue "s ARG 112": "NH1" <-> "NH2" Residue "s ASP 116": "OD1" <-> "OD2" Residue "s TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 90": "NH1" <-> "NH2" Residue "u ARG 112": "NH1" <-> "NH2" Residue "u ASP 116": "OD1" <-> "OD2" Residue "u TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 90": "NH1" <-> "NH2" Residue "w ARG 112": "NH1" <-> "NH2" Residue "w ASP 116": "OD1" <-> "OD2" Residue "w TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 90": "NH1" <-> "NH2" Residue "y ARG 112": "NH1" <-> "NH2" Residue "y ASP 116": "OD1" <-> "OD2" Residue "y TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA ARG 90": "NH1" <-> "NH2" Residue "AA ARG 112": "NH1" <-> "NH2" Residue "AA ASP 116": "OD1" <-> "OD2" Residue "AA TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC ARG 90": "NH1" <-> "NH2" Residue "AC ARG 112": "NH1" <-> "NH2" Residue "AC ASP 116": "OD1" <-> "OD2" Residue "AC TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE ARG 90": "NH1" <-> "NH2" Residue "AE ARG 112": "NH1" <-> "NH2" Residue "AE ASP 116": "OD1" <-> "OD2" Residue "AE TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG ARG 90": "NH1" <-> "NH2" Residue "AG ARG 112": "NH1" <-> "NH2" Residue "AG ASP 116": "OD1" <-> "OD2" Residue "AG TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI ARG 90": "NH1" <-> "NH2" Residue "AI ARG 112": "NH1" <-> "NH2" Residue "AI ASP 116": "OD1" <-> "OD2" Residue "AI TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK ARG 90": "NH1" <-> "NH2" Residue "AK ARG 112": "NH1" <-> "NH2" Residue "AK ASP 116": "OD1" <-> "OD2" Residue "AK TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM ARG 90": "NH1" <-> "NH2" Residue "AM ARG 112": "NH1" <-> "NH2" Residue "AM ASP 116": "OD1" <-> "OD2" Residue "AM TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AO PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AO PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AO ARG 90": "NH1" <-> "NH2" Residue "AO ARG 112": "NH1" <-> "NH2" Residue "AO ASP 116": "OD1" <-> "OD2" Residue "AO TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AO PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ ARG 90": "NH1" <-> "NH2" Residue "AQ ARG 112": "NH1" <-> "NH2" Residue "AQ ASP 116": "OD1" <-> "OD2" Residue "AQ TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS ARG 90": "NH1" <-> "NH2" Residue "AS ARG 112": "NH1" <-> "NH2" Residue "AS ASP 116": "OD1" <-> "OD2" Residue "AS TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AU PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AU PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AU ARG 90": "NH1" <-> "NH2" Residue "AU ARG 112": "NH1" <-> "NH2" Residue "AU ASP 116": "OD1" <-> "OD2" Residue "AU TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AU PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AW PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AW PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AW ARG 90": "NH1" <-> "NH2" Residue "AW ARG 112": "NH1" <-> "NH2" Residue "AW ASP 116": "OD1" <-> "OD2" Residue "AW TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AW PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AY PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AY PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AY ARG 90": "NH1" <-> "NH2" Residue "AY ARG 112": "NH1" <-> "NH2" Residue "AY ASP 116": "OD1" <-> "OD2" Residue "AY TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AY PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A0 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A0 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A0 ARG 90": "NH1" <-> "NH2" Residue "A0 ARG 112": "NH1" <-> "NH2" Residue "A0 ASP 116": "OD1" <-> "OD2" Residue "A0 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A0 PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A2 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A2 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A2 ARG 90": "NH1" <-> "NH2" Residue "A2 ARG 112": "NH1" <-> "NH2" Residue "A2 ASP 116": "OD1" <-> "OD2" Residue "A2 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A2 PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A4 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A4 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A4 ARG 90": "NH1" <-> "NH2" Residue "A4 ARG 112": "NH1" <-> "NH2" Residue "A4 ASP 116": "OD1" <-> "OD2" Residue "A4 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A4 PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 ARG 90": "NH1" <-> "NH2" Residue "A6 ARG 112": "NH1" <-> "NH2" Residue "A6 ASP 116": "OD1" <-> "OD2" Residue "A6 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A8 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A8 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A8 ARG 90": "NH1" <-> "NH2" Residue "A8 ARG 112": "NH1" <-> "NH2" Residue "A8 ASP 116": "OD1" <-> "OD2" Residue "A8 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A8 PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 62916 Number of models: 1 Model: "" Number of chains: 98 Chain: "B" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "D" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "E" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "F" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "G" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "H" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "I" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "J" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "K" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "L" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "M" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "N" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "O" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "P" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "Q" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "S" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "T" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "U" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "V" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "W" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "X" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "Y" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "Z" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "0" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "1" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "2" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "3" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "4" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "5" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "6" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "7" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "8" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "9" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "a" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "b" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "c" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "d" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "e" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "f" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "g" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "h" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "i" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "j" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "k" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "l" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "m" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "n" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "R" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "o" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "p" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "q" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "r" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "s" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "t" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "u" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "v" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "w" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "x" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "y" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "z" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "AA" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "AB" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "AC" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "AD" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "AE" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "AF" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "AG" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "AH" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "AI" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "AJ" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "AK" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "AL" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "AM" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "AN" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "AO" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "AP" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "AQ" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "AR" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "AS" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "AT" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "AU" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "AV" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "AW" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "AX" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "AY" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "AZ" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "A0" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "A1" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "A2" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "A3" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "A4" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "A5" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "A6" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "A7" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "A8" Number of atoms: 1219 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Conformer: "B" Number of residues, atoms: 155, 1210 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} bond proxies already assigned to first conformer: 1224 Chain: "A9" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Residues with excluded nonbonded symmetry interactions: 49 residue: pdb=" N AGLN B 39 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 39 " occ=0.50 residue: pdb=" N AGLN D 39 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN D 39 " occ=0.50 residue: pdb=" N AGLN F 39 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN F 39 " occ=0.50 residue: pdb=" N AGLN H 39 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN H 39 " occ=0.50 residue: pdb=" N AGLN J 39 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN J 39 " occ=0.50 residue: pdb=" N AGLN L 39 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN L 39 " occ=0.50 residue: pdb=" N AGLN N 39 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN N 39 " occ=0.50 residue: pdb=" N AGLN P 39 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN P 39 " occ=0.50 residue: pdb=" N AGLN S 39 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN S 39 " occ=0.50 residue: pdb=" N AGLN U 39 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN U 39 " occ=0.50 residue: pdb=" N AGLN W 39 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN W 39 " occ=0.50 residue: pdb=" N AGLN Y 39 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN Y 39 " occ=0.50 ... (remaining 37 not shown) Time building chain proxies: 42.96, per 1000 atoms: 0.68 Number of scatterers: 62916 At special positions: 0 Unit cell: (193.787, 193.787, 113.839, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 147 15.00 O 12740 8.00 N 11074 7.00 C 38906 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: 20.16 Conformation dependent library (CDL) restraints added in 14.5 seconds 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14700 Finding SS restraints... Secondary structure from input PDB file: 441 helices and 0 sheets defined 55.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.16 Creating SS restraints... Processing helix chain 'A' and resid 6 through 8 No H-bonds generated for 'chain 'A' and resid 6 through 8' Processing helix chain 'A' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEU A 13 " --> pdb=" O GLN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE A 24 " --> pdb=" O PRO A 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'B' and resid 6 through 8 No H-bonds generated for 'chain 'B' and resid 6 through 8' Processing helix chain 'B' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEU B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE B 24 " --> pdb=" O PRO B 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 removed outlier: 3.658A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 100 Processing helix chain 'B' and resid 103 through 128 removed outlier: 3.578A pdb=" N ASP B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 134 removed outlier: 3.539A pdb=" N LEU B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'D' and resid 6 through 8 No H-bonds generated for 'chain 'D' and resid 6 through 8' Processing helix chain 'D' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEU D 13 " --> pdb=" O GLN D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE D 24 " --> pdb=" O PRO D 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 85 removed outlier: 3.658A pdb=" N LEU D 83 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D 84 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 103 through 128 removed outlier: 3.578A pdb=" N ASP D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG D 134 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'F' and resid 6 through 8 No H-bonds generated for 'chain 'F' and resid 6 through 8' Processing helix chain 'F' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEU F 13 " --> pdb=" O GLN F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE F 24 " --> pdb=" O PRO F 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS F 27 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU F 83 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU F 84 " --> pdb=" O VAL F 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY F 85 " --> pdb=" O THR F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 100 Processing helix chain 'F' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP F 109 " --> pdb=" O ALA F 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP F 115 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU F 132 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG F 134 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'H' and resid 6 through 8 No H-bonds generated for 'chain 'H' and resid 6 through 8' Processing helix chain 'H' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEU H 13 " --> pdb=" O GLN H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 31 removed outlier: 3.741A pdb=" N ILE H 24 " --> pdb=" O PRO H 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS H 27 " --> pdb=" O LEU H 23 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN H 29 " --> pdb=" O ASN H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 46 removed outlier: 3.748A pdb=" N VAL H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 85 removed outlier: 3.658A pdb=" N LEU H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU H 84 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY H 85 " --> pdb=" O THR H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 100 Processing helix chain 'H' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG H 112 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP H 115 " --> pdb=" O THR H 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA H 120 " --> pdb=" O ASP H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU H 132 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG H 134 " --> pdb=" O VAL H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 145 Processing helix chain 'J' and resid 6 through 8 No H-bonds generated for 'chain 'J' and resid 6 through 8' Processing helix chain 'J' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEU J 13 " --> pdb=" O GLN J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE J 24 " --> pdb=" O PRO J 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS J 27 " --> pdb=" O LEU J 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN J 29 " --> pdb=" O ASN J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 46 removed outlier: 3.748A pdb=" N VAL J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU J 83 " --> pdb=" O LEU J 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU J 84 " --> pdb=" O VAL J 80 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY J 85 " --> pdb=" O THR J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 100 Processing helix chain 'J' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP J 109 " --> pdb=" O ALA J 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA J 110 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG J 112 " --> pdb=" O LEU J 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP J 115 " --> pdb=" O THR J 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA J 120 " --> pdb=" O ASP J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU J 132 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG J 134 " --> pdb=" O VAL J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 145 Processing helix chain 'L' and resid 6 through 8 No H-bonds generated for 'chain 'L' and resid 6 through 8' Processing helix chain 'L' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEU L 13 " --> pdb=" O GLN L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 31 removed outlier: 3.741A pdb=" N ILE L 24 " --> pdb=" O PRO L 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS L 27 " --> pdb=" O LEU L 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN L 29 " --> pdb=" O ASN L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU L 84 " --> pdb=" O VAL L 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY L 85 " --> pdb=" O THR L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 100 Processing helix chain 'L' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP L 109 " --> pdb=" O ALA L 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA L 110 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG L 112 " --> pdb=" O LEU L 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP L 115 " --> pdb=" O THR L 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA L 120 " --> pdb=" O ASP L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU L 132 " --> pdb=" O LEU L 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG L 134 " --> pdb=" O VAL L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 145 Processing helix chain 'N' and resid 6 through 8 No H-bonds generated for 'chain 'N' and resid 6 through 8' Processing helix chain 'N' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEU N 13 " --> pdb=" O GLN N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE N 24 " --> pdb=" O PRO N 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS N 27 " --> pdb=" O LEU N 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN N 29 " --> pdb=" O ASN N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 46 removed outlier: 3.748A pdb=" N VAL N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU N 84 " --> pdb=" O VAL N 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY N 85 " --> pdb=" O THR N 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 100 Processing helix chain 'N' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP N 109 " --> pdb=" O ALA N 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA N 110 " --> pdb=" O GLU N 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG N 112 " --> pdb=" O LEU N 108 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP N 115 " --> pdb=" O THR N 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA N 120 " --> pdb=" O ASP N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU N 132 " --> pdb=" O LEU N 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG N 134 " --> pdb=" O VAL N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 145 Processing helix chain 'P' and resid 6 through 8 No H-bonds generated for 'chain 'P' and resid 6 through 8' Processing helix chain 'P' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEU P 13 " --> pdb=" O GLN P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 31 removed outlier: 3.743A pdb=" N ILE P 24 " --> pdb=" O PRO P 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS P 27 " --> pdb=" O LEU P 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN P 29 " --> pdb=" O ASN P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL P 44 " --> pdb=" O ALA P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU P 84 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY P 85 " --> pdb=" O THR P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 100 Processing helix chain 'P' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP P 109 " --> pdb=" O ALA P 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA P 110 " --> pdb=" O GLU P 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG P 112 " --> pdb=" O LEU P 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP P 115 " --> pdb=" O THR P 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA P 120 " --> pdb=" O ASP P 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU P 132 " --> pdb=" O LEU P 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG P 134 " --> pdb=" O VAL P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 145 Processing helix chain 'S' and resid 6 through 8 No H-bonds generated for 'chain 'S' and resid 6 through 8' Processing helix chain 'S' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEU S 13 " --> pdb=" O GLN S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE S 24 " --> pdb=" O PRO S 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS S 27 " --> pdb=" O LEU S 23 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN S 29 " --> pdb=" O ASN S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU S 83 " --> pdb=" O LEU S 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU S 84 " --> pdb=" O VAL S 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY S 85 " --> pdb=" O THR S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 100 Processing helix chain 'S' and resid 103 through 128 removed outlier: 3.578A pdb=" N ASP S 109 " --> pdb=" O ALA S 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA S 110 " --> pdb=" O GLU S 106 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG S 112 " --> pdb=" O LEU S 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP S 115 " --> pdb=" O THR S 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA S 120 " --> pdb=" O ASP S 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU S 132 " --> pdb=" O LEU S 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG S 134 " --> pdb=" O VAL S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 140 through 145 Processing helix chain 'U' and resid 6 through 8 No H-bonds generated for 'chain 'U' and resid 6 through 8' Processing helix chain 'U' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEU U 13 " --> pdb=" O GLN U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE U 24 " --> pdb=" O PRO U 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS U 27 " --> pdb=" O LEU U 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN U 29 " --> pdb=" O ASN U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL U 44 " --> pdb=" O ALA U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU U 83 " --> pdb=" O LEU U 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU U 84 " --> pdb=" O VAL U 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY U 85 " --> pdb=" O THR U 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 100 Processing helix chain 'U' and resid 103 through 128 removed outlier: 3.578A pdb=" N ASP U 109 " --> pdb=" O ALA U 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA U 110 " --> pdb=" O GLU U 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG U 112 " --> pdb=" O LEU U 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP U 115 " --> pdb=" O THR U 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA U 120 " --> pdb=" O ASP U 116 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU U 132 " --> pdb=" O LEU U 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG U 134 " --> pdb=" O VAL U 130 " (cutoff:3.500A) Processing helix chain 'U' and resid 140 through 145 Processing helix chain 'W' and resid 6 through 8 No H-bonds generated for 'chain 'W' and resid 6 through 8' Processing helix chain 'W' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEU W 13 " --> pdb=" O GLN W 9 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE W 24 " --> pdb=" O PRO W 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS W 27 " --> pdb=" O LEU W 23 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN W 29 " --> pdb=" O ASN W 25 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 46 removed outlier: 3.748A pdb=" N VAL W 44 " --> pdb=" O ALA W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU W 83 " --> pdb=" O LEU W 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU W 84 " --> pdb=" O VAL W 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY W 85 " --> pdb=" O THR W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 96 through 100 Processing helix chain 'W' and resid 103 through 128 removed outlier: 3.578A pdb=" N ASP W 109 " --> pdb=" O ALA W 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA W 110 " --> pdb=" O GLU W 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG W 112 " --> pdb=" O LEU W 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP W 115 " --> pdb=" O THR W 111 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA W 120 " --> pdb=" O ASP W 116 " (cutoff:3.500A) Processing helix chain 'W' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU W 132 " --> pdb=" O LEU W 128 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG W 134 " --> pdb=" O VAL W 130 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 145 Processing helix chain 'Y' and resid 6 through 8 No H-bonds generated for 'chain 'Y' and resid 6 through 8' Processing helix chain 'Y' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEU Y 13 " --> pdb=" O GLN Y 9 " (cutoff:3.500A) Processing helix chain 'Y' and resid 19 through 31 removed outlier: 3.741A pdb=" N ILE Y 24 " --> pdb=" O PRO Y 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS Y 27 " --> pdb=" O LEU Y 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN Y 29 " --> pdb=" O ASN Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 46 removed outlier: 3.750A pdb=" N VAL Y 44 " --> pdb=" O ALA Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU Y 83 " --> pdb=" O LEU Y 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU Y 84 " --> pdb=" O VAL Y 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY Y 85 " --> pdb=" O THR Y 81 " (cutoff:3.500A) Processing helix chain 'Y' and resid 96 through 100 Processing helix chain 'Y' and resid 103 through 128 removed outlier: 3.578A pdb=" N ASP Y 109 " --> pdb=" O ALA Y 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA Y 110 " --> pdb=" O GLU Y 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG Y 112 " --> pdb=" O LEU Y 108 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP Y 115 " --> pdb=" O THR Y 111 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA Y 120 " --> pdb=" O ASP Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 128 through 134 removed outlier: 3.541A pdb=" N LEU Y 132 " --> pdb=" O LEU Y 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG Y 134 " --> pdb=" O VAL Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 140 through 145 Processing helix chain '0' and resid 6 through 8 No H-bonds generated for 'chain '0' and resid 6 through 8' Processing helix chain '0' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEU 0 13 " --> pdb=" O GLN 0 9 " (cutoff:3.500A) Processing helix chain '0' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE 0 24 " --> pdb=" O PRO 0 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS 0 27 " --> pdb=" O LEU 0 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN 0 29 " --> pdb=" O ASN 0 25 " (cutoff:3.500A) Processing helix chain '0' and resid 37 through 46 removed outlier: 3.748A pdb=" N VAL 0 44 " --> pdb=" O ALA 0 40 " (cutoff:3.500A) Processing helix chain '0' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU 0 83 " --> pdb=" O LEU 0 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU 0 84 " --> pdb=" O VAL 0 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY 0 85 " --> pdb=" O THR 0 81 " (cutoff:3.500A) Processing helix chain '0' and resid 96 through 100 Processing helix chain '0' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP 0 109 " --> pdb=" O ALA 0 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA 0 110 " --> pdb=" O GLU 0 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG 0 112 " --> pdb=" O LEU 0 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP 0 115 " --> pdb=" O THR 0 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA 0 120 " --> pdb=" O ASP 0 116 " (cutoff:3.500A) Processing helix chain '0' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU 0 132 " --> pdb=" O LEU 0 128 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG 0 134 " --> pdb=" O VAL 0 130 " (cutoff:3.500A) Processing helix chain '0' and resid 140 through 145 Processing helix chain '2' and resid 6 through 8 No H-bonds generated for 'chain '2' and resid 6 through 8' Processing helix chain '2' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEU 2 13 " --> pdb=" O GLN 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE 2 24 " --> pdb=" O PRO 2 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS 2 27 " --> pdb=" O LEU 2 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN 2 29 " --> pdb=" O ASN 2 25 " (cutoff:3.500A) Processing helix chain '2' and resid 37 through 46 removed outlier: 3.748A pdb=" N VAL 2 44 " --> pdb=" O ALA 2 40 " (cutoff:3.500A) Processing helix chain '2' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU 2 83 " --> pdb=" O LEU 2 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU 2 84 " --> pdb=" O VAL 2 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY 2 85 " --> pdb=" O THR 2 81 " (cutoff:3.500A) Processing helix chain '2' and resid 96 through 100 Processing helix chain '2' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP 2 109 " --> pdb=" O ALA 2 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA 2 110 " --> pdb=" O GLU 2 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG 2 112 " --> pdb=" O LEU 2 108 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP 2 115 " --> pdb=" O THR 2 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA 2 120 " --> pdb=" O ASP 2 116 " (cutoff:3.500A) Processing helix chain '2' and resid 128 through 134 removed outlier: 3.539A pdb=" N LEU 2 132 " --> pdb=" O LEU 2 128 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG 2 134 " --> pdb=" O VAL 2 130 " (cutoff:3.500A) Processing helix chain '2' and resid 140 through 145 Processing helix chain '4' and resid 6 through 8 No H-bonds generated for 'chain '4' and resid 6 through 8' Processing helix chain '4' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEU 4 13 " --> pdb=" O GLN 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE 4 24 " --> pdb=" O PRO 4 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS 4 27 " --> pdb=" O LEU 4 23 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN 4 29 " --> pdb=" O ASN 4 25 " (cutoff:3.500A) Processing helix chain '4' and resid 37 through 46 removed outlier: 3.750A pdb=" N VAL 4 44 " --> pdb=" O ALA 4 40 " (cutoff:3.500A) Processing helix chain '4' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU 4 83 " --> pdb=" O LEU 4 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU 4 84 " --> pdb=" O VAL 4 80 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY 4 85 " --> pdb=" O THR 4 81 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 100 Processing helix chain '4' and resid 103 through 128 removed outlier: 3.578A pdb=" N ASP 4 109 " --> pdb=" O ALA 4 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA 4 110 " --> pdb=" O GLU 4 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG 4 112 " --> pdb=" O LEU 4 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP 4 115 " --> pdb=" O THR 4 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA 4 120 " --> pdb=" O ASP 4 116 " (cutoff:3.500A) Processing helix chain '4' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU 4 132 " --> pdb=" O LEU 4 128 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG 4 134 " --> pdb=" O VAL 4 130 " (cutoff:3.500A) Processing helix chain '4' and resid 140 through 145 Processing helix chain '6' and resid 6 through 8 No H-bonds generated for 'chain '6' and resid 6 through 8' Processing helix chain '6' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEU 6 13 " --> pdb=" O GLN 6 9 " (cutoff:3.500A) Processing helix chain '6' and resid 19 through 31 removed outlier: 3.741A pdb=" N ILE 6 24 " --> pdb=" O PRO 6 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS 6 27 " --> pdb=" O LEU 6 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN 6 29 " --> pdb=" O ASN 6 25 " (cutoff:3.500A) Processing helix chain '6' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL 6 44 " --> pdb=" O ALA 6 40 " (cutoff:3.500A) Processing helix chain '6' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU 6 83 " --> pdb=" O LEU 6 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU 6 84 " --> pdb=" O VAL 6 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY 6 85 " --> pdb=" O THR 6 81 " (cutoff:3.500A) Processing helix chain '6' and resid 96 through 100 Processing helix chain '6' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP 6 109 " --> pdb=" O ALA 6 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA 6 110 " --> pdb=" O GLU 6 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP 6 115 " --> pdb=" O THR 6 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA 6 120 " --> pdb=" O ASP 6 116 " (cutoff:3.500A) Processing helix chain '6' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU 6 132 " --> pdb=" O LEU 6 128 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG 6 134 " --> pdb=" O VAL 6 130 " (cutoff:3.500A) Processing helix chain '6' and resid 140 through 145 Processing helix chain '8' and resid 6 through 8 No H-bonds generated for 'chain '8' and resid 6 through 8' Processing helix chain '8' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEU 8 13 " --> pdb=" O GLN 8 9 " (cutoff:3.500A) Processing helix chain '8' and resid 19 through 31 removed outlier: 3.741A pdb=" N ILE 8 24 " --> pdb=" O PRO 8 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS 8 27 " --> pdb=" O LEU 8 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN 8 29 " --> pdb=" O ASN 8 25 " (cutoff:3.500A) Processing helix chain '8' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL 8 44 " --> pdb=" O ALA 8 40 " (cutoff:3.500A) Processing helix chain '8' and resid 76 through 85 removed outlier: 3.658A pdb=" N LEU 8 83 " --> pdb=" O LEU 8 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU 8 84 " --> pdb=" O VAL 8 80 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY 8 85 " --> pdb=" O THR 8 81 " (cutoff:3.500A) Processing helix chain '8' and resid 96 through 100 Processing helix chain '8' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP 8 109 " --> pdb=" O ALA 8 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA 8 110 " --> pdb=" O GLU 8 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG 8 112 " --> pdb=" O LEU 8 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP 8 115 " --> pdb=" O THR 8 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA 8 120 " --> pdb=" O ASP 8 116 " (cutoff:3.500A) Processing helix chain '8' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU 8 132 " --> pdb=" O LEU 8 128 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG 8 134 " --> pdb=" O VAL 8 130 " (cutoff:3.500A) Processing helix chain '8' and resid 140 through 145 Processing helix chain 'a' and resid 6 through 8 No H-bonds generated for 'chain 'a' and resid 6 through 8' Processing helix chain 'a' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEU a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE a 24 " --> pdb=" O PRO a 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS a 27 " --> pdb=" O LEU a 23 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN a 29 " --> pdb=" O ASN a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL a 44 " --> pdb=" O ALA a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU a 83 " --> pdb=" O LEU a 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU a 84 " --> pdb=" O VAL a 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY a 85 " --> pdb=" O THR a 81 " (cutoff:3.500A) Processing helix chain 'a' and resid 96 through 100 Processing helix chain 'a' and resid 103 through 128 removed outlier: 3.578A pdb=" N ASP a 109 " --> pdb=" O ALA a 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA a 110 " --> pdb=" O GLU a 106 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG a 112 " --> pdb=" O LEU a 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP a 115 " --> pdb=" O THR a 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA a 120 " --> pdb=" O ASP a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU a 132 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG a 134 " --> pdb=" O VAL a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 140 through 145 Processing helix chain 'c' and resid 6 through 8 No H-bonds generated for 'chain 'c' and resid 6 through 8' Processing helix chain 'c' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEU c 13 " --> pdb=" O GLN c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 19 through 31 removed outlier: 3.741A pdb=" N ILE c 24 " --> pdb=" O PRO c 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS c 27 " --> pdb=" O LEU c 23 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN c 29 " --> pdb=" O ASN c 25 " (cutoff:3.500A) Processing helix chain 'c' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL c 44 " --> pdb=" O ALA c 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 76 through 85 removed outlier: 3.658A pdb=" N LEU c 83 " --> pdb=" O LEU c 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU c 84 " --> pdb=" O VAL c 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY c 85 " --> pdb=" O THR c 81 " (cutoff:3.500A) Processing helix chain 'c' and resid 96 through 100 Processing helix chain 'c' and resid 103 through 128 removed outlier: 3.578A pdb=" N ASP c 109 " --> pdb=" O ALA c 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA c 110 " --> pdb=" O GLU c 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG c 112 " --> pdb=" O LEU c 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP c 115 " --> pdb=" O THR c 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA c 120 " --> pdb=" O ASP c 116 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU c 132 " --> pdb=" O LEU c 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG c 134 " --> pdb=" O VAL c 130 " (cutoff:3.500A) Processing helix chain 'c' and resid 140 through 145 Processing helix chain 'e' and resid 6 through 8 No H-bonds generated for 'chain 'e' and resid 6 through 8' Processing helix chain 'e' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEU e 13 " --> pdb=" O GLN e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE e 24 " --> pdb=" O PRO e 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS e 27 " --> pdb=" O LEU e 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN e 29 " --> pdb=" O ASN e 25 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 46 removed outlier: 3.748A pdb=" N VAL e 44 " --> pdb=" O ALA e 40 " (cutoff:3.500A) Processing helix chain 'e' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU e 83 " --> pdb=" O LEU e 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU e 84 " --> pdb=" O VAL e 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY e 85 " --> pdb=" O THR e 81 " (cutoff:3.500A) Processing helix chain 'e' and resid 96 through 100 Processing helix chain 'e' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP e 109 " --> pdb=" O ALA e 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA e 110 " --> pdb=" O GLU e 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG e 112 " --> pdb=" O LEU e 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP e 115 " --> pdb=" O THR e 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA e 120 " --> pdb=" O ASP e 116 " (cutoff:3.500A) Processing helix chain 'e' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU e 132 " --> pdb=" O LEU e 128 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG e 134 " --> pdb=" O VAL e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 140 through 145 Processing helix chain 'g' and resid 6 through 8 No H-bonds generated for 'chain 'g' and resid 6 through 8' Processing helix chain 'g' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEU g 13 " --> pdb=" O GLN g 9 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE g 24 " --> pdb=" O PRO g 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS g 27 " --> pdb=" O LEU g 23 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN g 29 " --> pdb=" O ASN g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL g 44 " --> pdb=" O ALA g 40 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU g 83 " --> pdb=" O LEU g 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU g 84 " --> pdb=" O VAL g 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY g 85 " --> pdb=" O THR g 81 " (cutoff:3.500A) Processing helix chain 'g' and resid 96 through 100 Processing helix chain 'g' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP g 109 " --> pdb=" O ALA g 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA g 110 " --> pdb=" O GLU g 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG g 112 " --> pdb=" O LEU g 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP g 115 " --> pdb=" O THR g 111 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA g 120 " --> pdb=" O ASP g 116 " (cutoff:3.500A) Processing helix chain 'g' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU g 132 " --> pdb=" O LEU g 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG g 134 " --> pdb=" O VAL g 130 " (cutoff:3.500A) Processing helix chain 'g' and resid 140 through 145 Processing helix chain 'i' and resid 6 through 8 No H-bonds generated for 'chain 'i' and resid 6 through 8' Processing helix chain 'i' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEU i 13 " --> pdb=" O GLN i 9 " (cutoff:3.500A) Processing helix chain 'i' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE i 24 " --> pdb=" O PRO i 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS i 27 " --> pdb=" O LEU i 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN i 29 " --> pdb=" O ASN i 25 " (cutoff:3.500A) Processing helix chain 'i' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL i 44 " --> pdb=" O ALA i 40 " (cutoff:3.500A) Processing helix chain 'i' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU i 83 " --> pdb=" O LEU i 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU i 84 " --> pdb=" O VAL i 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY i 85 " --> pdb=" O THR i 81 " (cutoff:3.500A) Processing helix chain 'i' and resid 96 through 100 Processing helix chain 'i' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP i 109 " --> pdb=" O ALA i 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA i 110 " --> pdb=" O GLU i 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG i 112 " --> pdb=" O LEU i 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP i 115 " --> pdb=" O THR i 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA i 120 " --> pdb=" O ASP i 116 " (cutoff:3.500A) Processing helix chain 'i' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU i 132 " --> pdb=" O LEU i 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG i 134 " --> pdb=" O VAL i 130 " (cutoff:3.500A) Processing helix chain 'i' and resid 140 through 145 Processing helix chain 'k' and resid 6 through 8 No H-bonds generated for 'chain 'k' and resid 6 through 8' Processing helix chain 'k' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEU k 13 " --> pdb=" O GLN k 9 " (cutoff:3.500A) Processing helix chain 'k' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE k 24 " --> pdb=" O PRO k 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS k 27 " --> pdb=" O LEU k 23 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN k 29 " --> pdb=" O ASN k 25 " (cutoff:3.500A) Processing helix chain 'k' and resid 37 through 46 removed outlier: 3.748A pdb=" N VAL k 44 " --> pdb=" O ALA k 40 " (cutoff:3.500A) Processing helix chain 'k' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU k 84 " --> pdb=" O VAL k 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY k 85 " --> pdb=" O THR k 81 " (cutoff:3.500A) Processing helix chain 'k' and resid 96 through 100 Processing helix chain 'k' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP k 109 " --> pdb=" O ALA k 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA k 110 " --> pdb=" O GLU k 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG k 112 " --> pdb=" O LEU k 108 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP k 115 " --> pdb=" O THR k 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA k 120 " --> pdb=" O ASP k 116 " (cutoff:3.500A) Processing helix chain 'k' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU k 132 " --> pdb=" O LEU k 128 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG k 134 " --> pdb=" O VAL k 130 " (cutoff:3.500A) Processing helix chain 'k' and resid 140 through 145 Processing helix chain 'm' and resid 6 through 8 No H-bonds generated for 'chain 'm' and resid 6 through 8' Processing helix chain 'm' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEU m 13 " --> pdb=" O GLN m 9 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE m 24 " --> pdb=" O PRO m 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS m 27 " --> pdb=" O LEU m 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN m 29 " --> pdb=" O ASN m 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL m 44 " --> pdb=" O ALA m 40 " (cutoff:3.500A) Processing helix chain 'm' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU m 83 " --> pdb=" O LEU m 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU m 84 " --> pdb=" O VAL m 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY m 85 " --> pdb=" O THR m 81 " (cutoff:3.500A) Processing helix chain 'm' and resid 96 through 100 Processing helix chain 'm' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP m 109 " --> pdb=" O ALA m 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA m 110 " --> pdb=" O GLU m 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG m 112 " --> pdb=" O LEU m 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP m 115 " --> pdb=" O THR m 111 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA m 120 " --> pdb=" O ASP m 116 " (cutoff:3.500A) Processing helix chain 'm' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU m 132 " --> pdb=" O LEU m 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG m 134 " --> pdb=" O VAL m 130 " (cutoff:3.500A) Processing helix chain 'm' and resid 140 through 145 Processing helix chain 'o' and resid 6 through 8 No H-bonds generated for 'chain 'o' and resid 6 through 8' Processing helix chain 'o' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEU o 13 " --> pdb=" O GLN o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 19 through 31 removed outlier: 3.741A pdb=" N ILE o 24 " --> pdb=" O PRO o 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS o 27 " --> pdb=" O LEU o 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN o 29 " --> pdb=" O ASN o 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL o 44 " --> pdb=" O ALA o 40 " (cutoff:3.500A) Processing helix chain 'o' and resid 76 through 85 removed outlier: 3.658A pdb=" N LEU o 83 " --> pdb=" O LEU o 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU o 84 " --> pdb=" O VAL o 80 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY o 85 " --> pdb=" O THR o 81 " (cutoff:3.500A) Processing helix chain 'o' and resid 96 through 100 Processing helix chain 'o' and resid 103 through 128 removed outlier: 3.578A pdb=" N ASP o 109 " --> pdb=" O ALA o 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA o 110 " --> pdb=" O GLU o 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG o 112 " --> pdb=" O LEU o 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP o 115 " --> pdb=" O THR o 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA o 120 " --> pdb=" O ASP o 116 " (cutoff:3.500A) Processing helix chain 'o' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU o 132 " --> pdb=" O LEU o 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG o 134 " --> pdb=" O VAL o 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 140 through 145 Processing helix chain 'q' and resid 6 through 8 No H-bonds generated for 'chain 'q' and resid 6 through 8' Processing helix chain 'q' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEU q 13 " --> pdb=" O GLN q 9 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 31 removed outlier: 3.741A pdb=" N ILE q 24 " --> pdb=" O PRO q 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS q 27 " --> pdb=" O LEU q 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN q 29 " --> pdb=" O ASN q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 37 through 46 removed outlier: 3.748A pdb=" N VAL q 44 " --> pdb=" O ALA q 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 85 removed outlier: 3.658A pdb=" N LEU q 83 " --> pdb=" O LEU q 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU q 84 " --> pdb=" O VAL q 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY q 85 " --> pdb=" O THR q 81 " (cutoff:3.500A) Processing helix chain 'q' and resid 96 through 100 Processing helix chain 'q' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP q 109 " --> pdb=" O ALA q 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA q 110 " --> pdb=" O GLU q 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG q 112 " --> pdb=" O LEU q 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP q 115 " --> pdb=" O THR q 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA q 120 " --> pdb=" O ASP q 116 " (cutoff:3.500A) Processing helix chain 'q' and resid 128 through 134 removed outlier: 3.541A pdb=" N LEU q 132 " --> pdb=" O LEU q 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG q 134 " --> pdb=" O VAL q 130 " (cutoff:3.500A) Processing helix chain 'q' and resid 140 through 145 Processing helix chain 's' and resid 6 through 8 No H-bonds generated for 'chain 's' and resid 6 through 8' Processing helix chain 's' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEU s 13 " --> pdb=" O GLN s 9 " (cutoff:3.500A) Processing helix chain 's' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE s 24 " --> pdb=" O PRO s 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS s 27 " --> pdb=" O LEU s 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN s 29 " --> pdb=" O ASN s 25 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL s 44 " --> pdb=" O ALA s 40 " (cutoff:3.500A) Processing helix chain 's' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU s 83 " --> pdb=" O LEU s 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU s 84 " --> pdb=" O VAL s 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY s 85 " --> pdb=" O THR s 81 " (cutoff:3.500A) Processing helix chain 's' and resid 96 through 100 Processing helix chain 's' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP s 109 " --> pdb=" O ALA s 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA s 110 " --> pdb=" O GLU s 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG s 112 " --> pdb=" O LEU s 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP s 115 " --> pdb=" O THR s 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA s 120 " --> pdb=" O ASP s 116 " (cutoff:3.500A) Processing helix chain 's' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU s 132 " --> pdb=" O LEU s 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG s 134 " --> pdb=" O VAL s 130 " (cutoff:3.500A) Processing helix chain 's' and resid 140 through 145 Processing helix chain 'u' and resid 6 through 8 No H-bonds generated for 'chain 'u' and resid 6 through 8' Processing helix chain 'u' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEU u 13 " --> pdb=" O GLN u 9 " (cutoff:3.500A) Processing helix chain 'u' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE u 24 " --> pdb=" O PRO u 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS u 27 " --> pdb=" O LEU u 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN u 29 " --> pdb=" O ASN u 25 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL u 44 " --> pdb=" O ALA u 40 " (cutoff:3.500A) Processing helix chain 'u' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU u 83 " --> pdb=" O LEU u 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU u 84 " --> pdb=" O VAL u 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY u 85 " --> pdb=" O THR u 81 " (cutoff:3.500A) Processing helix chain 'u' and resid 96 through 100 Processing helix chain 'u' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP u 109 " --> pdb=" O ALA u 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA u 110 " --> pdb=" O GLU u 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG u 112 " --> pdb=" O LEU u 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP u 115 " --> pdb=" O THR u 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA u 120 " --> pdb=" O ASP u 116 " (cutoff:3.500A) Processing helix chain 'u' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU u 132 " --> pdb=" O LEU u 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG u 134 " --> pdb=" O VAL u 130 " (cutoff:3.500A) Processing helix chain 'u' and resid 140 through 145 Processing helix chain 'w' and resid 6 through 8 No H-bonds generated for 'chain 'w' and resid 6 through 8' Processing helix chain 'w' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEU w 13 " --> pdb=" O GLN w 9 " (cutoff:3.500A) Processing helix chain 'w' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILE w 24 " --> pdb=" O PRO w 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS w 27 " --> pdb=" O LEU w 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN w 29 " --> pdb=" O ASN w 25 " (cutoff:3.500A) Processing helix chain 'w' and resid 37 through 46 removed outlier: 3.749A pdb=" N VAL w 44 " --> pdb=" O ALA w 40 " (cutoff:3.500A) Processing helix chain 'w' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEU w 83 " --> pdb=" O LEU w 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU w 84 " --> pdb=" O VAL w 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY w 85 " --> pdb=" O THR w 81 " (cutoff:3.500A) Processing helix chain 'w' and resid 96 through 100 Processing helix chain 'w' and resid 103 through 128 removed outlier: 3.578A pdb=" N ASP w 109 " --> pdb=" O ALA w 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA w 110 " --> pdb=" O GLU w 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG w 112 " --> pdb=" O LEU w 108 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP w 115 " --> pdb=" O THR w 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA w 120 " --> pdb=" O ASP w 116 " (cutoff:3.500A) Processing helix chain 'w' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU w 132 " --> pdb=" O LEU w 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG w 134 " --> pdb=" O VAL w 130 " (cutoff:3.500A) Processing helix chain 'w' and resid 140 through 145 Processing helix chain 'y' and resid 6 through 8 No H-bonds generated for 'chain 'y' and resid 6 through 8' Processing helix chain 'y' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEU y 13 " --> pdb=" O GLN y 9 " (cutoff:3.500A) Processing helix chain 'y' and resid 19 through 31 removed outlier: 3.741A pdb=" N ILE y 24 " --> pdb=" O PRO y 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS y 27 " --> pdb=" O LEU y 23 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN y 29 " --> pdb=" O ASN y 25 " (cutoff:3.500A) Processing helix chain 'y' and resid 37 through 46 removed outlier: 3.748A pdb=" N VAL y 44 " --> pdb=" O ALA y 40 " (cutoff:3.500A) Processing helix chain 'y' and resid 76 through 85 removed outlier: 3.658A pdb=" N LEU y 83 " --> pdb=" O LEU y 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU y 84 " --> pdb=" O VAL y 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY y 85 " --> pdb=" O THR y 81 " (cutoff:3.500A) Processing helix chain 'y' and resid 96 through 100 Processing helix chain 'y' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASP y 109 " --> pdb=" O ALA y 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA y 110 " --> pdb=" O GLU y 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG y 112 " --> pdb=" O LEU y 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP y 115 " --> pdb=" O THR y 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA y 120 " --> pdb=" O ASP y 116 " (cutoff:3.500A) Processing helix chain 'y' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEU y 132 " --> pdb=" O LEU y 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG y 134 " --> pdb=" O VAL y 130 " (cutoff:3.500A) Processing helix chain 'y' and resid 140 through 145 Processing helix chain 'AA' and resid 6 through 8 No H-bonds generated for 'chain 'AA' and resid 6 through 8' Processing helix chain 'AA' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEUAA 13 " --> pdb=" O GLNAA 9 " (cutoff:3.500A) Processing helix chain 'AA' and resid 19 through 31 removed outlier: 3.741A pdb=" N ILEAA 24 " --> pdb=" O PROAA 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYSAA 27 " --> pdb=" O LEUAA 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASNAA 29 " --> pdb=" O ASNAA 25 " (cutoff:3.500A) Processing helix chain 'AA' and resid 37 through 46 removed outlier: 3.748A pdb=" N VALAA 44 " --> pdb=" O ALAAA 40 " (cutoff:3.500A) Processing helix chain 'AA' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEUAA 83 " --> pdb=" O LEUAA 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEUAA 84 " --> pdb=" O VALAA 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLYAA 85 " --> pdb=" O THRAA 81 " (cutoff:3.500A) Processing helix chain 'AA' and resid 96 through 100 Processing helix chain 'AA' and resid 103 through 128 removed outlier: 3.578A pdb=" N ASPAA 109 " --> pdb=" O ALAAA 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALAAA 110 " --> pdb=" O GLUAA 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARGAA 112 " --> pdb=" O LEUAA 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASPAA 115 " --> pdb=" O THRAA 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAAA 120 " --> pdb=" O ASPAA 116 " (cutoff:3.500A) Processing helix chain 'AA' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEUAA 132 " --> pdb=" O LEUAA 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARGAA 134 " --> pdb=" O VALAA 130 " (cutoff:3.500A) Processing helix chain 'AA' and resid 140 through 145 Processing helix chain 'AC' and resid 6 through 8 No H-bonds generated for 'chain 'AC' and resid 6 through 8' Processing helix chain 'AC' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEUAC 13 " --> pdb=" O GLNAC 9 " (cutoff:3.500A) Processing helix chain 'AC' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILEAC 24 " --> pdb=" O PROAC 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYSAC 27 " --> pdb=" O LEUAC 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASNAC 29 " --> pdb=" O ASNAC 25 " (cutoff:3.500A) Processing helix chain 'AC' and resid 37 through 46 removed outlier: 3.748A pdb=" N VALAC 44 " --> pdb=" O ALAAC 40 " (cutoff:3.500A) Processing helix chain 'AC' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEUAC 83 " --> pdb=" O LEUAC 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEUAC 84 " --> pdb=" O VALAC 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLYAC 85 " --> pdb=" O THRAC 81 " (cutoff:3.500A) Processing helix chain 'AC' and resid 96 through 100 Processing helix chain 'AC' and resid 103 through 128 removed outlier: 3.578A pdb=" N ASPAC 109 " --> pdb=" O ALAAC 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALAAC 110 " --> pdb=" O GLUAC 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARGAC 112 " --> pdb=" O LEUAC 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASPAC 115 " --> pdb=" O THRAC 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAAC 120 " --> pdb=" O ASPAC 116 " (cutoff:3.500A) Processing helix chain 'AC' and resid 128 through 134 removed outlier: 3.539A pdb=" N LEUAC 132 " --> pdb=" O LEUAC 128 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARGAC 134 " --> pdb=" O VALAC 130 " (cutoff:3.500A) Processing helix chain 'AC' and resid 140 through 145 Processing helix chain 'AE' and resid 6 through 8 No H-bonds generated for 'chain 'AE' and resid 6 through 8' Processing helix chain 'AE' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEUAE 13 " --> pdb=" O GLNAE 9 " (cutoff:3.500A) Processing helix chain 'AE' and resid 19 through 31 removed outlier: 3.741A pdb=" N ILEAE 24 " --> pdb=" O PROAE 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYSAE 27 " --> pdb=" O LEUAE 23 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASNAE 29 " --> pdb=" O ASNAE 25 " (cutoff:3.500A) Processing helix chain 'AE' and resid 37 through 46 removed outlier: 3.749A pdb=" N VALAE 44 " --> pdb=" O ALAAE 40 " (cutoff:3.500A) Processing helix chain 'AE' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEUAE 83 " --> pdb=" O LEUAE 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEUAE 84 " --> pdb=" O VALAE 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLYAE 85 " --> pdb=" O THRAE 81 " (cutoff:3.500A) Processing helix chain 'AE' and resid 96 through 100 Processing helix chain 'AE' and resid 103 through 128 removed outlier: 3.578A pdb=" N ASPAE 109 " --> pdb=" O ALAAE 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALAAE 110 " --> pdb=" O GLUAE 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARGAE 112 " --> pdb=" O LEUAE 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASPAE 115 " --> pdb=" O THRAE 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAAE 120 " --> pdb=" O ASPAE 116 " (cutoff:3.500A) Processing helix chain 'AE' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEUAE 132 " --> pdb=" O LEUAE 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARGAE 134 " --> pdb=" O VALAE 130 " (cutoff:3.500A) Processing helix chain 'AE' and resid 140 through 145 Processing helix chain 'AG' and resid 6 through 8 No H-bonds generated for 'chain 'AG' and resid 6 through 8' Processing helix chain 'AG' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEUAG 13 " --> pdb=" O GLNAG 9 " (cutoff:3.500A) Processing helix chain 'AG' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILEAG 24 " --> pdb=" O PROAG 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYSAG 27 " --> pdb=" O LEUAG 23 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASNAG 29 " --> pdb=" O ASNAG 25 " (cutoff:3.500A) Processing helix chain 'AG' and resid 37 through 46 removed outlier: 3.748A pdb=" N VALAG 44 " --> pdb=" O ALAAG 40 " (cutoff:3.500A) Processing helix chain 'AG' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEUAG 83 " --> pdb=" O LEUAG 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEUAG 84 " --> pdb=" O VALAG 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLYAG 85 " --> pdb=" O THRAG 81 " (cutoff:3.500A) Processing helix chain 'AG' and resid 96 through 100 Processing helix chain 'AG' and resid 103 through 128 removed outlier: 3.578A pdb=" N ASPAG 109 " --> pdb=" O ALAAG 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALAAG 110 " --> pdb=" O GLUAG 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARGAG 112 " --> pdb=" O LEUAG 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASPAG 115 " --> pdb=" O THRAG 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAAG 120 " --> pdb=" O ASPAG 116 " (cutoff:3.500A) Processing helix chain 'AG' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEUAG 132 " --> pdb=" O LEUAG 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARGAG 134 " --> pdb=" O VALAG 130 " (cutoff:3.500A) Processing helix chain 'AG' and resid 140 through 145 Processing helix chain 'AI' and resid 6 through 8 No H-bonds generated for 'chain 'AI' and resid 6 through 8' Processing helix chain 'AI' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEUAI 13 " --> pdb=" O GLNAI 9 " (cutoff:3.500A) Processing helix chain 'AI' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILEAI 24 " --> pdb=" O PROAI 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYSAI 27 " --> pdb=" O LEUAI 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASNAI 29 " --> pdb=" O ASNAI 25 " (cutoff:3.500A) Processing helix chain 'AI' and resid 37 through 46 removed outlier: 3.749A pdb=" N VALAI 44 " --> pdb=" O ALAAI 40 " (cutoff:3.500A) Processing helix chain 'AI' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEUAI 83 " --> pdb=" O LEUAI 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEUAI 84 " --> pdb=" O VALAI 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLYAI 85 " --> pdb=" O THRAI 81 " (cutoff:3.500A) Processing helix chain 'AI' and resid 96 through 100 Processing helix chain 'AI' and resid 103 through 128 removed outlier: 3.578A pdb=" N ASPAI 109 " --> pdb=" O ALAAI 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALAAI 110 " --> pdb=" O GLUAI 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARGAI 112 " --> pdb=" O LEUAI 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASPAI 115 " --> pdb=" O THRAI 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAAI 120 " --> pdb=" O ASPAI 116 " (cutoff:3.500A) Processing helix chain 'AI' and resid 128 through 134 removed outlier: 3.541A pdb=" N LEUAI 132 " --> pdb=" O LEUAI 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARGAI 134 " --> pdb=" O VALAI 130 " (cutoff:3.500A) Processing helix chain 'AI' and resid 140 through 145 Processing helix chain 'AK' and resid 6 through 8 No H-bonds generated for 'chain 'AK' and resid 6 through 8' Processing helix chain 'AK' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEUAK 13 " --> pdb=" O GLNAK 9 " (cutoff:3.500A) Processing helix chain 'AK' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILEAK 24 " --> pdb=" O PROAK 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYSAK 27 " --> pdb=" O LEUAK 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASNAK 29 " --> pdb=" O ASNAK 25 " (cutoff:3.500A) Processing helix chain 'AK' and resid 37 through 46 removed outlier: 3.749A pdb=" N VALAK 44 " --> pdb=" O ALAAK 40 " (cutoff:3.500A) Processing helix chain 'AK' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEUAK 83 " --> pdb=" O LEUAK 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEUAK 84 " --> pdb=" O VALAK 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLYAK 85 " --> pdb=" O THRAK 81 " (cutoff:3.500A) Processing helix chain 'AK' and resid 96 through 100 Processing helix chain 'AK' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASPAK 109 " --> pdb=" O ALAAK 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALAAK 110 " --> pdb=" O GLUAK 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARGAK 112 " --> pdb=" O LEUAK 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASPAK 115 " --> pdb=" O THRAK 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAAK 120 " --> pdb=" O ASPAK 116 " (cutoff:3.500A) Processing helix chain 'AK' and resid 128 through 134 removed outlier: 3.539A pdb=" N LEUAK 132 " --> pdb=" O LEUAK 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARGAK 134 " --> pdb=" O VALAK 130 " (cutoff:3.500A) Processing helix chain 'AK' and resid 140 through 145 Processing helix chain 'AM' and resid 6 through 8 No H-bonds generated for 'chain 'AM' and resid 6 through 8' Processing helix chain 'AM' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEUAM 13 " --> pdb=" O GLNAM 9 " (cutoff:3.500A) Processing helix chain 'AM' and resid 19 through 31 removed outlier: 3.741A pdb=" N ILEAM 24 " --> pdb=" O PROAM 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYSAM 27 " --> pdb=" O LEUAM 23 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASNAM 29 " --> pdb=" O ASNAM 25 " (cutoff:3.500A) Processing helix chain 'AM' and resid 37 through 46 removed outlier: 3.749A pdb=" N VALAM 44 " --> pdb=" O ALAAM 40 " (cutoff:3.500A) Processing helix chain 'AM' and resid 76 through 85 removed outlier: 3.658A pdb=" N LEUAM 83 " --> pdb=" O LEUAM 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEUAM 84 " --> pdb=" O VALAM 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLYAM 85 " --> pdb=" O THRAM 81 " (cutoff:3.500A) Processing helix chain 'AM' and resid 96 through 100 Processing helix chain 'AM' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASPAM 109 " --> pdb=" O ALAAM 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALAAM 110 " --> pdb=" O GLUAM 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARGAM 112 " --> pdb=" O LEUAM 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASPAM 115 " --> pdb=" O THRAM 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAAM 120 " --> pdb=" O ASPAM 116 " (cutoff:3.500A) Processing helix chain 'AM' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEUAM 132 " --> pdb=" O LEUAM 128 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARGAM 134 " --> pdb=" O VALAM 130 " (cutoff:3.500A) Processing helix chain 'AM' and resid 140 through 145 Processing helix chain 'AO' and resid 6 through 8 No H-bonds generated for 'chain 'AO' and resid 6 through 8' Processing helix chain 'AO' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEUAO 13 " --> pdb=" O GLNAO 9 " (cutoff:3.500A) Processing helix chain 'AO' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILEAO 24 " --> pdb=" O PROAO 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYSAO 27 " --> pdb=" O LEUAO 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASNAO 29 " --> pdb=" O ASNAO 25 " (cutoff:3.500A) Processing helix chain 'AO' and resid 37 through 46 removed outlier: 3.749A pdb=" N VALAO 44 " --> pdb=" O ALAAO 40 " (cutoff:3.500A) Processing helix chain 'AO' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEUAO 83 " --> pdb=" O LEUAO 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEUAO 84 " --> pdb=" O VALAO 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLYAO 85 " --> pdb=" O THRAO 81 " (cutoff:3.500A) Processing helix chain 'AO' and resid 96 through 100 Processing helix chain 'AO' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASPAO 109 " --> pdb=" O ALAAO 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALAAO 110 " --> pdb=" O GLUAO 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARGAO 112 " --> pdb=" O LEUAO 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASPAO 115 " --> pdb=" O THRAO 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAAO 120 " --> pdb=" O ASPAO 116 " (cutoff:3.500A) Processing helix chain 'AO' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEUAO 132 " --> pdb=" O LEUAO 128 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARGAO 134 " --> pdb=" O VALAO 130 " (cutoff:3.500A) Processing helix chain 'AO' and resid 140 through 145 Processing helix chain 'AQ' and resid 6 through 8 No H-bonds generated for 'chain 'AQ' and resid 6 through 8' Processing helix chain 'AQ' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEUAQ 13 " --> pdb=" O GLNAQ 9 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILEAQ 24 " --> pdb=" O PROAQ 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYSAQ 27 " --> pdb=" O LEUAQ 23 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASNAQ 29 " --> pdb=" O ASNAQ 25 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 37 through 46 removed outlier: 3.749A pdb=" N VALAQ 44 " --> pdb=" O ALAAQ 40 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEUAQ 83 " --> pdb=" O LEUAQ 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEUAQ 84 " --> pdb=" O VALAQ 80 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLYAQ 85 " --> pdb=" O THRAQ 81 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 96 through 100 Processing helix chain 'AQ' and resid 103 through 128 removed outlier: 3.578A pdb=" N ASPAQ 109 " --> pdb=" O ALAAQ 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALAAQ 110 " --> pdb=" O GLUAQ 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARGAQ 112 " --> pdb=" O LEUAQ 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASPAQ 115 " --> pdb=" O THRAQ 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAAQ 120 " --> pdb=" O ASPAQ 116 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEUAQ 132 " --> pdb=" O LEUAQ 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARGAQ 134 " --> pdb=" O VALAQ 130 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 140 through 145 Processing helix chain 'AS' and resid 6 through 8 No H-bonds generated for 'chain 'AS' and resid 6 through 8' Processing helix chain 'AS' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEUAS 13 " --> pdb=" O GLNAS 9 " (cutoff:3.500A) Processing helix chain 'AS' and resid 19 through 31 removed outlier: 3.741A pdb=" N ILEAS 24 " --> pdb=" O PROAS 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYSAS 27 " --> pdb=" O LEUAS 23 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASNAS 29 " --> pdb=" O ASNAS 25 " (cutoff:3.500A) Processing helix chain 'AS' and resid 37 through 46 removed outlier: 3.749A pdb=" N VALAS 44 " --> pdb=" O ALAAS 40 " (cutoff:3.500A) Processing helix chain 'AS' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEUAS 83 " --> pdb=" O LEUAS 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEUAS 84 " --> pdb=" O VALAS 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLYAS 85 " --> pdb=" O THRAS 81 " (cutoff:3.500A) Processing helix chain 'AS' and resid 96 through 100 Processing helix chain 'AS' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASPAS 109 " --> pdb=" O ALAAS 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALAAS 110 " --> pdb=" O GLUAS 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARGAS 112 " --> pdb=" O LEUAS 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASPAS 115 " --> pdb=" O THRAS 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAAS 120 " --> pdb=" O ASPAS 116 " (cutoff:3.500A) Processing helix chain 'AS' and resid 128 through 134 removed outlier: 3.541A pdb=" N LEUAS 132 " --> pdb=" O LEUAS 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARGAS 134 " --> pdb=" O VALAS 130 " (cutoff:3.500A) Processing helix chain 'AS' and resid 140 through 145 Processing helix chain 'AU' and resid 6 through 8 No H-bonds generated for 'chain 'AU' and resid 6 through 8' Processing helix chain 'AU' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEUAU 13 " --> pdb=" O GLNAU 9 " (cutoff:3.500A) Processing helix chain 'AU' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILEAU 24 " --> pdb=" O PROAU 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYSAU 27 " --> pdb=" O LEUAU 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASNAU 29 " --> pdb=" O ASNAU 25 " (cutoff:3.500A) Processing helix chain 'AU' and resid 37 through 46 removed outlier: 3.750A pdb=" N VALAU 44 " --> pdb=" O ALAAU 40 " (cutoff:3.500A) Processing helix chain 'AU' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEUAU 83 " --> pdb=" O LEUAU 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEUAU 84 " --> pdb=" O VALAU 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLYAU 85 " --> pdb=" O THRAU 81 " (cutoff:3.500A) Processing helix chain 'AU' and resid 96 through 100 Processing helix chain 'AU' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASPAU 109 " --> pdb=" O ALAAU 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALAAU 110 " --> pdb=" O GLUAU 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARGAU 112 " --> pdb=" O LEUAU 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASPAU 115 " --> pdb=" O THRAU 111 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALAAU 120 " --> pdb=" O ASPAU 116 " (cutoff:3.500A) Processing helix chain 'AU' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEUAU 132 " --> pdb=" O LEUAU 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARGAU 134 " --> pdb=" O VALAU 130 " (cutoff:3.500A) Processing helix chain 'AU' and resid 140 through 145 Processing helix chain 'AW' and resid 6 through 8 No H-bonds generated for 'chain 'AW' and resid 6 through 8' Processing helix chain 'AW' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEUAW 13 " --> pdb=" O GLNAW 9 " (cutoff:3.500A) Processing helix chain 'AW' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILEAW 24 " --> pdb=" O PROAW 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYSAW 27 " --> pdb=" O LEUAW 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASNAW 29 " --> pdb=" O ASNAW 25 " (cutoff:3.500A) Processing helix chain 'AW' and resid 37 through 46 removed outlier: 3.748A pdb=" N VALAW 44 " --> pdb=" O ALAAW 40 " (cutoff:3.500A) Processing helix chain 'AW' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEUAW 83 " --> pdb=" O LEUAW 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEUAW 84 " --> pdb=" O VALAW 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLYAW 85 " --> pdb=" O THRAW 81 " (cutoff:3.500A) Processing helix chain 'AW' and resid 96 through 100 Processing helix chain 'AW' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASPAW 109 " --> pdb=" O ALAAW 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALAAW 110 " --> pdb=" O GLUAW 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARGAW 112 " --> pdb=" O LEUAW 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASPAW 115 " --> pdb=" O THRAW 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAAW 120 " --> pdb=" O ASPAW 116 " (cutoff:3.500A) Processing helix chain 'AW' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEUAW 132 " --> pdb=" O LEUAW 128 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARGAW 134 " --> pdb=" O VALAW 130 " (cutoff:3.500A) Processing helix chain 'AW' and resid 140 through 145 Processing helix chain 'AY' and resid 6 through 8 No H-bonds generated for 'chain 'AY' and resid 6 through 8' Processing helix chain 'AY' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEUAY 13 " --> pdb=" O GLNAY 9 " (cutoff:3.500A) Processing helix chain 'AY' and resid 19 through 31 removed outlier: 3.741A pdb=" N ILEAY 24 " --> pdb=" O PROAY 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYSAY 27 " --> pdb=" O LEUAY 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASNAY 29 " --> pdb=" O ASNAY 25 " (cutoff:3.500A) Processing helix chain 'AY' and resid 37 through 46 removed outlier: 3.749A pdb=" N VALAY 44 " --> pdb=" O ALAAY 40 " (cutoff:3.500A) Processing helix chain 'AY' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEUAY 83 " --> pdb=" O LEUAY 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEUAY 84 " --> pdb=" O VALAY 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLYAY 85 " --> pdb=" O THRAY 81 " (cutoff:3.500A) Processing helix chain 'AY' and resid 96 through 100 Processing helix chain 'AY' and resid 103 through 128 removed outlier: 3.578A pdb=" N ASPAY 109 " --> pdb=" O ALAAY 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALAAY 110 " --> pdb=" O GLUAY 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARGAY 112 " --> pdb=" O LEUAY 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASPAY 115 " --> pdb=" O THRAY 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAAY 120 " --> pdb=" O ASPAY 116 " (cutoff:3.500A) Processing helix chain 'AY' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEUAY 132 " --> pdb=" O LEUAY 128 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARGAY 134 " --> pdb=" O VALAY 130 " (cutoff:3.500A) Processing helix chain 'AY' and resid 140 through 145 Processing helix chain 'A0' and resid 6 through 8 No H-bonds generated for 'chain 'A0' and resid 6 through 8' Processing helix chain 'A0' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEUA0 13 " --> pdb=" O GLNA0 9 " (cutoff:3.500A) Processing helix chain 'A0' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILEA0 24 " --> pdb=" O PROA0 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYSA0 27 " --> pdb=" O LEUA0 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASNA0 29 " --> pdb=" O ASNA0 25 " (cutoff:3.500A) Processing helix chain 'A0' and resid 37 through 46 removed outlier: 3.749A pdb=" N VALA0 44 " --> pdb=" O ALAA0 40 " (cutoff:3.500A) Processing helix chain 'A0' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEUA0 83 " --> pdb=" O LEUA0 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEUA0 84 " --> pdb=" O VALA0 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLYA0 85 " --> pdb=" O THRA0 81 " (cutoff:3.500A) Processing helix chain 'A0' and resid 96 through 100 Processing helix chain 'A0' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASPA0 109 " --> pdb=" O ALAA0 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALAA0 110 " --> pdb=" O GLUA0 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARGA0 112 " --> pdb=" O LEUA0 108 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASPA0 115 " --> pdb=" O THRA0 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAA0 120 " --> pdb=" O ASPA0 116 " (cutoff:3.500A) Processing helix chain 'A0' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEUA0 132 " --> pdb=" O LEUA0 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARGA0 134 " --> pdb=" O VALA0 130 " (cutoff:3.500A) Processing helix chain 'A0' and resid 140 through 145 Processing helix chain 'A2' and resid 6 through 8 No H-bonds generated for 'chain 'A2' and resid 6 through 8' Processing helix chain 'A2' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEUA2 13 " --> pdb=" O GLNA2 9 " (cutoff:3.500A) Processing helix chain 'A2' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILEA2 24 " --> pdb=" O PROA2 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYSA2 27 " --> pdb=" O LEUA2 23 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASNA2 29 " --> pdb=" O ASNA2 25 " (cutoff:3.500A) Processing helix chain 'A2' and resid 37 through 46 removed outlier: 3.749A pdb=" N VALA2 44 " --> pdb=" O ALAA2 40 " (cutoff:3.500A) Processing helix chain 'A2' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEUA2 83 " --> pdb=" O LEUA2 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEUA2 84 " --> pdb=" O VALA2 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLYA2 85 " --> pdb=" O THRA2 81 " (cutoff:3.500A) Processing helix chain 'A2' and resid 96 through 100 Processing helix chain 'A2' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASPA2 109 " --> pdb=" O ALAA2 105 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALAA2 110 " --> pdb=" O GLUA2 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARGA2 112 " --> pdb=" O LEUA2 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASPA2 115 " --> pdb=" O THRA2 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAA2 120 " --> pdb=" O ASPA2 116 " (cutoff:3.500A) Processing helix chain 'A2' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEUA2 132 " --> pdb=" O LEUA2 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARGA2 134 " --> pdb=" O VALA2 130 " (cutoff:3.500A) Processing helix chain 'A2' and resid 140 through 145 Processing helix chain 'A4' and resid 6 through 8 No H-bonds generated for 'chain 'A4' and resid 6 through 8' Processing helix chain 'A4' and resid 9 through 14 removed outlier: 3.775A pdb=" N LEUA4 13 " --> pdb=" O GLNA4 9 " (cutoff:3.500A) Processing helix chain 'A4' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILEA4 24 " --> pdb=" O PROA4 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYSA4 27 " --> pdb=" O LEUA4 23 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASNA4 29 " --> pdb=" O ASNA4 25 " (cutoff:3.500A) Processing helix chain 'A4' and resid 37 through 46 removed outlier: 3.748A pdb=" N VALA4 44 " --> pdb=" O ALAA4 40 " (cutoff:3.500A) Processing helix chain 'A4' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEUA4 83 " --> pdb=" O LEUA4 79 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEUA4 84 " --> pdb=" O VALA4 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLYA4 85 " --> pdb=" O THRA4 81 " (cutoff:3.500A) Processing helix chain 'A4' and resid 96 through 100 Processing helix chain 'A4' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASPA4 109 " --> pdb=" O ALAA4 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALAA4 110 " --> pdb=" O GLUA4 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARGA4 112 " --> pdb=" O LEUA4 108 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASPA4 115 " --> pdb=" O THRA4 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAA4 120 " --> pdb=" O ASPA4 116 " (cutoff:3.500A) Processing helix chain 'A4' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEUA4 132 " --> pdb=" O LEUA4 128 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARGA4 134 " --> pdb=" O VALA4 130 " (cutoff:3.500A) Processing helix chain 'A4' and resid 140 through 145 Processing helix chain 'A6' and resid 6 through 8 No H-bonds generated for 'chain 'A6' and resid 6 through 8' Processing helix chain 'A6' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEUA6 13 " --> pdb=" O GLNA6 9 " (cutoff:3.500A) Processing helix chain 'A6' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILEA6 24 " --> pdb=" O PROA6 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYSA6 27 " --> pdb=" O LEUA6 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASNA6 29 " --> pdb=" O ASNA6 25 " (cutoff:3.500A) Processing helix chain 'A6' and resid 37 through 46 removed outlier: 3.748A pdb=" N VALA6 44 " --> pdb=" O ALAA6 40 " (cutoff:3.500A) Processing helix chain 'A6' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEUA6 83 " --> pdb=" O LEUA6 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEUA6 84 " --> pdb=" O VALA6 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLYA6 85 " --> pdb=" O THRA6 81 " (cutoff:3.500A) Processing helix chain 'A6' and resid 96 through 100 Processing helix chain 'A6' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASPA6 109 " --> pdb=" O ALAA6 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALAA6 110 " --> pdb=" O GLUA6 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARGA6 112 " --> pdb=" O LEUA6 108 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASPA6 115 " --> pdb=" O THRA6 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAA6 120 " --> pdb=" O ASPA6 116 " (cutoff:3.500A) Processing helix chain 'A6' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEUA6 132 " --> pdb=" O LEUA6 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARGA6 134 " --> pdb=" O VALA6 130 " (cutoff:3.500A) Processing helix chain 'A6' and resid 140 through 145 Processing helix chain 'A8' and resid 6 through 8 No H-bonds generated for 'chain 'A8' and resid 6 through 8' Processing helix chain 'A8' and resid 9 through 14 removed outlier: 3.774A pdb=" N LEUA8 13 " --> pdb=" O GLNA8 9 " (cutoff:3.500A) Processing helix chain 'A8' and resid 19 through 31 removed outlier: 3.742A pdb=" N ILEA8 24 " --> pdb=" O PROA8 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYSA8 27 " --> pdb=" O LEUA8 23 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASNA8 29 " --> pdb=" O ASNA8 25 " (cutoff:3.500A) Processing helix chain 'A8' and resid 37 through 46 removed outlier: 3.748A pdb=" N VALA8 44 " --> pdb=" O ALAA8 40 " (cutoff:3.500A) Processing helix chain 'A8' and resid 76 through 85 removed outlier: 3.659A pdb=" N LEUA8 83 " --> pdb=" O LEUA8 79 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEUA8 84 " --> pdb=" O VALA8 80 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLYA8 85 " --> pdb=" O THRA8 81 " (cutoff:3.500A) Processing helix chain 'A8' and resid 96 through 100 Processing helix chain 'A8' and resid 103 through 128 removed outlier: 3.579A pdb=" N ASPA8 109 " --> pdb=" O ALAA8 105 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALAA8 110 " --> pdb=" O GLUA8 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARGA8 112 " --> pdb=" O LEUA8 108 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASPA8 115 " --> pdb=" O THRA8 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAA8 120 " --> pdb=" O ASPA8 116 " (cutoff:3.500A) Processing helix chain 'A8' and resid 128 through 134 removed outlier: 3.540A pdb=" N LEUA8 132 " --> pdb=" O LEUA8 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARGA8 134 " --> pdb=" O VALA8 130 " (cutoff:3.500A) Processing helix chain 'A8' and resid 140 through 145 1862 hydrogen bonds defined for protein. 5292 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: 16.56 Time building geometry restraints manager: 22.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13326 1.33 - 1.44: 15700 1.44 - 1.56: 34948 1.56 - 1.68: 461 1.68 - 1.79: 49 Bond restraints: 64484 Sorted by residual: bond pdb=" CA VAL g 44 " pdb=" CB VAL g 44 " ideal model delta sigma weight residual 1.544 1.494 0.050 1.25e-02 6.40e+03 1.63e+01 bond pdb=" CA VALA4 44 " pdb=" CB VALA4 44 " ideal model delta sigma weight residual 1.544 1.494 0.050 1.25e-02 6.40e+03 1.62e+01 bond pdb=" CA VALA0 44 " pdb=" CB VALA0 44 " ideal model delta sigma weight residual 1.544 1.494 0.050 1.25e-02 6.40e+03 1.61e+01 bond pdb=" CA VAL N 44 " pdb=" CB VAL N 44 " ideal model delta sigma weight residual 1.544 1.494 0.050 1.25e-02 6.40e+03 1.61e+01 bond pdb=" CA VAL o 44 " pdb=" CB VAL o 44 " ideal model delta sigma weight residual 1.544 1.494 0.050 1.25e-02 6.40e+03 1.61e+01 ... (remaining 64479 not shown) Histogram of bond angle deviations from ideal: 96.04 - 103.66: 2618 103.66 - 111.27: 25935 111.27 - 118.88: 24552 118.88 - 126.50: 34164 126.50 - 134.11: 1519 Bond angle restraints: 88788 Sorted by residual: angle pdb=" N LEUAK 23 " pdb=" CA LEUAK 23 " pdb=" C LEUAK 23 " ideal model delta sigma weight residual 111.07 127.11 -16.04 1.07e+00 8.73e-01 2.25e+02 angle pdb=" N LEU w 23 " pdb=" CA LEU w 23 " pdb=" C LEU w 23 " ideal model delta sigma weight residual 111.07 127.11 -16.04 1.07e+00 8.73e-01 2.25e+02 angle pdb=" N LEU W 23 " pdb=" CA LEU W 23 " pdb=" C LEU W 23 " ideal model delta sigma weight residual 111.07 127.11 -16.04 1.07e+00 8.73e-01 2.25e+02 angle pdb=" N LEU 8 23 " pdb=" CA LEU 8 23 " pdb=" C LEU 8 23 " ideal model delta sigma weight residual 111.07 127.10 -16.03 1.07e+00 8.73e-01 2.25e+02 angle pdb=" N LEU m 23 " pdb=" CA LEU m 23 " pdb=" C LEU m 23 " ideal model delta sigma weight residual 111.07 127.10 -16.03 1.07e+00 8.73e-01 2.25e+02 ... (remaining 88783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.36: 35930 34.36 - 68.71: 2094 68.71 - 103.07: 196 103.07 - 137.43: 0 137.43 - 171.79: 49 Dihedral angle restraints: 38269 sinusoidal: 15778 harmonic: 22491 Sorted by residual: dihedral pdb=" O4' UAT 5 " pdb=" C1' UAT 5 " pdb=" N1 UAT 5 " pdb=" C2 UAT 5 " ideal model delta sinusoidal sigma weight residual -160.00 11.79 -171.79 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U E 5 " pdb=" C1' U E 5 " pdb=" N1 U E 5 " pdb=" C2 U E 5 " ideal model delta sinusoidal sigma weight residual -160.00 11.78 -171.78 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U f 5 " pdb=" C1' U f 5 " pdb=" N1 U f 5 " pdb=" C2 U f 5 " ideal model delta sinusoidal sigma weight residual -160.00 11.78 -171.78 1 1.50e+01 4.44e-03 8.49e+01 ... (remaining 38266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 8468 0.152 - 0.305: 1391 0.305 - 0.457: 480 0.457 - 0.610: 98 0.610 - 0.762: 98 Chirality restraints: 10535 Sorted by residual: chirality pdb=" CA GLN e 38 " pdb=" N GLN e 38 " pdb=" C GLN e 38 " pdb=" CB GLN e 38 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" CA GLN g 38 " pdb=" N GLN g 38 " pdb=" C GLN g 38 " pdb=" CB GLN g 38 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" CA GLNAG 38 " pdb=" N GLNAG 38 " pdb=" C GLNAG 38 " pdb=" CB GLNAG 38 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.45e+01 ... (remaining 10532 not shown) Planarity restraints: 11123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP W 17 " 0.128 2.00e-02 2.50e+03 5.77e-02 8.32e+01 pdb=" CG TRP W 17 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP W 17 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP W 17 " -0.048 2.00e-02 2.50e+03 pdb=" NE1 TRP W 17 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP W 17 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP W 17 " -0.056 2.00e-02 2.50e+03 pdb=" CZ2 TRP W 17 " 0.049 2.00e-02 2.50e+03 pdb=" CZ3 TRP W 17 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP W 17 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRPAE 17 " -0.128 2.00e-02 2.50e+03 5.77e-02 8.31e+01 pdb=" CG TRPAE 17 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TRPAE 17 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRPAE 17 " 0.047 2.00e-02 2.50e+03 pdb=" NE1 TRPAE 17 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRPAE 17 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRPAE 17 " 0.056 2.00e-02 2.50e+03 pdb=" CZ2 TRPAE 17 " -0.050 2.00e-02 2.50e+03 pdb=" CZ3 TRPAE 17 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRPAE 17 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP k 17 " 0.128 2.00e-02 2.50e+03 5.77e-02 8.31e+01 pdb=" CG TRP k 17 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP k 17 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP k 17 " -0.048 2.00e-02 2.50e+03 pdb=" NE1 TRP k 17 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP k 17 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP k 17 " -0.056 2.00e-02 2.50e+03 pdb=" CZ2 TRP k 17 " 0.049 2.00e-02 2.50e+03 pdb=" CZ3 TRP k 17 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP k 17 " 0.039 2.00e-02 2.50e+03 ... (remaining 11120 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 194 2.27 - 2.92: 35950 2.92 - 3.58: 91036 3.58 - 4.24: 156950 4.24 - 4.90: 250847 Nonbonded interactions: 534977 Sorted by model distance: nonbonded pdb=" O3' G Q 6 " pdb=" P A T 4 " model vdw 1.607 3.400 nonbonded pdb=" O3' G C 6 " pdb=" P A E 4 " model vdw 1.607 3.400 nonbonded pdb=" O3' G G 6 " pdb=" P A I 4 " model vdw 1.607 3.400 nonbonded pdb=" O3' GA5 6 " pdb=" P AA7 4 " model vdw 1.607 3.400 nonbonded pdb=" O3' G Z 6 " pdb=" P A 1 4 " model vdw 1.607 3.400 ... (remaining 534972 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' and (resid 3 through 38 or resid 40 through 157)) selection = (chain '2' and (resid 3 through 38 or resid 40 through 157)) selection = (chain '4' and (resid 3 through 38 or resid 40 through 157)) selection = (chain '6' and (resid 3 through 38 or resid 40 through 157)) selection = (chain '8' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'A' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'A0' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'A2' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'A4' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'A6' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'A8' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'AA' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'AC' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'AE' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'AG' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'AI' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'AK' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'AM' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'AO' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'AQ' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'AS' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'AU' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'AW' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'AY' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'B' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'D' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'F' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'H' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'J' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'L' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'N' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'P' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'S' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'U' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'W' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'Y' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'a' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'c' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'e' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'g' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'i' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'k' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'm' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'o' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'q' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 's' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'u' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'w' and (resid 3 through 38 or resid 40 through 157)) selection = (chain 'y' and (resid 3 through 38 or resid 40 through 157)) } ncs_group { reference = chain '1' selection = chain '3' selection = chain '5' selection = chain '7' selection = chain '9' selection = chain 'A1' selection = chain 'A3' selection = chain 'A5' selection = chain 'A7' selection = chain 'A9' selection = chain 'AB' selection = chain 'AD' selection = chain 'AF' selection = chain 'AH' selection = chain 'AJ' selection = chain 'AL' selection = chain 'AN' selection = chain 'AP' selection = chain 'AR' selection = chain 'AT' selection = chain 'AV' selection = chain 'AX' selection = chain 'AZ' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'p' selection = chain 'r' selection = chain 't' selection = chain 'v' selection = chain 'x' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 28.810 Check model and map are aligned: 0.720 Set scattering table: 0.450 Process input model: 159.860 Find NCS groups from input model: 3.660 Set up NCS constraints: 0.780 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: 0.020 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 202.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 0.081 64484 Z= 0.719 Angle : 2.341 18.246 88788 Z= 1.616 Chirality : 0.155 0.762 10535 Planarity : 0.014 0.080 11123 Dihedral : 21.081 171.787 23569 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 79.64 Ramachandran Plot: Outliers : 13.53 % Allowed : 21.09 % Favored : 65.39 % Rotamer Outliers : 14.71 % Cbeta Deviations : 6.00 % 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: -7.24 (0.06), residues: 7644 helix: -4.69 (0.04), residues: 3283 sheet: None (None), residues: 0 loop : -5.16 (0.07), residues: 4361 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2698 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 931 poor density : 1767 time to evaluate : 5.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 931 outliers final: 224 residues processed: 2540 average time/residue: 0.6823 time to fit residues: 2785.5176 Evaluate side-chains 1450 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1226 time to evaluate : 5.483 Switching outliers to nearest non-outliers outliers start: 224 outliers final: 10 residues processed: 224 average time/residue: 0.6176 time to fit residues: 237.1877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 620 optimal weight: 2.9990 chunk 557 optimal weight: 0.9990 chunk 309 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 375 optimal weight: 8.9990 chunk 297 optimal weight: 2.9990 chunk 576 optimal weight: 1.9990 chunk 222 optimal weight: 6.9990 chunk 350 optimal weight: 3.9990 chunk 428 optimal weight: 0.9990 chunk 667 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B B 57 GLN B 101 ASN D 34 GLN D 39 GLN B D 57 GLN D 101 ASN F 34 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN B F 91 ASN F 101 ASN H 33 ASN H 39 GLN B H 101 ASN J 33 ASN J 34 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN B J 57 GLN J 101 ASN L 33 ASN L 39 GLN B L 73 ASN L 101 ASN N 33 ASN N 34 GLN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN B N 57 GLN N 101 ASN P 33 ASN ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 GLN B P 47 GLN P 57 GLN S 39 GLN B S 73 ASN S 101 ASN U 33 ASN ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 GLN B U 57 GLN U 101 ASN W 33 ASN ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 39 GLN B W 73 ASN W 101 ASN Y 33 ASN Y 34 GLN Y 39 GLN B Y 73 ASN Y 101 ASN 0 33 ASN 0 34 GLN ** 0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 39 GLN B 0 57 GLN 0 73 ASN 0 101 ASN 2 33 ASN ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 39 GLN B 2 57 GLN 2 101 ASN 4 39 GLN B 4 101 ASN 6 33 ASN 6 34 GLN ** 6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 39 GLN B 6 101 ASN 8 33 ASN 8 39 GLN B 8 57 GLN 8 101 ASN ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 GLN B a 57 GLN a 101 ASN a 126 ASN c 33 ASN ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 39 GLN B c 47 GLN c 101 ASN c 126 ASN e 33 ASN ** e 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 39 GLN B e 57 GLN e 73 ASN e 101 ASN e 126 ASN g 33 ASN ** g 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 39 GLN B g 101 ASN i 33 ASN i 34 GLN i 39 GLN B i 101 ASN i 126 ASN k 33 ASN k 34 GLN ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 39 GLN B k 57 GLN k 101 ASN k 126 ASN m 33 ASN m 34 GLN ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 39 GLN B m 57 GLN m 101 ASN m 126 ASN A 33 ASN A 34 GLN A 39 GLN B A 57 GLN A 101 ASN A 126 ASN ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 39 GLN B o 101 ASN q 33 ASN q 34 GLN ** q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 39 GLN B q 101 ASN q 126 ASN s 33 ASN ** s 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 39 GLN B s 57 GLN s 73 ASN s 101 ASN u 34 GLN ** u 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 GLN B u 57 GLN u 101 ASN w 33 ASN ** w 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 39 GLN B w 57 GLN w 73 ASN w 101 ASN y 33 ASN y 34 GLN ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 39 GLN B y 101 ASN AA 33 ASN AA 39 GLN B AA 101 ASN AA 126 ASN AC 34 GLN ** AC 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 39 GLN B AC 57 GLN AC 101 ASN ** AE 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 34 GLN AE 39 GLN B AE 57 GLN AE 73 ASN AE 101 ASN ** AG 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 33 ASN ** AG 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 39 GLN B AG 101 ASN AG 126 ASN AI 34 GLN ** AI 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 39 GLN B AI 73 ASN AI 91 ASN AI 101 ASN AI 126 ASN ** AK 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 39 GLN B AK 101 ASN AK 126 ASN ** AM 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 33 ASN ** AM 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 39 GLN B AM 57 GLN AM 73 ASN AM 101 ASN ** AO 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 33 ASN AO 34 GLN ** AO 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 39 GLN B AO 101 ASN AO 126 ASN AQ 33 ASN ** AQ 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 39 GLN B AQ 101 ASN AQ 126 ASN ** AS 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 39 GLN B AS 57 GLN AS 101 ASN AS 126 ASN ** AU 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 39 GLN B AU 57 GLN AU 73 ASN AU 101 ASN ** AW 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 39 GLN B AW 57 GLN AW 101 ASN AW 126 ASN AY 33 ASN AY 39 GLN B AY 57 GLN AY 101 ASN AY 126 ASN ** A0 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A0 39 GLN B A0 57 GLN A0 101 ASN A0 126 ASN ** A2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 33 ASN ** A2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 39 GLN B A2 57 GLN A2 73 ASN A2 101 ASN ** A4 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 33 ASN A4 34 GLN ** A4 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 39 GLN B A4 57 GLN A4 101 ASN A4 126 ASN ** A6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 33 ASN ** A6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 39 GLN B A6 47 GLN A6 101 ASN A6 126 ASN ** A8 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 33 ASN A8 34 GLN ** A8 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 39 GLN B A8 57 GLN A8 73 ASN A8 101 ASN A8 126 ASN Total number of N/Q/H flips: 218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 64484 Z= 0.278 Angle : 0.944 13.015 88788 Z= 0.466 Chirality : 0.048 0.248 10535 Planarity : 0.008 0.075 11123 Dihedral : 17.040 163.649 9947 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 1.96 % Allowed : 12.35 % Favored : 85.69 % Rotamer Outliers : 6.17 % 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: -5.29 (0.07), residues: 7644 helix: -3.27 (0.06), residues: 3969 sheet: None (None), residues: 0 loop : -3.84 (0.08), residues: 3675 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1982 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 1620 time to evaluate : 6.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 362 outliers final: 185 residues processed: 1893 average time/residue: 0.6017 time to fit residues: 1926.1495 Evaluate side-chains 1277 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1092 time to evaluate : 5.301 Switching outliers to nearest non-outliers outliers start: 185 outliers final: 0 residues processed: 185 average time/residue: 0.4426 time to fit residues: 163.9191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 370 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 555 optimal weight: 6.9990 chunk 454 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 668 optimal weight: 0.6980 chunk 722 optimal weight: 5.9990 chunk 595 optimal weight: 7.9990 chunk 663 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 536 optimal weight: 5.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN J 57 GLN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 GLN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 GLN ** P 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 57 GLN ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 57 GLN ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 33 ASN 0 33 ASN ** 0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 47 GLN 0 57 GLN ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 57 GLN 6 33 ASN 6 34 GLN ** 6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 57 GLN ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 47 GLN ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN g 33 ASN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 33 ASN ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 33 ASN ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 47 GLN m 57 GLN A 38 GLN A 57 GLN ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 126 ASN ** s 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 57 GLN u 57 GLN w 33 ASN w 57 GLN y 33 ASN ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 57 GLN ** AG 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 33 ASN ** AG 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 47 GLN AM 57 GLN AM 126 ASN ** AO 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 33 ASN ** AQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 33 ASN ** AU 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 47 GLN AU 57 GLN ** AW 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 38 GLN ** AW 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 57 GLN ** AY 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A0 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A0 57 GLN ** A0 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 33 ASN ** A2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 57 GLN ** A4 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 33 ASN ** A4 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 33 ASN ** A6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 57 GLN A8 73 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 64484 Z= 0.356 Angle : 0.915 10.765 88788 Z= 0.452 Chirality : 0.049 0.214 10535 Planarity : 0.007 0.072 11123 Dihedral : 17.141 171.156 9947 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 1.81 % Allowed : 9.90 % Favored : 88.29 % Rotamer Outliers : 4.73 % 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: -4.58 (0.08), residues: 7644 helix: -3.15 (0.05), residues: 4263 sheet: None (None), residues: 0 loop : -2.74 (0.10), residues: 3381 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1397 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1131 time to evaluate : 5.354 Fit side-chains outliers start: 266 outliers final: 152 residues processed: 1325 average time/residue: 0.5708 time to fit residues: 1309.0734 Evaluate side-chains 1068 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 916 time to evaluate : 5.343 Switching outliers to nearest non-outliers outliers start: 152 outliers final: 0 residues processed: 152 average time/residue: 0.4479 time to fit residues: 137.2481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 660 optimal weight: 7.9990 chunk 502 optimal weight: 5.9990 chunk 347 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 319 optimal weight: 2.9990 chunk 449 optimal weight: 2.9990 chunk 671 optimal weight: 4.9990 chunk 710 optimal weight: 9.9990 chunk 350 optimal weight: 1.9990 chunk 636 optimal weight: 0.6980 chunk 191 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 47 GLN B 57 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN A D 57 GLN ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 GLN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 GLN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 GLN ** P 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 GLN A U 57 GLN ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 GLN W 57 GLN ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 57 GLN ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 57 GLN ** 4 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 33 ASN ** 6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 47 GLN 8 57 GLN a 39 GLN A ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN ** g 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 57 GLN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 33 ASN ** m 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 57 GLN A 33 ASN A 57 GLN ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 47 GLN q 57 GLN ** s 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 GLN A u 57 GLN w 33 ASN ** w 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 34 GLN AA 47 GLN AA 57 GLN ** AA 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 57 GLN ** AG 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 73 ASN ** AK 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 57 GLN ** AK 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 57 GLN ** AO 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 33 ASN ** AQ 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 57 GLN ** AU 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 33 ASN ** AU 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 57 GLN ** AW 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 57 GLN ** AY 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A0 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A0 57 GLN ** A0 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 29 ASN A2 33 ASN ** A2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 57 GLN ** A6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 34 GLN ** A6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 57 GLN ** A6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 57 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 64484 Z= 0.225 Angle : 0.789 14.291 88788 Z= 0.382 Chirality : 0.045 0.187 10535 Planarity : 0.007 0.078 11123 Dihedral : 16.764 167.481 9947 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 1.31 % Allowed : 9.15 % Favored : 89.54 % Rotamer Outliers : 2.52 % 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: -3.64 (0.08), residues: 7644 helix: -2.17 (0.06), residues: 3871 sheet: None (None), residues: 0 loop : -2.67 (0.09), residues: 3773 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 956 time to evaluate : 5.363 Fit side-chains outliers start: 119 outliers final: 59 residues processed: 1042 average time/residue: 0.5941 time to fit residues: 1067.6179 Evaluate side-chains 859 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 800 time to evaluate : 5.304 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.4532 time to fit residues: 58.1276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 591 optimal weight: 1.9990 chunk 403 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 528 optimal weight: 7.9990 chunk 293 optimal weight: 9.9990 chunk 606 optimal weight: 9.9990 chunk 491 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 362 optimal weight: 5.9990 chunk 637 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 GLN ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN H 34 GLN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 GLN J 57 GLN J 73 ASN L 34 GLN N 57 GLN ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 57 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 39 GLN A ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 47 GLN ** 6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 33 ASN 8 57 GLN a 34 GLN ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN ** e 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 45 GLN ** e 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 34 GLN ** g 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 ASN i 47 GLN ** i 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 33 ASN m 34 GLN ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN o 34 GLN ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 47 GLN q 33 ASN ** q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 GLN ** u 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 57 GLN w 34 GLN ** w 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 57 GLN AG 29 ASN ** AG 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 57 GLN ** AG 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 57 GLN ** AM 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 38 GLN AM 57 GLN ** AO 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 57 GLN AU 29 ASN ** AU 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 57 GLN ** AW 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 57 GLN ** AY 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A0 29 ASN ** A0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A0 57 GLN ** A0 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 33 ASN ** A2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 34 GLN ** A4 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 57 GLN ** A6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 34 GLN ** A6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 57 GLN ** A6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 57 GLN A8 73 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.6380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 64484 Z= 0.208 Angle : 0.751 12.468 88788 Z= 0.363 Chirality : 0.044 0.242 10535 Planarity : 0.006 0.075 11123 Dihedral : 16.431 168.382 9947 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 1.32 % Allowed : 8.80 % Favored : 89.88 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.08), residues: 7644 helix: -1.72 (0.07), residues: 3920 sheet: None (None), residues: 0 loop : -2.67 (0.10), residues: 3724 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 832 time to evaluate : 5.370 Fit side-chains outliers start: 125 outliers final: 45 residues processed: 919 average time/residue: 0.6218 time to fit residues: 989.9514 Evaluate side-chains 796 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 751 time to evaluate : 5.340 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.4775 time to fit residues: 47.8116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 239 optimal weight: 8.9990 chunk 639 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 417 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 711 optimal weight: 3.9990 chunk 590 optimal weight: 5.9990 chunk 329 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 373 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN D 29 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 GLN ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 ASN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN J 34 GLN J 39 GLN A J 47 GLN J 57 GLN L 34 GLN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 33 ASN P 57 GLN ** P 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 ASN ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 57 GLN ** 6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 57 GLN a 34 GLN a 57 GLN ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN e 57 GLN g 34 GLN ** g 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 29 ASN i 57 GLN k 34 GLN ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 33 ASN m 34 GLN ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 57 GLN ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 GLN A 57 GLN ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 39 GLN A ** q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 29 ASN u 34 GLN u 57 GLN ** w 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 39 GLN A ** AA 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 29 ASN AE 57 GLN ** AG 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 29 ASN AI 34 GLN ** AI 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 45 GLN AK 34 GLN AK 57 GLN AM 29 ASN ** AM 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 57 GLN ** AO 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 33 ASN ** AQ 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 34 GLN AS 57 GLN ** AS 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 47 GLN AU 57 GLN AW 34 GLN AW 47 GLN AW 57 GLN ** AW 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 34 GLN AY 57 GLN ** AY 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A0 57 GLN ** A0 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 29 ASN ** A4 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 57 GLN A6 29 ASN A6 34 GLN ** A6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 57 GLN A8 29 ASN A8 57 GLN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.6481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.065 64484 Z= 0.467 Angle : 0.914 11.629 88788 Z= 0.463 Chirality : 0.052 0.257 10535 Planarity : 0.008 0.089 11123 Dihedral : 16.955 175.894 9947 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 1.57 % Allowed : 11.84 % Favored : 86.58 % Rotamer Outliers : 3.44 % 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: -4.00 (0.08), residues: 7644 helix: -2.56 (0.06), residues: 4312 sheet: None (None), residues: 0 loop : -2.66 (0.11), residues: 3332 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1110 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 930 time to evaluate : 5.437 Fit side-chains outliers start: 180 outliers final: 102 residues processed: 1051 average time/residue: 0.5895 time to fit residues: 1071.4128 Evaluate side-chains 992 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 890 time to evaluate : 5.337 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 0 residues processed: 102 average time/residue: 0.4556 time to fit residues: 95.8111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 685 optimal weight: 5.9990 chunk 80 optimal weight: 0.0470 chunk 405 optimal weight: 0.1980 chunk 519 optimal weight: 8.9990 chunk 402 optimal weight: 0.9980 chunk 598 optimal weight: 10.0000 chunk 397 optimal weight: 7.9990 chunk 708 optimal weight: 3.9990 chunk 443 optimal weight: 1.9990 chunk 431 optimal weight: 4.9990 chunk 327 optimal weight: 1.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN A B 57 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 GLN ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 GLN L 34 GLN L 39 GLN A ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN A ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 GLN A ** P 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 34 GLN ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 47 GLN 0 34 GLN ** 0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 39 GLN A ** 6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 57 GLN ** 6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 39 GLN A ** 8 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 34 GLN ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 34 GLN ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 47 GLN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN ** e 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 34 GLN ** g 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 39 GLN A ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 39 GLN A ** k 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 33 ASN ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 47 GLN ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 GLN o 34 GLN ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 39 GLN A ** o 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 45 GLN ** q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 GLN s 57 GLN u 34 GLN ** u 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 57 GLN w 34 GLN ** w 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 57 GLN ** AC 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 57 GLN ** AE 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 34 GLN ** AK 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 45 GLN AK 57 GLN ** AM 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 38 GLN AM 57 GLN ** AM 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 57 GLN ** AU 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 29 ASN ** AW 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 47 GLN ** AW 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 29 ASN ** AY 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A0 57 GLN ** A0 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 34 GLN ** A6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 57 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.6825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 64484 Z= 0.193 Angle : 0.739 11.653 88788 Z= 0.362 Chirality : 0.043 0.254 10535 Planarity : 0.006 0.081 11123 Dihedral : 16.320 170.683 9947 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 1.92 % Allowed : 7.72 % Favored : 90.36 % Rotamer Outliers : 1.65 % 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: -3.29 (0.09), residues: 7644 helix: -1.84 (0.07), residues: 4263 sheet: None (None), residues: 0 loop : -2.58 (0.11), residues: 3381 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 867 time to evaluate : 5.309 Fit side-chains outliers start: 61 outliers final: 15 residues processed: 909 average time/residue: 0.6171 time to fit residues: 967.6308 Evaluate side-chains 793 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 778 time to evaluate : 5.371 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4908 time to fit residues: 20.6091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 438 optimal weight: 7.9990 chunk 282 optimal weight: 10.0000 chunk 423 optimal weight: 4.9990 chunk 213 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 450 optimal weight: 10.0000 chunk 482 optimal weight: 7.9990 chunk 350 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 556 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN H 29 ASN ** H 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 ASN J 34 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 GLN L 29 ASN L 34 GLN L 47 GLN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 GLN ** P 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 140 ASN U 34 GLN ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 34 GLN ** 0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 45 GLN ** 4 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 57 GLN ** 6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 34 GLN ** a 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN ** e 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 57 GLN g 34 GLN ** g 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 34 GLN ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 34 GLN ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 57 GLN ** m 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 140 ASN A 29 ASN A 34 GLN A 47 GLN ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 57 GLN ** s 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 34 GLN ** u 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 57 GLN ** w 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 57 GLN ** AC 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 57 GLN ** AG 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 34 GLN ** AK 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 9 GLN ** AM 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 57 GLN AW 29 ASN AW 34 GLN ** AW 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 47 GLN ** AW 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 34 GLN ** AY 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A0 57 GLN ** A0 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 34 GLN ** A2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 34 GLN ** A6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 57 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.6804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 64484 Z= 0.352 Angle : 0.830 11.246 88788 Z= 0.418 Chirality : 0.048 0.267 10535 Planarity : 0.007 0.078 11123 Dihedral : 16.562 175.214 9947 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 1.91 % Allowed : 10.51 % Favored : 87.58 % Rotamer Outliers : 2.06 % 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: -3.70 (0.08), residues: 7644 helix: -2.15 (0.07), residues: 4361 sheet: None (None), residues: 0 loop : -2.79 (0.11), residues: 3283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 863 time to evaluate : 5.331 Fit side-chains outliers start: 88 outliers final: 36 residues processed: 928 average time/residue: 0.5750 time to fit residues: 931.1817 Evaluate side-chains 890 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 854 time to evaluate : 5.589 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.4764 time to fit residues: 39.0001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 644 optimal weight: 6.9990 chunk 678 optimal weight: 1.9990 chunk 619 optimal weight: 5.9990 chunk 660 optimal weight: 8.9990 chunk 397 optimal weight: 2.9990 chunk 287 optimal weight: 7.9990 chunk 518 optimal weight: 0.8980 chunk 202 optimal weight: 3.9990 chunk 596 optimal weight: 6.9990 chunk 624 optimal weight: 10.0000 chunk 657 optimal weight: 0.0870 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 GLN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 29 ASN ** 6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 34 GLN ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 29 ASN e 33 ASN ** e 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 34 GLN ** g 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 34 GLN ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 GLN ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 29 ASN o 34 GLN ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 34 GLN ** q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 57 GLN ** s 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 57 GLN ** w 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 57 GLN ** AC 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 57 GLN ** AG 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 34 GLN ** AK 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 57 GLN ** AM 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 33 ASN ** AQ 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 57 GLN ** AU 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 29 ASN ** AW 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 47 GLN ** AW 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 34 GLN ** AY 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A0 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 34 GLN ** A6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 57 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.7001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 64484 Z= 0.221 Angle : 0.752 12.853 88788 Z= 0.371 Chirality : 0.044 0.267 10535 Planarity : 0.006 0.076 11123 Dihedral : 16.258 173.351 9947 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 1.87 % Allowed : 8.35 % Favored : 89.78 % Rotamer Outliers : 1.26 % 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: -3.18 (0.09), residues: 7644 helix: -1.73 (0.07), residues: 4263 sheet: None (None), residues: 0 loop : -2.56 (0.11), residues: 3381 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 826 time to evaluate : 5.345 Fit side-chains outliers start: 35 outliers final: 13 residues processed: 849 average time/residue: 0.5727 time to fit residues: 853.2125 Evaluate side-chains 792 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 779 time to evaluate : 5.257 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4691 time to fit residues: 18.2973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 433 optimal weight: 10.0000 chunk 698 optimal weight: 9.9990 chunk 426 optimal weight: 3.9990 chunk 331 optimal weight: 9.9990 chunk 485 optimal weight: 0.0870 chunk 732 optimal weight: 8.9990 chunk 673 optimal weight: 10.0000 chunk 583 optimal weight: 0.0980 chunk 60 optimal weight: 10.0000 chunk 450 optimal weight: 5.9990 chunk 357 optimal weight: 10.0000 overall best weight: 3.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN J 34 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 GLN L 29 ASN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 GLN ** P 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 GLN ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 29 ASN ** Y 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 34 GLN ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 34 GLN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN g 34 GLN ** g 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 34 GLN ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 34 GLN ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 34 GLN ** q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 57 GLN ** s 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 47 GLN u 57 GLN ** w 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 34 GLN ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 ASN ** AA 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 57 GLN ** AC 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 57 GLN ** AG 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 34 GLN ** AK 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 38 GLN ** AK 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 33 ASN ** AO 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 73 ASN ** AQ 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 57 GLN ** AU 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 34 GLN ** AW 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A0 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 34 GLN ** A6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 57 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.6974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 64484 Z= 0.311 Angle : 0.802 11.542 88788 Z= 0.402 Chirality : 0.047 0.280 10535 Planarity : 0.007 0.077 11123 Dihedral : 16.381 175.405 9947 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 1.71 % Allowed : 10.20 % Favored : 88.09 % Rotamer Outliers : 1.38 % 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: -3.54 (0.09), residues: 7644 helix: -1.95 (0.07), residues: 4361 sheet: None (None), residues: 0 loop : -2.82 (0.10), residues: 3283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15288 Ramachandran restraints generated. 7644 Oldfield, 0 Emsley, 7644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 847 time to evaluate : 5.356 Fit side-chains outliers start: 43 outliers final: 23 residues processed: 871 average time/residue: 0.5765 time to fit residues: 878.8366 Evaluate side-chains 846 residues out of total 6566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 823 time to evaluate : 5.329 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4906 time to fit residues: 28.0467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 463 optimal weight: 0.0980 chunk 621 optimal weight: 2.9990 chunk 178 optimal weight: 0.0970 chunk 537 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 584 optimal weight: 0.8980 chunk 244 optimal weight: 0.2980 chunk 599 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 GLN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 33 ASN ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 GLN ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 29 ASN a 34 GLN ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 34 GLN ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 47 GLN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 34 GLN ** k 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 39 GLN A ** m 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 GLN A o 29 ASN o 34 GLN ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 34 GLN ** q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 57 GLN ** w 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 57 GLN ** AC 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 47 GLN AE 57 GLN AG 9 GLN ** AG 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 73 ASN AK 34 GLN ** AK 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 57 GLN ** AM 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 33 ASN ** AO 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 29 ASN ** AQ 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 57 GLN ** AU 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 34 GLN ** AW 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 47 GLN ** AW 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 33 ASN AY 34 GLN ** AY 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A0 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 126 ASN ** A4 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 57 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.130419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.110407 restraints weight = 505167.109| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 5.37 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.7245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 64484 Z= 0.180 Angle : 0.714 11.866 88788 Z= 0.348 Chirality : 0.042 0.269 10535 Planarity : 0.006 0.075 11123 Dihedral : 15.884 170.807 9947 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 1.84 % Allowed : 6.91 % Favored : 91.25 % Rotamer Outliers : 0.98 % 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: -3.04 (0.09), residues: 7644 helix: -1.34 (0.07), residues: 4214 sheet: None (None), residues: 0 loop : -2.91 (0.10), residues: 3430 =============================================================================== Job complete usr+sys time: 18790.32 seconds wall clock time: 328 minutes 26.57 seconds (19706.57 seconds total)