Starting phenix.real_space_refine (version: dev) on Sat Dec 17 10:00:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kh1_22873/12_2022/7kh1_22873.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kh1_22873/12_2022/7kh1_22873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kh1_22873/12_2022/7kh1_22873.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kh1_22873/12_2022/7kh1_22873.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kh1_22873/12_2022/7kh1_22873.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kh1_22873/12_2022/7kh1_22873.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.019 sd= 0.584 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A1 TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 GLU 83": "OE1" <-> "OE2" Residue "A1 GLU 109": "OE1" <-> "OE2" Residue "A1 GLU 135": "OE1" <-> "OE2" Residue "A1 ARG 137": "NH1" <-> "NH2" Residue "A1 GLU 141": "OE1" <-> "OE2" Residue "B1 TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 GLU 83": "OE1" <-> "OE2" Residue "B1 GLU 109": "OE1" <-> "OE2" Residue "B1 GLU 135": "OE1" <-> "OE2" Residue "B1 ARG 137": "NH1" <-> "NH2" Residue "B1 GLU 141": "OE1" <-> "OE2" Residue "C1 TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 GLU 83": "OE1" <-> "OE2" Residue "C1 GLU 109": "OE1" <-> "OE2" Residue "C1 GLU 135": "OE1" <-> "OE2" Residue "C1 ARG 137": "NH1" <-> "NH2" Residue "C1 GLU 141": "OE1" <-> "OE2" Residue "D1 TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 GLU 83": "OE1" <-> "OE2" Residue "D1 GLU 109": "OE1" <-> "OE2" Residue "D1 GLU 135": "OE1" <-> "OE2" Residue "D1 ARG 137": "NH1" <-> "NH2" Residue "D1 GLU 141": "OE1" <-> "OE2" Residue "E1 TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E1 GLU 83": "OE1" <-> "OE2" Residue "E1 GLU 109": "OE1" <-> "OE2" Residue "E1 GLU 135": "OE1" <-> "OE2" Residue "E1 ARG 137": "NH1" <-> "NH2" Residue "E1 GLU 141": "OE1" <-> "OE2" Residue "F1 TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F1 GLU 83": "OE1" <-> "OE2" Residue "F1 GLU 109": "OE1" <-> "OE2" Residue "F1 GLU 135": "OE1" <-> "OE2" Residue "F1 ARG 137": "NH1" <-> "NH2" Residue "F1 GLU 141": "OE1" <-> "OE2" Residue "A2 PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A2 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A2 TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A2 TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A2 PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A2 ASP 65": "OD1" <-> "OD2" Residue "A2 ARG 68": "NH1" <-> "NH2" Residue "A2 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A2 PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A2 ARG 122": "NH1" <-> "NH2" Residue "A2 GLU 142": "OE1" <-> "OE2" Residue "A2 ASP 179": "OD1" <-> "OD2" Residue "A2 GLU 180": "OE1" <-> "OE2" Residue "B2 PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 ASP 65": "OD1" <-> "OD2" Residue "B2 ARG 68": "NH1" <-> "NH2" Residue "B2 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 ARG 122": "NH1" <-> "NH2" Residue "B2 GLU 142": "OE1" <-> "OE2" Residue "B2 ASP 179": "OD1" <-> "OD2" Residue "B2 GLU 180": "OE1" <-> "OE2" Residue "C2 PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 ASP 65": "OD1" <-> "OD2" Residue "C2 ARG 68": "NH1" <-> "NH2" Residue "C2 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 ARG 122": "NH1" <-> "NH2" Residue "C2 GLU 142": "OE1" <-> "OE2" Residue "C2 ASP 179": "OD1" <-> "OD2" Residue "C2 GLU 180": "OE1" <-> "OE2" Residue "D2 PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 ASP 65": "OD1" <-> "OD2" Residue "D2 ARG 68": "NH1" <-> "NH2" Residue "D2 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 ARG 122": "NH1" <-> "NH2" Residue "D2 GLU 142": "OE1" <-> "OE2" Residue "D2 ASP 179": "OD1" <-> "OD2" Residue "D2 GLU 180": "OE1" <-> "OE2" Residue "E2 PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E2 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E2 TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E2 TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E2 PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E2 ASP 65": "OD1" <-> "OD2" Residue "E2 ARG 68": "NH1" <-> "NH2" Residue "E2 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E2 PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E2 ARG 122": "NH1" <-> "NH2" Residue "E2 GLU 142": "OE1" <-> "OE2" Residue "E2 ASP 179": "OD1" <-> "OD2" Residue "E2 GLU 180": "OE1" <-> "OE2" Residue "F2 PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 ASP 65": "OD1" <-> "OD2" Residue "F2 ARG 68": "NH1" <-> "NH2" Residue "F2 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 ARG 122": "NH1" <-> "NH2" Residue "F2 GLU 142": "OE1" <-> "OE2" Residue "F2 ASP 179": "OD1" <-> "OD2" Residue "F2 GLU 180": "OE1" <-> "OE2" Residue "A3 GLU 9": "OE1" <-> "OE2" Residue "A3 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A3 GLU 59": "OE1" <-> "OE2" Residue "A3 TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A3 GLU 146": "OE1" <-> "OE2" Residue "A3 GLU 155": "OE1" <-> "OE2" Residue "A3 PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A3 TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A3 GLU 240": "OE1" <-> "OE2" Residue "B3 GLU 9": "OE1" <-> "OE2" Residue "B3 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 GLU 59": "OE1" <-> "OE2" Residue "B3 TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 GLU 146": "OE1" <-> "OE2" Residue "B3 GLU 155": "OE1" <-> "OE2" Residue "B3 PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 GLU 240": "OE1" <-> "OE2" Residue "C3 GLU 9": "OE1" <-> "OE2" Residue "C3 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C3 GLU 59": "OE1" <-> "OE2" Residue "C3 TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C3 GLU 146": "OE1" <-> "OE2" Residue "C3 GLU 155": "OE1" <-> "OE2" Residue "C3 PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C3 TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C3 GLU 240": "OE1" <-> "OE2" Residue "D3 GLU 9": "OE1" <-> "OE2" Residue "D3 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D3 GLU 59": "OE1" <-> "OE2" Residue "D3 TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D3 GLU 146": "OE1" <-> "OE2" Residue "D3 GLU 155": "OE1" <-> "OE2" Residue "D3 PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D3 TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D3 GLU 240": "OE1" <-> "OE2" Residue "E3 GLU 9": "OE1" <-> "OE2" Residue "E3 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E3 GLU 59": "OE1" <-> "OE2" Residue "E3 TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E3 GLU 146": "OE1" <-> "OE2" Residue "E3 GLU 155": "OE1" <-> "OE2" Residue "E3 PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E3 TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E3 GLU 240": "OE1" <-> "OE2" Residue "F3 GLU 9": "OE1" <-> "OE2" Residue "F3 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F3 GLU 59": "OE1" <-> "OE2" Residue "F3 TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F3 GLU 146": "OE1" <-> "OE2" Residue "F3 GLU 155": "OE1" <-> "OE2" Residue "F3 PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F3 TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F3 GLU 240": "OE1" <-> "OE2" Residue "A4 PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A4 ARG 90": "NH1" <-> "NH2" Residue "A4 GLU 107": "OE1" <-> "OE2" Residue "B4 PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B4 ARG 90": "NH1" <-> "NH2" Residue "B4 GLU 107": "OE1" <-> "OE2" Residue "C4 PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C4 ARG 90": "NH1" <-> "NH2" Residue "C4 GLU 107": "OE1" <-> "OE2" Residue "D4 PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D4 ARG 90": "NH1" <-> "NH2" Residue "D4 GLU 107": "OE1" <-> "OE2" Residue "E4 PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E4 ARG 90": "NH1" <-> "NH2" Residue "E4 GLU 107": "OE1" <-> "OE2" Residue "F4 PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F4 ARG 90": "NH1" <-> "NH2" Residue "F4 GLU 107": "OE1" <-> "OE2" Residue "A5 GLU 7": "OE1" <-> "OE2" Residue "A5 GLU 17": "OE1" <-> "OE2" Residue "A5 GLU 28": "OE1" <-> "OE2" Residue "A5 PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A5 GLU 179": "OE1" <-> "OE2" Residue "A5 ASP 237": "OD1" <-> "OD2" Residue "A5 ASP 328": "OD1" <-> "OD2" Residue "A5 ASP 379": "OD1" <-> "OD2" Residue "B5 GLU 28": "OE1" <-> "OE2" Residue "B5 ARG 93": "NH1" <-> "NH2" Residue "B5 ASP 172": "OD1" <-> "OD2" Residue "B5 ASP 221": "OD1" <-> "OD2" Residue "B5 TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C5 GLU 17": "OE1" <-> "OE2" Residue "C5 GLU 28": "OE1" <-> "OE2" Residue "C5 ASP 37": "OD1" <-> "OD2" Residue "C5 TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C5 PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C5 GLU 180": "OE1" <-> "OE2" Residue "C5 ASP 237": "OD1" <-> "OD2" Residue "C5 ASP 328": "OD1" <-> "OD2" Residue "D5 GLU 28": "OE1" <-> "OE2" Residue "D5 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 GLU 57": "OE1" <-> "OE2" Residue "D5 ARG 93": "NH1" <-> "NH2" Residue "D5 ASP 172": "OD1" <-> "OD2" Residue "D5 GLU 180": "OE1" <-> "OE2" Residue "D5 ASP 221": "OD1" <-> "OD2" Residue "D5 TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 ASP 348": "OD1" <-> "OD2" Residue "D5 PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E5 GLU 7": "OE1" <-> "OE2" Residue "E5 GLU 17": "OE1" <-> "OE2" Residue "E5 GLU 28": "OE1" <-> "OE2" Residue "E5 ASP 42": "OD1" <-> "OD2" Residue "E5 TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E5 PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E5 GLU 179": "OE1" <-> "OE2" Residue "E5 GLU 180": "OE1" <-> "OE2" Residue "E5 ASP 328": "OD1" <-> "OD2" Residue "F5 PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F5 GLU 39": "OE1" <-> "OE2" Residue "F5 GLU 57": "OE1" <-> "OE2" Residue "F5 ASP 75": "OD1" <-> "OD2" Residue "F5 ARG 93": "NH1" <-> "NH2" Residue "F5 ASP 172": "OD1" <-> "OD2" Residue "F5 GLU 179": "OE1" <-> "OE2" Residue "F5 GLU 180": "OE1" <-> "OE2" Residue "F5 ASP 221": "OD1" <-> "OD2" Residue "F5 PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F5 TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F5 GLU 342": "OE1" <-> "OE2" Residue "F5 TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F5 PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G5 GLU 7": "OE1" <-> "OE2" Residue "G5 GLU 17": "OE1" <-> "OE2" Residue "G5 GLU 28": "OE1" <-> "OE2" Residue "G5 ASP 37": "OD1" <-> "OD2" Residue "G5 PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G5 ASP 237": "OD1" <-> "OD2" Residue "G5 ASP 328": "OD1" <-> "OD2" Residue "G5 ASP 379": "OD1" <-> "OD2" Residue "H5 GLU 17": "OE1" <-> "OE2" Residue "H5 GLU 28": "OE1" <-> "OE2" Residue "H5 ARG 93": "NH1" <-> "NH2" Residue "H5 PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H5 ASP 172": "OD1" <-> "OD2" Residue "H5 ASP 221": "OD1" <-> "OD2" Residue "H5 ASP 311": "OD1" <-> "OD2" Residue "H5 TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H5 ASP 348": "OD1" <-> "OD2" Residue "H5 PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I5 GLU 17": "OE1" <-> "OE2" Residue "I5 GLU 28": "OE1" <-> "OE2" Residue "I5 ASP 37": "OD1" <-> "OD2" Residue "I5 TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I5 PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I5 ASP 237": "OD1" <-> "OD2" Residue "I5 ASP 328": "OD1" <-> "OD2" Residue "J5 PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J5 GLU 28": "OE1" <-> "OE2" Residue "J5 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J5 ARG 93": "NH1" <-> "NH2" Residue "J5 ASP 172": "OD1" <-> "OD2" Residue "J5 GLU 180": "OE1" <-> "OE2" Residue "J5 ASP 221": "OD1" <-> "OD2" Residue "J5 TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J5 ASP 348": "OD1" <-> "OD2" Residue "J5 PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K5 GLU 7": "OE1" <-> "OE2" Residue "K5 GLU 17": "OE1" <-> "OE2" Residue "K5 GLU 28": "OE1" <-> "OE2" Residue "K5 ASP 42": "OD1" <-> "OD2" Residue "K5 TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K5 PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K5 ASP 172": "OD1" <-> "OD2" Residue "K5 GLU 180": "OE1" <-> "OE2" Residue "K5 ASP 328": "OD1" <-> "OD2" Residue "L5 PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L5 GLU 39": "OE1" <-> "OE2" Residue "L5 ARG 93": "NH1" <-> "NH2" Residue "L5 ASP 172": "OD1" <-> "OD2" Residue "L5 GLU 179": "OE1" <-> "OE2" Residue "L5 GLU 180": "OE1" <-> "OE2" Residue "L5 ASP 221": "OD1" <-> "OD2" Residue "L5 PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L5 TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L5 GLU 342": "OE1" <-> "OE2" Residue "L5 TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L5 PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 ASP 71": "OD1" <-> "OD2" Residue "A6 TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 GLU 330": "OE1" <-> "OE2" Residue "A6 GLU 342": "OE1" <-> "OE2" Residue "A6 GLU 419": "OE1" <-> "OE2" Residue "A6 GLU 467": "OE1" <-> "OE2" Residue "B6 ASP 71": "OD1" <-> "OD2" Residue "B6 TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B6 TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B6 GLU 330": "OE1" <-> "OE2" Residue "B6 GLU 342": "OE1" <-> "OE2" Residue "B6 GLU 419": "OE1" <-> "OE2" Residue "B6 GLU 467": "OE1" <-> "OE2" Residue "C6 ASP 71": "OD1" <-> "OD2" Residue "C6 TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C6 TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C6 GLU 330": "OE1" <-> "OE2" Residue "C6 GLU 342": "OE1" <-> "OE2" Residue "C6 GLU 419": "OE1" <-> "OE2" Residue "C6 GLU 467": "OE1" <-> "OE2" Residue "D6 ASP 71": "OD1" <-> "OD2" Residue "D6 TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 GLU 330": "OE1" <-> "OE2" Residue "D6 GLU 342": "OE1" <-> "OE2" Residue "D6 GLU 419": "OE1" <-> "OE2" Residue "D6 GLU 467": "OE1" <-> "OE2" Residue "E6 ASP 71": "OD1" <-> "OD2" Residue "E6 TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E6 TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E6 GLU 330": "OE1" <-> "OE2" Residue "E6 GLU 342": "OE1" <-> "OE2" Residue "E6 TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E6 GLU 419": "OE1" <-> "OE2" Residue "E6 GLU 467": "OE1" <-> "OE2" Residue "F6 ASP 71": "OD1" <-> "OD2" Residue "F6 TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F6 TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F6 GLU 330": "OE1" <-> "OE2" Residue "F6 GLU 342": "OE1" <-> "OE2" Residue "F6 GLU 419": "OE1" <-> "OE2" Residue "F6 GLU 467": "OE1" <-> "OE2" Residue "A7 ASP 42": "OD1" <-> "OD2" Residue "A7 TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A7 ASP 103": "OD1" <-> "OD2" Residue "A7 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B7 ASP 42": "OD1" <-> "OD2" Residue "B7 TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B7 ASP 103": "OD1" <-> "OD2" Residue "B7 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C7 ASP 42": "OD1" <-> "OD2" Residue "C7 TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C7 ASP 103": "OD1" <-> "OD2" Residue "C7 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D7 ASP 42": "OD1" <-> "OD2" Residue "D7 TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D7 ASP 103": "OD1" <-> "OD2" Residue "D7 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E7 ASP 42": "OD1" <-> "OD2" Residue "E7 TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E7 ASP 103": "OD1" <-> "OD2" Residue "E7 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F7 ASP 42": "OD1" <-> "OD2" Residue "F7 TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F7 ASP 103": "OD1" <-> "OD2" Residue "F7 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 97344 Number of models: 1 Model: "" Number of chains: 48 Chain: "A1" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1091 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "B1" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1091 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "C1" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1091 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "D1" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1091 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "E1" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1091 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "F1" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1091 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "A2" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain breaks: 1 Chain: "B2" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain breaks: 1 Chain: "C2" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain breaks: 1 Chain: "D2" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain breaks: 1 Chain: "E2" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain breaks: 1 Chain: "F2" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain breaks: 1 Chain: "A3" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1944 Classifications: {'peptide': 250} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 10, 'TRANS': 239} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B3" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1944 Classifications: {'peptide': 250} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 10, 'TRANS': 239} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C3" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1944 Classifications: {'peptide': 250} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 10, 'TRANS': 239} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D3" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1944 Classifications: {'peptide': 250} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 10, 'TRANS': 239} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E3" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1944 Classifications: {'peptide': 250} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 10, 'TRANS': 239} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F3" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1944 Classifications: {'peptide': 250} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 10, 'TRANS': 239} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A4" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "B4" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "C4" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "D4" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "E4" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "F4" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "A5" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3101 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 389} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B5" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3103 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 14, 'TRANS': 389} Chain: "C5" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3101 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 389} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D5" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3103 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 14, 'TRANS': 389} Chain: "E5" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3101 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 389} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F5" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3103 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 14, 'TRANS': 389} Chain: "G5" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3101 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 389} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H5" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3103 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 14, 'TRANS': 389} Chain: "I5" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3101 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 389} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J5" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3103 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 14, 'TRANS': 389} Chain: "K5" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3101 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 389} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L5" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3103 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 14, 'TRANS': 389} Chain: "A6" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3721 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 11, 'TRANS': 485} Chain: "B6" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3721 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 11, 'TRANS': 485} Chain: "C6" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3721 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 11, 'TRANS': 485} Chain: "D6" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3721 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 11, 'TRANS': 485} Chain: "E6" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3721 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 11, 'TRANS': 485} Chain: "F6" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3721 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 11, 'TRANS': 485} Chain: "A7" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 883 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain: "B7" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 883 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain: "C7" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 883 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain: "D7" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 883 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain: "E7" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 883 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain: "F7" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 883 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 1, 'TRANS': 108} Time building chain proxies: 39.79, per 1000 atoms: 0.41 Number of scatterers: 97344 At special positions: 0 Unit cell: (213.03, 214.65, 166.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 216 16.00 O 19950 8.00 N 16338 7.00 C 60840 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: 32.20 Conformation dependent library (CDL) restraints added in 11.4 seconds 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23436 Finding SS restraints... Secondary structure from input PDB file: 348 helices and 182 sheets defined 30.3% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'A1' and resid 69 through 80 Processing helix chain 'B1' and resid 69 through 80 Processing helix chain 'C1' and resid 69 through 80 Processing helix chain 'D1' and resid 69 through 80 Processing helix chain 'E1' and resid 69 through 80 Processing helix chain 'F1' and resid 69 through 80 Processing helix chain 'A2' and resid 2 through 10 removed outlier: 3.579A pdb=" N LEUA2 10 " --> pdb=" O ASNA2 6 " (cutoff:3.500A) Processing helix chain 'A2' and resid 19 through 48 removed outlier: 3.867A pdb=" N TYRA2 36 " --> pdb=" O THRA2 32 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLYA2 44 " --> pdb=" O ILEA2 40 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASNA2 45 " --> pdb=" O ALAA2 41 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASPA2 48 " --> pdb=" O GLYA2 44 " (cutoff:3.500A) Processing helix chain 'A2' and resid 54 through 64 Processing helix chain 'A2' and resid 117 through 133 removed outlier: 3.690A pdb=" N ILEA2 133 " --> pdb=" O ALAA2 129 " (cutoff:3.500A) Processing helix chain 'A2' and resid 145 through 154 removed outlier: 3.857A pdb=" N VALA2 149 " --> pdb=" O SERA2 145 " (cutoff:3.500A) Processing helix chain 'A2' and resid 177 through 186 removed outlier: 3.656A pdb=" N LEUA2 181 " --> pdb=" O ASPA2 177 " (cutoff:3.500A) Processing helix chain 'B2' and resid 2 through 10 removed outlier: 3.578A pdb=" N LEUB2 10 " --> pdb=" O ASNB2 6 " (cutoff:3.500A) Processing helix chain 'B2' and resid 19 through 48 removed outlier: 3.867A pdb=" N TYRB2 36 " --> pdb=" O THRB2 32 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLYB2 44 " --> pdb=" O ILEB2 40 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASNB2 45 " --> pdb=" O ALAB2 41 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASPB2 48 " --> pdb=" O GLYB2 44 " (cutoff:3.500A) Processing helix chain 'B2' and resid 54 through 64 Processing helix chain 'B2' and resid 117 through 133 removed outlier: 3.689A pdb=" N ILEB2 133 " --> pdb=" O ALAB2 129 " (cutoff:3.500A) Processing helix chain 'B2' and resid 145 through 154 removed outlier: 3.857A pdb=" N VALB2 149 " --> pdb=" O SERB2 145 " (cutoff:3.500A) Processing helix chain 'B2' and resid 177 through 186 removed outlier: 3.656A pdb=" N LEUB2 181 " --> pdb=" O ASPB2 177 " (cutoff:3.500A) Processing helix chain 'C2' and resid 2 through 10 removed outlier: 3.578A pdb=" N LEUC2 10 " --> pdb=" O ASNC2 6 " (cutoff:3.500A) Processing helix chain 'C2' and resid 19 through 48 removed outlier: 3.867A pdb=" N TYRC2 36 " --> pdb=" O THRC2 32 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLYC2 44 " --> pdb=" O ILEC2 40 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASNC2 45 " --> pdb=" O ALAC2 41 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASPC2 48 " --> pdb=" O GLYC2 44 " (cutoff:3.500A) Processing helix chain 'C2' and resid 54 through 64 Processing helix chain 'C2' and resid 117 through 133 removed outlier: 3.689A pdb=" N ILEC2 133 " --> pdb=" O ALAC2 129 " (cutoff:3.500A) Processing helix chain 'C2' and resid 145 through 154 removed outlier: 3.857A pdb=" N VALC2 149 " --> pdb=" O SERC2 145 " (cutoff:3.500A) Processing helix chain 'C2' and resid 177 through 186 removed outlier: 3.656A pdb=" N LEUC2 181 " --> pdb=" O ASPC2 177 " (cutoff:3.500A) Processing helix chain 'D2' and resid 2 through 10 removed outlier: 3.578A pdb=" N LEUD2 10 " --> pdb=" O ASND2 6 " (cutoff:3.500A) Processing helix chain 'D2' and resid 19 through 48 removed outlier: 3.868A pdb=" N TYRD2 36 " --> pdb=" O THRD2 32 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLYD2 44 " --> pdb=" O ILED2 40 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASND2 45 " --> pdb=" O ALAD2 41 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASPD2 48 " --> pdb=" O GLYD2 44 " (cutoff:3.500A) Processing helix chain 'D2' and resid 54 through 64 Processing helix chain 'D2' and resid 117 through 133 removed outlier: 3.690A pdb=" N ILED2 133 " --> pdb=" O ALAD2 129 " (cutoff:3.500A) Processing helix chain 'D2' and resid 145 through 154 removed outlier: 3.856A pdb=" N VALD2 149 " --> pdb=" O SERD2 145 " (cutoff:3.500A) Processing helix chain 'D2' and resid 177 through 186 removed outlier: 3.656A pdb=" N LEUD2 181 " --> pdb=" O ASPD2 177 " (cutoff:3.500A) Processing helix chain 'E2' and resid 2 through 10 removed outlier: 3.578A pdb=" N LEUE2 10 " --> pdb=" O ASNE2 6 " (cutoff:3.500A) Processing helix chain 'E2' and resid 19 through 48 removed outlier: 3.866A pdb=" N TYRE2 36 " --> pdb=" O THRE2 32 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLYE2 44 " --> pdb=" O ILEE2 40 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASNE2 45 " --> pdb=" O ALAE2 41 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASPE2 48 " --> pdb=" O GLYE2 44 " (cutoff:3.500A) Processing helix chain 'E2' and resid 54 through 64 Processing helix chain 'E2' and resid 117 through 133 removed outlier: 3.690A pdb=" N ILEE2 133 " --> pdb=" O ALAE2 129 " (cutoff:3.500A) Processing helix chain 'E2' and resid 145 through 154 removed outlier: 3.857A pdb=" N VALE2 149 " --> pdb=" O SERE2 145 " (cutoff:3.500A) Processing helix chain 'E2' and resid 177 through 186 removed outlier: 3.656A pdb=" N LEUE2 181 " --> pdb=" O ASPE2 177 " (cutoff:3.500A) Processing helix chain 'F2' and resid 2 through 10 removed outlier: 3.579A pdb=" N LEUF2 10 " --> pdb=" O ASNF2 6 " (cutoff:3.500A) Processing helix chain 'F2' and resid 19 through 48 removed outlier: 3.867A pdb=" N TYRF2 36 " --> pdb=" O THRF2 32 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLYF2 44 " --> pdb=" O ILEF2 40 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASNF2 45 " --> pdb=" O ALAF2 41 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASPF2 48 " --> pdb=" O GLYF2 44 " (cutoff:3.500A) Processing helix chain 'F2' and resid 54 through 64 Processing helix chain 'F2' and resid 117 through 133 removed outlier: 3.690A pdb=" N ILEF2 133 " --> pdb=" O ALAF2 129 " (cutoff:3.500A) Processing helix chain 'F2' and resid 145 through 154 removed outlier: 3.856A pdb=" N VALF2 149 " --> pdb=" O SERF2 145 " (cutoff:3.500A) Processing helix chain 'F2' and resid 177 through 186 removed outlier: 3.656A pdb=" N LEUF2 181 " --> pdb=" O ASPF2 177 " (cutoff:3.500A) Processing helix chain 'A3' and resid 4 through 11 removed outlier: 3.520A pdb=" N VALA3 8 " --> pdb=" O VALA3 4 " (cutoff:3.500A) Processing helix chain 'A3' and resid 104 through 128 removed outlier: 3.502A pdb=" N ILEA3 108 " --> pdb=" O GLNA3 104 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASPA3 117 " --> pdb=" O SERA3 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALAA3 118 " --> pdb=" O GLNA3 114 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ALAA3 121 " --> pdb=" O ASPA3 117 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ALAA3 122 " --> pdb=" O ALAA3 118 " (cutoff:3.500A) Processing helix chain 'A3' and resid 132 through 137 Processing helix chain 'A3' and resid 145 through 161 removed outlier: 3.632A pdb=" N ARGA3 161 " --> pdb=" O LEUA3 157 " (cutoff:3.500A) Processing helix chain 'A3' and resid 215 through 220 removed outlier: 4.651A pdb=" N GLYA3 220 " --> pdb=" O LYSA3 216 " (cutoff:3.500A) Processing helix chain 'A3' and resid 232 through 236 Processing helix chain 'A3' and resid 244 through 249 removed outlier: 3.526A pdb=" N VALA3 248 " --> pdb=" O LEUA3 244 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLYA3 249 " --> pdb=" O SERA3 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A3' and resid 244 through 249' Processing helix chain 'B3' and resid 4 through 11 removed outlier: 3.519A pdb=" N VALB3 8 " --> pdb=" O VALB3 4 " (cutoff:3.500A) Processing helix chain 'B3' and resid 104 through 128 removed outlier: 3.503A pdb=" N ILEB3 108 " --> pdb=" O GLNB3 104 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASPB3 117 " --> pdb=" O SERB3 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALAB3 118 " --> pdb=" O GLNB3 114 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ALAB3 121 " --> pdb=" O ASPB3 117 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ALAB3 122 " --> pdb=" O ALAB3 118 " (cutoff:3.500A) Processing helix chain 'B3' and resid 132 through 137 Processing helix chain 'B3' and resid 145 through 161 removed outlier: 3.631A pdb=" N ARGB3 161 " --> pdb=" O LEUB3 157 " (cutoff:3.500A) Processing helix chain 'B3' and resid 215 through 220 removed outlier: 4.650A pdb=" N GLYB3 220 " --> pdb=" O LYSB3 216 " (cutoff:3.500A) Processing helix chain 'B3' and resid 232 through 236 Processing helix chain 'B3' and resid 244 through 249 removed outlier: 3.526A pdb=" N VALB3 248 " --> pdb=" O LEUB3 244 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLYB3 249 " --> pdb=" O SERB3 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B3' and resid 244 through 249' Processing helix chain 'C3' and resid 4 through 11 removed outlier: 3.521A pdb=" N VALC3 8 " --> pdb=" O VALC3 4 " (cutoff:3.500A) Processing helix chain 'C3' and resid 104 through 128 removed outlier: 3.502A pdb=" N ILEC3 108 " --> pdb=" O GLNC3 104 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASPC3 117 " --> pdb=" O SERC3 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALAC3 118 " --> pdb=" O GLNC3 114 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ALAC3 121 " --> pdb=" O ASPC3 117 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ALAC3 122 " --> pdb=" O ALAC3 118 " (cutoff:3.500A) Processing helix chain 'C3' and resid 132 through 137 Processing helix chain 'C3' and resid 145 through 161 removed outlier: 3.632A pdb=" N ARGC3 161 " --> pdb=" O LEUC3 157 " (cutoff:3.500A) Processing helix chain 'C3' and resid 215 through 220 removed outlier: 4.650A pdb=" N GLYC3 220 " --> pdb=" O LYSC3 216 " (cutoff:3.500A) Processing helix chain 'C3' and resid 232 through 236 Processing helix chain 'C3' and resid 244 through 249 removed outlier: 3.527A pdb=" N VALC3 248 " --> pdb=" O LEUC3 244 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLYC3 249 " --> pdb=" O SERC3 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'C3' and resid 244 through 249' Processing helix chain 'D3' and resid 4 through 11 removed outlier: 3.520A pdb=" N VALD3 8 " --> pdb=" O VALD3 4 " (cutoff:3.500A) Processing helix chain 'D3' and resid 104 through 128 removed outlier: 3.503A pdb=" N ILED3 108 " --> pdb=" O GLND3 104 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASPD3 117 " --> pdb=" O SERD3 113 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALAD3 118 " --> pdb=" O GLND3 114 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ALAD3 121 " --> pdb=" O ASPD3 117 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ALAD3 122 " --> pdb=" O ALAD3 118 " (cutoff:3.500A) Processing helix chain 'D3' and resid 132 through 137 Processing helix chain 'D3' and resid 145 through 161 removed outlier: 3.631A pdb=" N ARGD3 161 " --> pdb=" O LEUD3 157 " (cutoff:3.500A) Processing helix chain 'D3' and resid 215 through 220 removed outlier: 4.650A pdb=" N GLYD3 220 " --> pdb=" O LYSD3 216 " (cutoff:3.500A) Processing helix chain 'D3' and resid 232 through 236 Processing helix chain 'D3' and resid 244 through 249 removed outlier: 3.527A pdb=" N VALD3 248 " --> pdb=" O LEUD3 244 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLYD3 249 " --> pdb=" O SERD3 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'D3' and resid 244 through 249' Processing helix chain 'E3' and resid 4 through 11 removed outlier: 3.519A pdb=" N VALE3 8 " --> pdb=" O VALE3 4 " (cutoff:3.500A) Processing helix chain 'E3' and resid 104 through 128 removed outlier: 3.502A pdb=" N ILEE3 108 " --> pdb=" O GLNE3 104 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASPE3 117 " --> pdb=" O SERE3 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALAE3 118 " --> pdb=" O GLNE3 114 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ALAE3 121 " --> pdb=" O ASPE3 117 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ALAE3 122 " --> pdb=" O ALAE3 118 " (cutoff:3.500A) Processing helix chain 'E3' and resid 132 through 137 Processing helix chain 'E3' and resid 145 through 161 removed outlier: 3.631A pdb=" N ARGE3 161 " --> pdb=" O LEUE3 157 " (cutoff:3.500A) Processing helix chain 'E3' and resid 215 through 220 removed outlier: 4.650A pdb=" N GLYE3 220 " --> pdb=" O LYSE3 216 " (cutoff:3.500A) Processing helix chain 'E3' and resid 232 through 236 Processing helix chain 'E3' and resid 244 through 249 removed outlier: 3.526A pdb=" N VALE3 248 " --> pdb=" O LEUE3 244 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLYE3 249 " --> pdb=" O SERE3 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'E3' and resid 244 through 249' Processing helix chain 'F3' and resid 4 through 11 removed outlier: 3.520A pdb=" N VALF3 8 " --> pdb=" O VALF3 4 " (cutoff:3.500A) Processing helix chain 'F3' and resid 104 through 128 removed outlier: 3.502A pdb=" N ILEF3 108 " --> pdb=" O GLNF3 104 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASPF3 117 " --> pdb=" O SERF3 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALAF3 118 " --> pdb=" O GLNF3 114 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ALAF3 121 " --> pdb=" O ASPF3 117 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ALAF3 122 " --> pdb=" O ALAF3 118 " (cutoff:3.500A) Processing helix chain 'F3' and resid 132 through 137 Processing helix chain 'F3' and resid 145 through 161 removed outlier: 3.632A pdb=" N ARGF3 161 " --> pdb=" O LEUF3 157 " (cutoff:3.500A) Processing helix chain 'F3' and resid 215 through 220 removed outlier: 4.651A pdb=" N GLYF3 220 " --> pdb=" O LYSF3 216 " (cutoff:3.500A) Processing helix chain 'F3' and resid 232 through 236 Processing helix chain 'F3' and resid 244 through 249 removed outlier: 3.527A pdb=" N VALF3 248 " --> pdb=" O LEUF3 244 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLYF3 249 " --> pdb=" O SERF3 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'F3' and resid 244 through 249' Processing helix chain 'A4' and resid 90 through 94 removed outlier: 4.512A pdb=" N PHEA4 94 " --> pdb=" O ALAA4 91 " (cutoff:3.500A) Processing helix chain 'A4' and resid 105 through 114 removed outlier: 3.825A pdb=" N GLNA4 111 " --> pdb=" O GLUA4 107 " (cutoff:3.500A) Processing helix chain 'B4' and resid 90 through 94 removed outlier: 4.512A pdb=" N PHEB4 94 " --> pdb=" O ALAB4 91 " (cutoff:3.500A) Processing helix chain 'B4' and resid 105 through 114 removed outlier: 3.826A pdb=" N GLNB4 111 " --> pdb=" O GLUB4 107 " (cutoff:3.500A) Processing helix chain 'C4' and resid 90 through 94 removed outlier: 4.512A pdb=" N PHEC4 94 " --> pdb=" O ALAC4 91 " (cutoff:3.500A) Processing helix chain 'C4' and resid 105 through 114 removed outlier: 3.826A pdb=" N GLNC4 111 " --> pdb=" O GLUC4 107 " (cutoff:3.500A) Processing helix chain 'D4' and resid 90 through 94 removed outlier: 4.512A pdb=" N PHED4 94 " --> pdb=" O ALAD4 91 " (cutoff:3.500A) Processing helix chain 'D4' and resid 105 through 114 removed outlier: 3.826A pdb=" N GLND4 111 " --> pdb=" O GLUD4 107 " (cutoff:3.500A) Processing helix chain 'E4' and resid 90 through 94 removed outlier: 4.511A pdb=" N PHEE4 94 " --> pdb=" O ALAE4 91 " (cutoff:3.500A) Processing helix chain 'E4' and resid 105 through 114 removed outlier: 3.825A pdb=" N GLNE4 111 " --> pdb=" O GLUE4 107 " (cutoff:3.500A) Processing helix chain 'F4' and resid 90 through 94 removed outlier: 4.512A pdb=" N PHEF4 94 " --> pdb=" O ALAF4 91 " (cutoff:3.500A) Processing helix chain 'F4' and resid 105 through 114 removed outlier: 3.825A pdb=" N GLNF4 111 " --> pdb=" O GLUF4 107 " (cutoff:3.500A) Processing helix chain 'A5' and resid 14 through 30 Processing helix chain 'A5' and resid 40 through 66 Processing helix chain 'A5' and resid 75 through 80 removed outlier: 3.893A pdb=" N ILEA5 80 " --> pdb=" O META5 76 " (cutoff:3.500A) Processing helix chain 'A5' and resid 80 through 85 Processing helix chain 'A5' and resid 181 through 192 removed outlier: 3.973A pdb=" N SERA5 192 " --> pdb=" O ARGA5 188 " (cutoff:3.500A) Processing helix chain 'A5' and resid 199 through 208 removed outlier: 4.143A pdb=" N ILEA5 204 " --> pdb=" O THRA5 200 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYRA5 205 " --> pdb=" O ILEA5 201 " (cutoff:3.500A) Processing helix chain 'A5' and resid 235 through 240 removed outlier: 3.629A pdb=" N LEUA5 239 " --> pdb=" O PROA5 236 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASNA5 240 " --> pdb=" O ASPA5 237 " (cutoff:3.500A) Processing helix chain 'A5' and resid 260 through 272 Processing helix chain 'A5' and resid 330 through 338 Processing helix chain 'A5' and resid 348 through 353 Processing helix chain 'A5' and resid 354 through 357 Processing helix chain 'B5' and resid 14 through 30 Processing helix chain 'B5' and resid 40 through 66 Processing helix chain 'B5' and resid 74 through 82 Processing helix chain 'B5' and resid 181 through 192 removed outlier: 3.833A pdb=" N LEUB5 187 " --> pdb=" O GLUB5 183 " (cutoff:3.500A) Processing helix chain 'B5' and resid 194 through 198 removed outlier: 3.938A pdb=" N GLNB5 198 " --> pdb=" O ASNB5 195 " (cutoff:3.500A) Processing helix chain 'B5' and resid 200 through 209 removed outlier: 4.009A pdb=" N TYRB5 205 " --> pdb=" O ILEB5 201 " (cutoff:3.500A) Processing helix chain 'B5' and resid 235 through 239 removed outlier: 3.580A pdb=" N ILEB5 238 " --> pdb=" O ASNB5 235 " (cutoff:3.500A) Processing helix chain 'B5' and resid 260 through 271 Processing helix chain 'B5' and resid 328 through 337 Processing helix chain 'B5' and resid 349 through 356 removed outlier: 3.666A pdb=" N TYRB5 353 " --> pdb=" O ALAB5 349 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLNB5 354 " --> pdb=" O ASPB5 350 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLNB5 355 " --> pdb=" O ALAB5 351 " (cutoff:3.500A) Processing helix chain 'C5' and resid 14 through 30 Processing helix chain 'C5' and resid 40 through 66 Processing helix chain 'C5' and resid 75 through 80 removed outlier: 3.873A pdb=" N ILEC5 80 " --> pdb=" O METC5 76 " (cutoff:3.500A) Processing helix chain 'C5' and resid 80 through 85 Processing helix chain 'C5' and resid 181 through 192 removed outlier: 3.975A pdb=" N SERC5 192 " --> pdb=" O ARGC5 188 " (cutoff:3.500A) Processing helix chain 'C5' and resid 199 through 208 removed outlier: 4.185A pdb=" N ILEC5 204 " --> pdb=" O THRC5 200 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYRC5 205 " --> pdb=" O ILEC5 201 " (cutoff:3.500A) Processing helix chain 'C5' and resid 235 through 240 removed outlier: 3.603A pdb=" N LEUC5 239 " --> pdb=" O PROC5 236 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASNC5 240 " --> pdb=" O ASPC5 237 " (cutoff:3.500A) Processing helix chain 'C5' and resid 260 through 272 Processing helix chain 'C5' and resid 330 through 338 Processing helix chain 'C5' and resid 348 through 353 Processing helix chain 'C5' and resid 354 through 357 Processing helix chain 'D5' and resid 14 through 30 Processing helix chain 'D5' and resid 40 through 66 Processing helix chain 'D5' and resid 74 through 82 Processing helix chain 'D5' and resid 181 through 192 removed outlier: 3.828A pdb=" N LEUD5 187 " --> pdb=" O GLUD5 183 " (cutoff:3.500A) Processing helix chain 'D5' and resid 194 through 198 removed outlier: 3.927A pdb=" N GLND5 198 " --> pdb=" O ASND5 195 " (cutoff:3.500A) Processing helix chain 'D5' and resid 200 through 209 removed outlier: 4.025A pdb=" N TYRD5 205 " --> pdb=" O ILED5 201 " (cutoff:3.500A) Processing helix chain 'D5' and resid 235 through 239 removed outlier: 3.615A pdb=" N ILED5 238 " --> pdb=" O ASND5 235 " (cutoff:3.500A) Processing helix chain 'D5' and resid 260 through 271 Processing helix chain 'D5' and resid 328 through 337 Processing helix chain 'D5' and resid 348 through 356 removed outlier: 3.612A pdb=" N LEUD5 352 " --> pdb=" O ASPD5 348 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYRD5 353 " --> pdb=" O ALAD5 349 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLND5 354 " --> pdb=" O ASPD5 350 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLND5 355 " --> pdb=" O ALAD5 351 " (cutoff:3.500A) Processing helix chain 'E5' and resid 14 through 30 Processing helix chain 'E5' and resid 40 through 66 Processing helix chain 'E5' and resid 75 through 80 removed outlier: 3.817A pdb=" N ILEE5 80 " --> pdb=" O METE5 76 " (cutoff:3.500A) Processing helix chain 'E5' and resid 80 through 85 Processing helix chain 'E5' and resid 181 through 192 removed outlier: 3.980A pdb=" N SERE5 192 " --> pdb=" O ARGE5 188 " (cutoff:3.500A) Processing helix chain 'E5' and resid 199 through 208 removed outlier: 4.171A pdb=" N ILEE5 204 " --> pdb=" O THRE5 200 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYRE5 205 " --> pdb=" O ILEE5 201 " (cutoff:3.500A) Processing helix chain 'E5' and resid 235 through 240 removed outlier: 3.634A pdb=" N LEUE5 239 " --> pdb=" O PROE5 236 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASNE5 240 " --> pdb=" O ASPE5 237 " (cutoff:3.500A) Processing helix chain 'E5' and resid 260 through 272 Processing helix chain 'E5' and resid 330 through 338 Processing helix chain 'E5' and resid 348 through 353 Processing helix chain 'E5' and resid 354 through 357 Processing helix chain 'F5' and resid 14 through 30 Processing helix chain 'F5' and resid 40 through 66 Processing helix chain 'F5' and resid 74 through 82 Processing helix chain 'F5' and resid 181 through 192 removed outlier: 3.831A pdb=" N LEUF5 187 " --> pdb=" O GLUF5 183 " (cutoff:3.500A) Processing helix chain 'F5' and resid 194 through 198 removed outlier: 3.952A pdb=" N GLNF5 198 " --> pdb=" O ASNF5 195 " (cutoff:3.500A) Processing helix chain 'F5' and resid 200 through 209 removed outlier: 4.016A pdb=" N TYRF5 205 " --> pdb=" O ILEF5 201 " (cutoff:3.500A) Processing helix chain 'F5' and resid 235 through 239 removed outlier: 3.617A pdb=" N ILEF5 238 " --> pdb=" O ASNF5 235 " (cutoff:3.500A) Processing helix chain 'F5' and resid 260 through 271 Processing helix chain 'F5' and resid 328 through 337 Processing helix chain 'F5' and resid 348 through 356 removed outlier: 3.697A pdb=" N LEUF5 352 " --> pdb=" O ASPF5 348 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYRF5 353 " --> pdb=" O ALAF5 349 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLNF5 354 " --> pdb=" O ASPF5 350 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLNF5 355 " --> pdb=" O ALAF5 351 " (cutoff:3.500A) Processing helix chain 'G5' and resid 14 through 30 Processing helix chain 'G5' and resid 40 through 66 Processing helix chain 'G5' and resid 75 through 80 removed outlier: 3.884A pdb=" N ILEG5 80 " --> pdb=" O METG5 76 " (cutoff:3.500A) Processing helix chain 'G5' and resid 80 through 85 Processing helix chain 'G5' and resid 181 through 192 removed outlier: 3.975A pdb=" N SERG5 192 " --> pdb=" O ARGG5 188 " (cutoff:3.500A) Processing helix chain 'G5' and resid 199 through 208 removed outlier: 4.147A pdb=" N ILEG5 204 " --> pdb=" O THRG5 200 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYRG5 205 " --> pdb=" O ILEG5 201 " (cutoff:3.500A) Processing helix chain 'G5' and resid 235 through 240 removed outlier: 3.629A pdb=" N LEUG5 239 " --> pdb=" O PROG5 236 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASNG5 240 " --> pdb=" O ASPG5 237 " (cutoff:3.500A) Processing helix chain 'G5' and resid 260 through 272 Processing helix chain 'G5' and resid 330 through 338 Processing helix chain 'G5' and resid 348 through 353 Processing helix chain 'G5' and resid 354 through 357 Processing helix chain 'H5' and resid 14 through 30 Processing helix chain 'H5' and resid 40 through 66 Processing helix chain 'H5' and resid 74 through 82 Processing helix chain 'H5' and resid 181 through 192 removed outlier: 3.819A pdb=" N LEUH5 187 " --> pdb=" O GLUH5 183 " (cutoff:3.500A) Processing helix chain 'H5' and resid 194 through 198 removed outlier: 3.932A pdb=" N GLNH5 198 " --> pdb=" O ASNH5 195 " (cutoff:3.500A) Processing helix chain 'H5' and resid 200 through 209 removed outlier: 4.005A pdb=" N TYRH5 205 " --> pdb=" O ILEH5 201 " (cutoff:3.500A) Processing helix chain 'H5' and resid 235 through 239 removed outlier: 3.580A pdb=" N ILEH5 238 " --> pdb=" O ASNH5 235 " (cutoff:3.500A) Processing helix chain 'H5' and resid 260 through 271 Processing helix chain 'H5' and resid 328 through 337 Processing helix chain 'H5' and resid 349 through 356 removed outlier: 3.648A pdb=" N TYRH5 353 " --> pdb=" O ALAH5 349 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLNH5 354 " --> pdb=" O ASPH5 350 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLNH5 355 " --> pdb=" O ALAH5 351 " (cutoff:3.500A) Processing helix chain 'I5' and resid 14 through 30 Processing helix chain 'I5' and resid 40 through 66 Processing helix chain 'I5' and resid 75 through 80 removed outlier: 3.869A pdb=" N ILEI5 80 " --> pdb=" O METI5 76 " (cutoff:3.500A) Processing helix chain 'I5' and resid 80 through 85 Processing helix chain 'I5' and resid 181 through 192 removed outlier: 3.979A pdb=" N SERI5 192 " --> pdb=" O ARGI5 188 " (cutoff:3.500A) Processing helix chain 'I5' and resid 199 through 208 removed outlier: 4.184A pdb=" N ILEI5 204 " --> pdb=" O THRI5 200 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYRI5 205 " --> pdb=" O ILEI5 201 " (cutoff:3.500A) Processing helix chain 'I5' and resid 235 through 240 removed outlier: 3.605A pdb=" N LEUI5 239 " --> pdb=" O PROI5 236 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASNI5 240 " --> pdb=" O ASPI5 237 " (cutoff:3.500A) Processing helix chain 'I5' and resid 260 through 272 Processing helix chain 'I5' and resid 330 through 338 Processing helix chain 'I5' and resid 348 through 353 Processing helix chain 'I5' and resid 354 through 357 Processing helix chain 'J5' and resid 14 through 30 Processing helix chain 'J5' and resid 40 through 66 Processing helix chain 'J5' and resid 74 through 82 Processing helix chain 'J5' and resid 181 through 192 removed outlier: 3.831A pdb=" N LEUJ5 187 " --> pdb=" O GLUJ5 183 " (cutoff:3.500A) Processing helix chain 'J5' and resid 194 through 198 removed outlier: 3.933A pdb=" N GLNJ5 198 " --> pdb=" O ASNJ5 195 " (cutoff:3.500A) Processing helix chain 'J5' and resid 200 through 209 removed outlier: 4.023A pdb=" N TYRJ5 205 " --> pdb=" O ILEJ5 201 " (cutoff:3.500A) Processing helix chain 'J5' and resid 235 through 239 removed outlier: 3.602A pdb=" N ILEJ5 238 " --> pdb=" O ASNJ5 235 " (cutoff:3.500A) Processing helix chain 'J5' and resid 260 through 271 Processing helix chain 'J5' and resid 328 through 338 removed outlier: 3.857A pdb=" N LEUJ5 338 " --> pdb=" O ASNJ5 334 " (cutoff:3.500A) Processing helix chain 'J5' and resid 348 through 356 removed outlier: 3.643A pdb=" N LEUJ5 352 " --> pdb=" O ASPJ5 348 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYRJ5 353 " --> pdb=" O ALAJ5 349 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLNJ5 354 " --> pdb=" O ASPJ5 350 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLNJ5 355 " --> pdb=" O ALAJ5 351 " (cutoff:3.500A) Processing helix chain 'K5' and resid 14 through 30 Processing helix chain 'K5' and resid 40 through 66 Processing helix chain 'K5' and resid 75 through 80 removed outlier: 3.812A pdb=" N ILEK5 80 " --> pdb=" O METK5 76 " (cutoff:3.500A) Processing helix chain 'K5' and resid 80 through 85 Processing helix chain 'K5' and resid 181 through 192 removed outlier: 3.979A pdb=" N SERK5 192 " --> pdb=" O ARGK5 188 " (cutoff:3.500A) Processing helix chain 'K5' and resid 199 through 208 removed outlier: 4.171A pdb=" N ILEK5 204 " --> pdb=" O THRK5 200 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYRK5 205 " --> pdb=" O ILEK5 201 " (cutoff:3.500A) Processing helix chain 'K5' and resid 235 through 240 removed outlier: 3.631A pdb=" N LEUK5 239 " --> pdb=" O PROK5 236 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASNK5 240 " --> pdb=" O ASPK5 237 " (cutoff:3.500A) Processing helix chain 'K5' and resid 260 through 272 Processing helix chain 'K5' and resid 330 through 338 Processing helix chain 'K5' and resid 348 through 353 Processing helix chain 'K5' and resid 354 through 357 Processing helix chain 'L5' and resid 14 through 30 Processing helix chain 'L5' and resid 40 through 66 Processing helix chain 'L5' and resid 74 through 82 Processing helix chain 'L5' and resid 181 through 192 removed outlier: 3.828A pdb=" N LEUL5 187 " --> pdb=" O GLUL5 183 " (cutoff:3.500A) Processing helix chain 'L5' and resid 194 through 198 removed outlier: 3.949A pdb=" N GLNL5 198 " --> pdb=" O ASNL5 195 " (cutoff:3.500A) Processing helix chain 'L5' and resid 200 through 209 removed outlier: 4.020A pdb=" N TYRL5 205 " --> pdb=" O ILEL5 201 " (cutoff:3.500A) Processing helix chain 'L5' and resid 235 through 239 removed outlier: 3.568A pdb=" N ILEL5 238 " --> pdb=" O ASNL5 235 " (cutoff:3.500A) Processing helix chain 'L5' and resid 260 through 271 Processing helix chain 'L5' and resid 328 through 337 Processing helix chain 'L5' and resid 348 through 356 removed outlier: 3.690A pdb=" N LEUL5 352 " --> pdb=" O ASPL5 348 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYRL5 353 " --> pdb=" O ALAL5 349 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLNL5 354 " --> pdb=" O ASPL5 350 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLNL5 355 " --> pdb=" O ALAL5 351 " (cutoff:3.500A) Processing helix chain 'A6' and resid 3 through 7 removed outlier: 3.658A pdb=" N GLUA6 6 " --> pdb=" O SERA6 3 " (cutoff:3.500A) Processing helix chain 'A6' and resid 48 through 57 removed outlier: 3.606A pdb=" N VALA6 52 " --> pdb=" O THRA6 48 " (cutoff:3.500A) Processing helix chain 'A6' and resid 60 through 71 Processing helix chain 'A6' and resid 75 through 79 Processing helix chain 'A6' and resid 111 through 117 Processing helix chain 'A6' and resid 146 through 158 removed outlier: 3.621A pdb=" N VALA6 150 " --> pdb=" O GLUA6 146 " (cutoff:3.500A) Processing helix chain 'A6' and resid 195 through 200 Processing helix chain 'A6' and resid 223 through 225 No H-bonds generated for 'chain 'A6' and resid 223 through 225' Processing helix chain 'A6' and resid 226 through 235 removed outlier: 3.746A pdb=" N ILEA6 230 " --> pdb=" O GLYA6 226 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLUA6 233 " --> pdb=" O ALAA6 229 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASNA6 235 " --> pdb=" O LYSA6 231 " (cutoff:3.500A) Processing helix chain 'A6' and resid 246 through 248 No H-bonds generated for 'chain 'A6' and resid 246 through 248' Processing helix chain 'A6' and resid 249 through 260 Processing helix chain 'A6' and resid 269 through 273 Processing helix chain 'A6' and resid 279 through 288 Processing helix chain 'A6' and resid 302 through 313 removed outlier: 4.164A pdb=" N ALAA6 306 " --> pdb=" O ARGA6 302 " (cutoff:3.500A) Processing helix chain 'A6' and resid 339 through 350 Processing helix chain 'A6' and resid 371 through 396 removed outlier: 3.881A pdb=" N THRA6 396 " --> pdb=" O LEUA6 392 " (cutoff:3.500A) Processing helix chain 'A6' and resid 403 through 424 Processing helix chain 'A6' and resid 440 through 452 Processing helix chain 'A6' and resid 459 through 463 Processing helix chain 'B6' and resid 3 through 7 removed outlier: 3.659A pdb=" N GLUB6 6 " --> pdb=" O SERB6 3 " (cutoff:3.500A) Processing helix chain 'B6' and resid 48 through 57 removed outlier: 3.604A pdb=" N VALB6 52 " --> pdb=" O THRB6 48 " (cutoff:3.500A) Processing helix chain 'B6' and resid 60 through 71 Processing helix chain 'B6' and resid 75 through 79 Processing helix chain 'B6' and resid 111 through 117 Processing helix chain 'B6' and resid 146 through 158 removed outlier: 3.620A pdb=" N VALB6 150 " --> pdb=" O GLUB6 146 " (cutoff:3.500A) Processing helix chain 'B6' and resid 195 through 200 Processing helix chain 'B6' and resid 223 through 225 No H-bonds generated for 'chain 'B6' and resid 223 through 225' Processing helix chain 'B6' and resid 226 through 235 removed outlier: 3.745A pdb=" N ILEB6 230 " --> pdb=" O GLYB6 226 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLUB6 233 " --> pdb=" O ALAB6 229 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASNB6 235 " --> pdb=" O LYSB6 231 " (cutoff:3.500A) Processing helix chain 'B6' and resid 246 through 248 No H-bonds generated for 'chain 'B6' and resid 246 through 248' Processing helix chain 'B6' and resid 249 through 260 Processing helix chain 'B6' and resid 269 through 273 Processing helix chain 'B6' and resid 279 through 288 Processing helix chain 'B6' and resid 302 through 313 removed outlier: 4.164A pdb=" N ALAB6 306 " --> pdb=" O ARGB6 302 " (cutoff:3.500A) Processing helix chain 'B6' and resid 339 through 350 Processing helix chain 'B6' and resid 371 through 396 removed outlier: 3.882A pdb=" N THRB6 396 " --> pdb=" O LEUB6 392 " (cutoff:3.500A) Processing helix chain 'B6' and resid 403 through 424 Processing helix chain 'B6' and resid 440 through 452 Processing helix chain 'B6' and resid 459 through 463 Processing helix chain 'C6' and resid 3 through 7 removed outlier: 3.659A pdb=" N GLUC6 6 " --> pdb=" O SERC6 3 " (cutoff:3.500A) Processing helix chain 'C6' and resid 48 through 57 removed outlier: 3.605A pdb=" N VALC6 52 " --> pdb=" O THRC6 48 " (cutoff:3.500A) Processing helix chain 'C6' and resid 60 through 71 Processing helix chain 'C6' and resid 75 through 79 Processing helix chain 'C6' and resid 111 through 117 Processing helix chain 'C6' and resid 146 through 158 removed outlier: 3.620A pdb=" N VALC6 150 " --> pdb=" O GLUC6 146 " (cutoff:3.500A) Processing helix chain 'C6' and resid 195 through 200 Processing helix chain 'C6' and resid 223 through 225 No H-bonds generated for 'chain 'C6' and resid 223 through 225' Processing helix chain 'C6' and resid 226 through 235 removed outlier: 3.746A pdb=" N ILEC6 230 " --> pdb=" O GLYC6 226 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLUC6 233 " --> pdb=" O ALAC6 229 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASNC6 235 " --> pdb=" O LYSC6 231 " (cutoff:3.500A) Processing helix chain 'C6' and resid 246 through 248 No H-bonds generated for 'chain 'C6' and resid 246 through 248' Processing helix chain 'C6' and resid 249 through 260 Processing helix chain 'C6' and resid 269 through 273 Processing helix chain 'C6' and resid 279 through 288 Processing helix chain 'C6' and resid 302 through 313 removed outlier: 4.163A pdb=" N ALAC6 306 " --> pdb=" O ARGC6 302 " (cutoff:3.500A) Processing helix chain 'C6' and resid 339 through 350 Processing helix chain 'C6' and resid 371 through 396 removed outlier: 3.882A pdb=" N THRC6 396 " --> pdb=" O LEUC6 392 " (cutoff:3.500A) Processing helix chain 'C6' and resid 403 through 424 Processing helix chain 'C6' and resid 440 through 452 Processing helix chain 'C6' and resid 459 through 463 Processing helix chain 'D6' and resid 3 through 7 removed outlier: 3.659A pdb=" N GLUD6 6 " --> pdb=" O SERD6 3 " (cutoff:3.500A) Processing helix chain 'D6' and resid 48 through 57 removed outlier: 3.606A pdb=" N VALD6 52 " --> pdb=" O THRD6 48 " (cutoff:3.500A) Processing helix chain 'D6' and resid 60 through 71 Processing helix chain 'D6' and resid 75 through 79 Processing helix chain 'D6' and resid 111 through 117 Processing helix chain 'D6' and resid 146 through 158 removed outlier: 3.621A pdb=" N VALD6 150 " --> pdb=" O GLUD6 146 " (cutoff:3.500A) Processing helix chain 'D6' and resid 195 through 200 Processing helix chain 'D6' and resid 223 through 225 No H-bonds generated for 'chain 'D6' and resid 223 through 225' Processing helix chain 'D6' and resid 226 through 235 removed outlier: 3.746A pdb=" N ILED6 230 " --> pdb=" O GLYD6 226 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLUD6 233 " --> pdb=" O ALAD6 229 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASND6 235 " --> pdb=" O LYSD6 231 " (cutoff:3.500A) Processing helix chain 'D6' and resid 246 through 248 No H-bonds generated for 'chain 'D6' and resid 246 through 248' Processing helix chain 'D6' and resid 249 through 260 Processing helix chain 'D6' and resid 269 through 273 Processing helix chain 'D6' and resid 279 through 288 Processing helix chain 'D6' and resid 302 through 313 removed outlier: 4.164A pdb=" N ALAD6 306 " --> pdb=" O ARGD6 302 " (cutoff:3.500A) Processing helix chain 'D6' and resid 339 through 350 Processing helix chain 'D6' and resid 371 through 396 removed outlier: 3.881A pdb=" N THRD6 396 " --> pdb=" O LEUD6 392 " (cutoff:3.500A) Processing helix chain 'D6' and resid 403 through 424 Processing helix chain 'D6' and resid 440 through 452 Processing helix chain 'D6' and resid 459 through 463 Processing helix chain 'E6' and resid 3 through 7 removed outlier: 3.658A pdb=" N GLUE6 6 " --> pdb=" O SERE6 3 " (cutoff:3.500A) Processing helix chain 'E6' and resid 48 through 57 removed outlier: 3.604A pdb=" N VALE6 52 " --> pdb=" O THRE6 48 " (cutoff:3.500A) Processing helix chain 'E6' and resid 60 through 71 Processing helix chain 'E6' and resid 75 through 79 Processing helix chain 'E6' and resid 111 through 117 Processing helix chain 'E6' and resid 146 through 158 removed outlier: 3.620A pdb=" N VALE6 150 " --> pdb=" O GLUE6 146 " (cutoff:3.500A) Processing helix chain 'E6' and resid 195 through 200 Processing helix chain 'E6' and resid 223 through 225 No H-bonds generated for 'chain 'E6' and resid 223 through 225' Processing helix chain 'E6' and resid 226 through 235 removed outlier: 3.745A pdb=" N ILEE6 230 " --> pdb=" O GLYE6 226 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLUE6 233 " --> pdb=" O ALAE6 229 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASNE6 235 " --> pdb=" O LYSE6 231 " (cutoff:3.500A) Processing helix chain 'E6' and resid 246 through 248 No H-bonds generated for 'chain 'E6' and resid 246 through 248' Processing helix chain 'E6' and resid 249 through 260 Processing helix chain 'E6' and resid 269 through 273 Processing helix chain 'E6' and resid 279 through 288 Processing helix chain 'E6' and resid 302 through 313 removed outlier: 4.164A pdb=" N ALAE6 306 " --> pdb=" O ARGE6 302 " (cutoff:3.500A) Processing helix chain 'E6' and resid 339 through 350 Processing helix chain 'E6' and resid 371 through 396 removed outlier: 3.881A pdb=" N THRE6 396 " --> pdb=" O LEUE6 392 " (cutoff:3.500A) Processing helix chain 'E6' and resid 403 through 424 Processing helix chain 'E6' and resid 440 through 452 Processing helix chain 'E6' and resid 459 through 463 Processing helix chain 'F6' and resid 3 through 7 removed outlier: 3.659A pdb=" N GLUF6 6 " --> pdb=" O SERF6 3 " (cutoff:3.500A) Processing helix chain 'F6' and resid 48 through 57 removed outlier: 3.605A pdb=" N VALF6 52 " --> pdb=" O THRF6 48 " (cutoff:3.500A) Processing helix chain 'F6' and resid 60 through 71 Processing helix chain 'F6' and resid 75 through 79 Processing helix chain 'F6' and resid 111 through 117 Processing helix chain 'F6' and resid 146 through 158 removed outlier: 3.620A pdb=" N VALF6 150 " --> pdb=" O GLUF6 146 " (cutoff:3.500A) Processing helix chain 'F6' and resid 195 through 200 Processing helix chain 'F6' and resid 223 through 225 No H-bonds generated for 'chain 'F6' and resid 223 through 225' Processing helix chain 'F6' and resid 226 through 235 removed outlier: 3.747A pdb=" N ILEF6 230 " --> pdb=" O GLYF6 226 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLUF6 233 " --> pdb=" O ALAF6 229 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASNF6 235 " --> pdb=" O LYSF6 231 " (cutoff:3.500A) Processing helix chain 'F6' and resid 246 through 248 No H-bonds generated for 'chain 'F6' and resid 246 through 248' Processing helix chain 'F6' and resid 249 through 260 Processing helix chain 'F6' and resid 269 through 273 Processing helix chain 'F6' and resid 279 through 288 Processing helix chain 'F6' and resid 302 through 313 removed outlier: 4.163A pdb=" N ALAF6 306 " --> pdb=" O ARGF6 302 " (cutoff:3.500A) Processing helix chain 'F6' and resid 339 through 350 Processing helix chain 'F6' and resid 371 through 396 removed outlier: 3.882A pdb=" N THRF6 396 " --> pdb=" O LEUF6 392 " (cutoff:3.500A) Processing helix chain 'F6' and resid 403 through 424 Processing helix chain 'F6' and resid 440 through 452 Processing helix chain 'F6' and resid 459 through 463 Processing helix chain 'A7' and resid 26 through 36 Processing helix chain 'A7' and resid 62 through 76 Processing helix chain 'B7' and resid 26 through 36 Processing helix chain 'B7' and resid 62 through 76 Processing helix chain 'C7' and resid 26 through 36 Processing helix chain 'C7' and resid 62 through 76 Processing helix chain 'D7' and resid 26 through 36 Processing helix chain 'D7' and resid 62 through 76 Processing helix chain 'E7' and resid 26 through 36 Processing helix chain 'E7' and resid 62 through 76 Processing helix chain 'F7' and resid 26 through 36 Processing helix chain 'F7' and resid 62 through 76 Processing sheet with id=AA1, first strand: chain 'A1' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A1' and resid 4 through 6 removed outlier: 7.165A pdb=" N GLYA1 89 " --> pdb=" O GLUA1 109 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLUA1 109 " --> pdb=" O GLYA1 89 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N META1 91 " --> pdb=" O THRA1 107 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N THRA1 107 " --> pdb=" O META1 91 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ARGA1 93 " --> pdb=" O THRA1 105 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N THRA1 105 " --> pdb=" O ARGA1 93 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYRA1 95 " --> pdb=" O LYSA1 103 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYSA1 103 " --> pdb=" O TYRA1 95 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLUA1 97 " --> pdb=" O LEUA1 101 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEUA1 101 " --> pdb=" O GLUA1 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A1' and resid 113 through 115 removed outlier: 6.671A pdb=" N VALA1 133 " --> pdb=" O THRA1 114 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEUA1 29 " --> pdb=" O ASPB1 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A1' and resid 38 through 42 removed outlier: 3.892A pdb=" N LEUB3 72 " --> pdb=" O ILEA1 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A1' and resid 119 through 121 removed outlier: 4.187A pdb=" N LEUF1 29 " --> pdb=" O ASPA1 121 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VALF1 133 " --> pdb=" O THRF1 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B1' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'B1' and resid 4 through 6 removed outlier: 7.165A pdb=" N GLYB1 89 " --> pdb=" O GLUB1 109 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLUB1 109 " --> pdb=" O GLYB1 89 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N METB1 91 " --> pdb=" O THRB1 107 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N THRB1 107 " --> pdb=" O METB1 91 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARGB1 93 " --> pdb=" O THRB1 105 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N THRB1 105 " --> pdb=" O ARGB1 93 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYRB1 95 " --> pdb=" O LYSB1 103 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYSB1 103 " --> pdb=" O TYRB1 95 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLUB1 97 " --> pdb=" O LEUB1 101 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEUB1 101 " --> pdb=" O GLUB1 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B1' and resid 113 through 115 removed outlier: 6.671A pdb=" N VALB1 133 " --> pdb=" O THRB1 114 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEUB1 29 " --> pdb=" O ASPC1 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B1' and resid 38 through 42 removed outlier: 3.872A pdb=" N LEUC3 72 " --> pdb=" O ILEB1 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C1' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'C1' and resid 4 through 6 removed outlier: 7.166A pdb=" N GLYC1 89 " --> pdb=" O GLUC1 109 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLUC1 109 " --> pdb=" O GLYC1 89 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N METC1 91 " --> pdb=" O THRC1 107 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THRC1 107 " --> pdb=" O METC1 91 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARGC1 93 " --> pdb=" O THRC1 105 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N THRC1 105 " --> pdb=" O ARGC1 93 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYRC1 95 " --> pdb=" O LYSC1 103 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYSC1 103 " --> pdb=" O TYRC1 95 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLUC1 97 " --> pdb=" O LEUC1 101 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEUC1 101 " --> pdb=" O GLUC1 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C1' and resid 113 through 115 removed outlier: 6.671A pdb=" N VALC1 133 " --> pdb=" O THRC1 114 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEUC1 29 " --> pdb=" O ASPD1 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C1' and resid 38 through 42 removed outlier: 3.960A pdb=" N LEUD3 72 " --> pdb=" O ILEC1 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D1' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'D1' and resid 4 through 6 removed outlier: 7.166A pdb=" N GLYD1 89 " --> pdb=" O GLUD1 109 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLUD1 109 " --> pdb=" O GLYD1 89 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N METD1 91 " --> pdb=" O THRD1 107 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N THRD1 107 " --> pdb=" O METD1 91 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARGD1 93 " --> pdb=" O THRD1 105 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N THRD1 105 " --> pdb=" O ARGD1 93 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYRD1 95 " --> pdb=" O LYSD1 103 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYSD1 103 " --> pdb=" O TYRD1 95 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLUD1 97 " --> pdb=" O LEUD1 101 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEUD1 101 " --> pdb=" O GLUD1 97 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D1' and resid 113 through 115 removed outlier: 6.670A pdb=" N VALD1 133 " --> pdb=" O THRD1 114 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ALAD1 28 " --> pdb=" O METD1 64 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEUD1 29 " --> pdb=" O ASPE1 121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D1' and resid 38 through 42 removed outlier: 3.819A pdb=" N LEUE3 72 " --> pdb=" O ILED1 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E1' and resid 4 through 6 Processing sheet with id=AC1, first strand: chain 'E1' and resid 4 through 6 removed outlier: 7.166A pdb=" N GLYE1 89 " --> pdb=" O GLUE1 109 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLUE1 109 " --> pdb=" O GLYE1 89 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N METE1 91 " --> pdb=" O THRE1 107 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THRE1 107 " --> pdb=" O METE1 91 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARGE1 93 " --> pdb=" O THRE1 105 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N THRE1 105 " --> pdb=" O ARGE1 93 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYRE1 95 " --> pdb=" O LYSE1 103 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYSE1 103 " --> pdb=" O TYRE1 95 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLUE1 97 " --> pdb=" O LEUE1 101 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEUE1 101 " --> pdb=" O GLUE1 97 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E1' and resid 113 through 115 removed outlier: 6.670A pdb=" N VALE1 133 " --> pdb=" O THRE1 114 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ALAE1 28 " --> pdb=" O METE1 64 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEUE1 29 " --> pdb=" O ASPF1 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E1' and resid 38 through 42 removed outlier: 3.978A pdb=" N LEUF3 72 " --> pdb=" O ILEE1 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F1' and resid 4 through 6 Processing sheet with id=AC5, first strand: chain 'F1' and resid 4 through 6 removed outlier: 7.166A pdb=" N GLYF1 89 " --> pdb=" O GLUF1 109 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLUF1 109 " --> pdb=" O GLYF1 89 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N METF1 91 " --> pdb=" O THRF1 107 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N THRF1 107 " --> pdb=" O METF1 91 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARGF1 93 " --> pdb=" O THRF1 105 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N THRF1 105 " --> pdb=" O ARGF1 93 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYRF1 95 " --> pdb=" O LYSF1 103 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYSF1 103 " --> pdb=" O TYRF1 95 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLUF1 97 " --> pdb=" O LEUF1 101 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEUF1 101 " --> pdb=" O GLUF1 97 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F1' and resid 38 through 42 removed outlier: 3.932A pdb=" N LEUA3 72 " --> pdb=" O ILEF1 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A2' and resid 158 through 162 Processing sheet with id=AC8, first strand: chain 'B2' and resid 158 through 162 Processing sheet with id=AC9, first strand: chain 'C2' and resid 158 through 162 Processing sheet with id=AD1, first strand: chain 'D2' and resid 158 through 162 Processing sheet with id=AD2, first strand: chain 'E2' and resid 158 through 162 Processing sheet with id=AD3, first strand: chain 'F2' and resid 158 through 162 Processing sheet with id=AD4, first strand: chain 'A3' and resid 164 through 168 removed outlier: 5.411A pdb=" N VALA3 166 " --> pdb=" O LYSA3 174 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYSA3 174 " --> pdb=" O VALA3 166 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VALA3 168 " --> pdb=" O ASPA3 172 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASPA3 172 " --> pdb=" O VALA3 168 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEUA3 178 " --> pdb=" O GLNA3 199 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLNA3 199 " --> pdb=" O LEUA3 178 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VALA3 68 " --> pdb=" O ARGA3 30 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARGA3 30 " --> pdb=" O VALA3 68 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASPB3 172 " --> pdb=" O VALB3 168 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VALB3 168 " --> pdb=" O ASPB3 172 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYSB3 174 " --> pdb=" O VALB3 166 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VALB3 166 " --> pdb=" O LYSB3 174 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B3' and resid 164 through 168 removed outlier: 5.410A pdb=" N VALB3 166 " --> pdb=" O LYSB3 174 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYSB3 174 " --> pdb=" O VALB3 166 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VALB3 168 " --> pdb=" O ASPB3 172 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASPB3 172 " --> pdb=" O VALB3 168 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEUB3 178 " --> pdb=" O GLNB3 199 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLNB3 199 " --> pdb=" O LEUB3 178 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VALB3 68 " --> pdb=" O ARGB3 30 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ARGB3 30 " --> pdb=" O VALB3 68 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASPC3 172 " --> pdb=" O VALC3 168 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VALC3 168 " --> pdb=" O ASPC3 172 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYSC3 174 " --> pdb=" O VALC3 166 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VALC3 166 " --> pdb=" O LYSC3 174 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C3' and resid 164 through 168 removed outlier: 5.410A pdb=" N VALC3 166 " --> pdb=" O LYSC3 174 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYSC3 174 " --> pdb=" O VALC3 166 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VALC3 168 " --> pdb=" O ASPC3 172 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASPC3 172 " --> pdb=" O VALC3 168 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEUC3 178 " --> pdb=" O GLNC3 199 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLNC3 199 " --> pdb=" O LEUC3 178 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VALC3 68 " --> pdb=" O ARGC3 30 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARGC3 30 " --> pdb=" O VALC3 68 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASPD3 172 " --> pdb=" O VALD3 168 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VALD3 168 " --> pdb=" O ASPD3 172 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYSD3 174 " --> pdb=" O VALD3 166 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VALD3 166 " --> pdb=" O LYSD3 174 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D3' and resid 164 through 168 removed outlier: 5.411A pdb=" N VALD3 166 " --> pdb=" O LYSD3 174 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYSD3 174 " --> pdb=" O VALD3 166 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VALD3 168 " --> pdb=" O ASPD3 172 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASPD3 172 " --> pdb=" O VALD3 168 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEUD3 178 " --> pdb=" O GLND3 199 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLND3 199 " --> pdb=" O LEUD3 178 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VALD3 68 " --> pdb=" O ARGD3 30 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ARGD3 30 " --> pdb=" O VALD3 68 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASPE3 172 " --> pdb=" O VALE3 168 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VALE3 168 " --> pdb=" O ASPE3 172 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYSE3 174 " --> pdb=" O VALE3 166 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VALE3 166 " --> pdb=" O LYSE3 174 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E3' and resid 164 through 168 removed outlier: 5.410A pdb=" N VALE3 166 " --> pdb=" O LYSE3 174 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYSE3 174 " --> pdb=" O VALE3 166 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VALE3 168 " --> pdb=" O ASPE3 172 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASPE3 172 " --> pdb=" O VALE3 168 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEUE3 178 " --> pdb=" O GLNE3 199 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLNE3 199 " --> pdb=" O LEUE3 178 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VALE3 68 " --> pdb=" O ARGE3 30 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ARGE3 30 " --> pdb=" O VALE3 68 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASPF3 172 " --> pdb=" O VALF3 168 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VALF3 168 " --> pdb=" O ASPF3 172 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYSF3 174 " --> pdb=" O VALF3 166 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VALF3 166 " --> pdb=" O LYSF3 174 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F3' and resid 164 through 168 removed outlier: 5.411A pdb=" N VALF3 166 " --> pdb=" O LYSF3 174 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYSF3 174 " --> pdb=" O VALF3 166 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VALF3 168 " --> pdb=" O ASPF3 172 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASPF3 172 " --> pdb=" O VALF3 168 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEUF3 178 " --> pdb=" O GLNF3 199 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLNF3 199 " --> pdb=" O LEUF3 178 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VALF3 68 " --> pdb=" O ARGF3 30 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARGF3 30 " --> pdb=" O VALF3 68 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASPA3 172 " --> pdb=" O VALA3 168 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VALA3 168 " --> pdb=" O ASPA3 172 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYSA3 174 " --> pdb=" O VALA3 166 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VALA3 166 " --> pdb=" O LYSA3 174 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A3' and resid 226 through 227 removed outlier: 7.044A pdb=" N TRPF4 37 " --> pdb=" O LYSF4 59 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYSF4 59 " --> pdb=" O TRPF4 37 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N METF4 39 " --> pdb=" O GLYF4 57 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VALF4 41 " --> pdb=" O ILEF4 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B3' and resid 226 through 227 removed outlier: 7.043A pdb=" N TRPA4 37 " --> pdb=" O LYSA4 59 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYSA4 59 " --> pdb=" O TRPA4 37 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N META4 39 " --> pdb=" O GLYA4 57 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VALA4 41 " --> pdb=" O ILEA4 55 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C3' and resid 226 through 227 removed outlier: 7.044A pdb=" N TRPB4 37 " --> pdb=" O LYSB4 59 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYSB4 59 " --> pdb=" O TRPB4 37 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N METB4 39 " --> pdb=" O GLYB4 57 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VALB4 41 " --> pdb=" O ILEB4 55 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D3' and resid 226 through 227 removed outlier: 7.043A pdb=" N TRPC4 37 " --> pdb=" O LYSC4 59 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYSC4 59 " --> pdb=" O TRPC4 37 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N METC4 39 " --> pdb=" O GLYC4 57 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VALC4 41 " --> pdb=" O ILEC4 55 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E3' and resid 226 through 227 removed outlier: 7.044A pdb=" N TRPD4 37 " --> pdb=" O LYSD4 59 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYSD4 59 " --> pdb=" O TRPD4 37 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N METD4 39 " --> pdb=" O GLYD4 57 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VALD4 41 " --> pdb=" O ILED4 55 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F3' and resid 226 through 227 removed outlier: 7.044A pdb=" N TRPE4 37 " --> pdb=" O LYSE4 59 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYSE4 59 " --> pdb=" O TRPE4 37 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N METE4 39 " --> pdb=" O GLYE4 57 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VALE4 41 " --> pdb=" O ILEE4 55 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A4' and resid 2 through 3 removed outlier: 4.094A pdb=" N ASPA4 75 " --> pdb=" O ILEA4 104 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B4' and resid 2 through 3 removed outlier: 4.093A pdb=" N ASPB4 75 " --> pdb=" O ILEB4 104 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C4' and resid 2 through 3 removed outlier: 4.094A pdb=" N ASPC4 75 " --> pdb=" O ILEC4 104 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D4' and resid 2 through 3 removed outlier: 4.094A pdb=" N ASPD4 75 " --> pdb=" O ILED4 104 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E4' and resid 2 through 3 removed outlier: 4.093A pdb=" N ASPE4 75 " --> pdb=" O ILEE4 104 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F4' and resid 2 through 3 removed outlier: 4.093A pdb=" N ASPF4 75 " --> pdb=" O ILEF4 104 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A5' and resid 4 through 6 Processing sheet with id=AF5, first strand: chain 'A5' and resid 156 through 157 removed outlier: 3.735A pdb=" N SERA5 166 " --> pdb=" O ASNA5 101 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A5' and resid 106 through 108 Processing sheet with id=AF7, first strand: chain 'A5' and resid 232 through 233 removed outlier: 4.018A pdb=" N GLYA5 232 " --> pdb=" O ASPA5 221 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASPA5 221 " --> pdb=" O GLYA5 232 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASPA5 216 " --> pdb=" O GLUA5 257 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N META5 252 " --> pdb=" O LYSA5 277 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A5' and resid 280 through 288 Processing sheet with id=AF9, first strand: chain 'A5' and resid 313 through 315 Processing sheet with id=AG1, first strand: chain 'A5' and resid 318 through 319 removed outlier: 6.191A pdb=" N ALAA5 318 " --> pdb=" O VALA5 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'B5' and resid 4 through 6 Processing sheet with id=AG3, first strand: chain 'B5' and resid 93 through 100 removed outlier: 5.167A pdb=" N SERB5 94 " --> pdb=" O SERB5 141 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B5' and resid 232 through 233 removed outlier: 4.024A pdb=" N ASPB5 216 " --> pdb=" O GLUB5 257 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLUB5 257 " --> pdb=" O ASPB5 216 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THRB5 251 " --> pdb=" O ASNB5 222 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VALB5 254 " --> pdb=" O LYSB5 277 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B5' and resid 280 through 289 removed outlier: 3.647A pdb=" N ASPB5 286 " --> pdb=" O ILEB5 298 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILEB5 298 " --> pdb=" O ASPB5 286 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEUB5 288 " --> pdb=" O PHEB5 296 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHEB5 296 " --> pdb=" O LEUB5 288 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B5' and resid 363 through 365 Processing sheet with id=AG7, first strand: chain 'B5' and resid 363 through 365 removed outlier: 3.731A pdb=" N THRB5 398 " --> pdb=" O VALB5 314 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEUB5 316 " --> pdb=" O THRB5 398 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLNB5 320 " --> pdb=" O VALB5 402 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B5' and resid 347 through 348 Processing sheet with id=AG9, first strand: chain 'C5' and resid 4 through 6 Processing sheet with id=AH1, first strand: chain 'C5' and resid 156 through 157 removed outlier: 3.759A pdb=" N SERC5 166 " --> pdb=" O ASNC5 101 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C5' and resid 106 through 108 Processing sheet with id=AH3, first strand: chain 'C5' and resid 232 through 233 removed outlier: 3.993A pdb=" N GLYC5 232 " --> pdb=" O ASPC5 221 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASPC5 216 " --> pdb=" O GLUC5 257 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N METC5 252 " --> pdb=" O LYSC5 277 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C5' and resid 280 through 288 Processing sheet with id=AH5, first strand: chain 'C5' and resid 313 through 315 Processing sheet with id=AH6, first strand: chain 'C5' and resid 318 through 319 removed outlier: 6.184A pdb=" N ALAC5 318 " --> pdb=" O VALC5 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'D5' and resid 4 through 6 Processing sheet with id=AH8, first strand: chain 'D5' and resid 93 through 100 removed outlier: 5.163A pdb=" N SERD5 94 " --> pdb=" O SERD5 141 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D5' and resid 232 through 233 removed outlier: 4.016A pdb=" N ASPD5 216 " --> pdb=" O GLUD5 257 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLUD5 257 " --> pdb=" O ASPD5 216 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THRD5 251 " --> pdb=" O ASND5 222 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VALD5 254 " --> pdb=" O LYSD5 277 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'D5' and resid 280 through 289 removed outlier: 3.698A pdb=" N ASPD5 286 " --> pdb=" O ILED5 298 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILED5 298 " --> pdb=" O ASPD5 286 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEUD5 288 " --> pdb=" O PHED5 296 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHED5 296 " --> pdb=" O LEUD5 288 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D5' and resid 363 through 365 Processing sheet with id=AI3, first strand: chain 'D5' and resid 363 through 365 removed outlier: 3.716A pdb=" N THRD5 398 " --> pdb=" O VALD5 314 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEUD5 316 " --> pdb=" O THRD5 398 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLND5 320 " --> pdb=" O VALD5 402 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E5' and resid 4 through 6 Processing sheet with id=AI5, first strand: chain 'E5' and resid 156 through 157 removed outlier: 3.742A pdb=" N SERE5 166 " --> pdb=" O ASNE5 101 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E5' and resid 106 through 108 Processing sheet with id=AI7, first strand: chain 'E5' and resid 232 through 233 removed outlier: 4.038A pdb=" N GLYE5 232 " --> pdb=" O ASPE5 221 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASPE5 221 " --> pdb=" O GLYE5 232 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASPE5 216 " --> pdb=" O GLUE5 257 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N METE5 252 " --> pdb=" O LYSE5 277 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E5' and resid 280 through 288 Processing sheet with id=AI9, first strand: chain 'E5' and resid 313 through 315 Processing sheet with id=AJ1, first strand: chain 'E5' and resid 318 through 319 removed outlier: 6.176A pdb=" N ALAE5 318 " --> pdb=" O VALE5 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'F5' and resid 4 through 6 Processing sheet with id=AJ3, first strand: chain 'F5' and resid 95 through 100 Processing sheet with id=AJ4, first strand: chain 'F5' and resid 232 through 233 removed outlier: 4.037A pdb=" N ASPF5 216 " --> pdb=" O GLUF5 257 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLUF5 257 " --> pdb=" O ASPF5 216 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THRF5 251 " --> pdb=" O ASNF5 222 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VALF5 254 " --> pdb=" O LYSF5 277 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'F5' and resid 280 through 289 removed outlier: 3.672A pdb=" N ASPF5 286 " --> pdb=" O ILEF5 298 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILEF5 298 " --> pdb=" O ASPF5 286 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEUF5 288 " --> pdb=" O PHEF5 296 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHEF5 296 " --> pdb=" O LEUF5 288 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F5' and resid 363 through 365 Processing sheet with id=AJ7, first strand: chain 'F5' and resid 363 through 365 removed outlier: 3.722A pdb=" N THRF5 398 " --> pdb=" O VALF5 314 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLNF5 320 " --> pdb=" O VALF5 402 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'G5' and resid 4 through 6 Processing sheet with id=AJ9, first strand: chain 'G5' and resid 156 through 157 removed outlier: 3.714A pdb=" N SERG5 166 " --> pdb=" O ASNG5 101 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'G5' and resid 106 through 108 Processing sheet with id=AK2, first strand: chain 'G5' and resid 232 through 233 removed outlier: 4.020A pdb=" N GLYG5 232 " --> pdb=" O ASPG5 221 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASPG5 221 " --> pdb=" O GLYG5 232 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASPG5 216 " --> pdb=" O GLUG5 257 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N METG5 252 " --> pdb=" O LYSG5 277 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'G5' and resid 280 through 288 Processing sheet with id=AK4, first strand: chain 'G5' and resid 313 through 315 Processing sheet with id=AK5, first strand: chain 'G5' and resid 318 through 319 removed outlier: 6.157A pdb=" N ALAG5 318 " --> pdb=" O VALG5 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK5 Processing sheet with id=AK6, first strand: chain 'H5' and resid 4 through 6 Processing sheet with id=AK7, first strand: chain 'H5' and resid 93 through 100 removed outlier: 5.164A pdb=" N SERH5 94 " --> pdb=" O SERH5 141 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'H5' and resid 232 through 233 removed outlier: 4.022A pdb=" N ASPH5 216 " --> pdb=" O GLUH5 257 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLUH5 257 " --> pdb=" O ASPH5 216 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THRH5 251 " --> pdb=" O ASNH5 222 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VALH5 254 " --> pdb=" O LYSH5 277 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'H5' and resid 280 through 289 removed outlier: 3.644A pdb=" N ASPH5 286 " --> pdb=" O ILEH5 298 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILEH5 298 " --> pdb=" O ASPH5 286 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEUH5 288 " --> pdb=" O PHEH5 296 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHEH5 296 " --> pdb=" O LEUH5 288 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'H5' and resid 364 through 365 Processing sheet with id=AL2, first strand: chain 'H5' and resid 364 through 365 removed outlier: 3.732A pdb=" N THRH5 398 " --> pdb=" O VALH5 314 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEUH5 316 " --> pdb=" O THRH5 398 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'H5' and resid 347 through 348 Processing sheet with id=AL4, first strand: chain 'I5' and resid 4 through 6 Processing sheet with id=AL5, first strand: chain 'I5' and resid 156 through 157 removed outlier: 3.760A pdb=" N SERI5 166 " --> pdb=" O ASNI5 101 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'I5' and resid 106 through 108 Processing sheet with id=AL7, first strand: chain 'I5' and resid 232 through 233 removed outlier: 3.997A pdb=" N GLYI5 232 " --> pdb=" O ASPI5 221 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASPI5 216 " --> pdb=" O GLUI5 257 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N METI5 252 " --> pdb=" O LYSI5 277 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'I5' and resid 280 through 288 Processing sheet with id=AL9, first strand: chain 'I5' and resid 313 through 315 Processing sheet with id=AM1, first strand: chain 'I5' and resid 318 through 319 removed outlier: 6.172A pdb=" N ALAI5 318 " --> pdb=" O VALI5 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM1 Processing sheet with id=AM2, first strand: chain 'J5' and resid 4 through 6 Processing sheet with id=AM3, first strand: chain 'J5' and resid 93 through 100 removed outlier: 5.171A pdb=" N SERJ5 94 " --> pdb=" O SERJ5 141 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'J5' and resid 232 through 233 removed outlier: 4.013A pdb=" N ASPJ5 216 " --> pdb=" O GLUJ5 257 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLUJ5 257 " --> pdb=" O ASPJ5 216 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THRJ5 251 " --> pdb=" O ASNJ5 222 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'J5' and resid 280 through 289 removed outlier: 3.698A pdb=" N ASPJ5 286 " --> pdb=" O ILEJ5 298 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILEJ5 298 " --> pdb=" O ASPJ5 286 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEUJ5 288 " --> pdb=" O PHEJ5 296 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHEJ5 296 " --> pdb=" O LEUJ5 288 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'J5' and resid 363 through 365 Processing sheet with id=AM7, first strand: chain 'J5' and resid 363 through 365 removed outlier: 3.717A pdb=" N THRJ5 398 " --> pdb=" O VALJ5 314 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEUJ5 316 " --> pdb=" O THRJ5 398 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLNJ5 320 " --> pdb=" O VALJ5 402 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'K5' and resid 4 through 6 Processing sheet with id=AM9, first strand: chain 'K5' and resid 156 through 157 removed outlier: 3.744A pdb=" N SERK5 166 " --> pdb=" O ASNK5 101 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'K5' and resid 106 through 108 Processing sheet with id=AN2, first strand: chain 'K5' and resid 232 through 233 removed outlier: 4.026A pdb=" N GLYK5 232 " --> pdb=" O ASPK5 221 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASPK5 221 " --> pdb=" O GLYK5 232 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASPK5 216 " --> pdb=" O GLUK5 257 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N METK5 252 " --> pdb=" O LYSK5 277 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'K5' and resid 280 through 288 Processing sheet with id=AN4, first strand: chain 'K5' and resid 313 through 315 Processing sheet with id=AN5, first strand: chain 'K5' and resid 318 through 319 removed outlier: 6.149A pdb=" N ALAK5 318 " --> pdb=" O VALK5 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN5 Processing sheet with id=AN6, first strand: chain 'L5' and resid 4 through 6 Processing sheet with id=AN7, first strand: chain 'L5' and resid 93 through 100 removed outlier: 5.133A pdb=" N SERL5 94 " --> pdb=" O SERL5 141 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'L5' and resid 232 through 233 removed outlier: 4.037A pdb=" N ASPL5 216 " --> pdb=" O GLUL5 257 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLUL5 257 " --> pdb=" O ASPL5 216 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THRL5 251 " --> pdb=" O ASNL5 222 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VALL5 254 " --> pdb=" O LYSL5 277 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'L5' and resid 280 through 289 removed outlier: 3.667A pdb=" N ASPL5 286 " --> pdb=" O ILEL5 298 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILEL5 298 " --> pdb=" O ASPL5 286 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEUL5 288 " --> pdb=" O PHEL5 296 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHEL5 296 " --> pdb=" O LEUL5 288 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'L5' and resid 363 through 365 Processing sheet with id=AO2, first strand: chain 'L5' and resid 363 through 365 removed outlier: 3.724A pdb=" N THRL5 398 " --> pdb=" O VALL5 314 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLNL5 320 " --> pdb=" O VALL5 402 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'A6' and resid 9 through 12 removed outlier: 6.180A pdb=" N ARGA6 9 " --> pdb=" O ILEF6 491 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILEF6 493 " --> pdb=" O ARGA6 9 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SERA6 11 " --> pdb=" O ILEF6 493 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'A6' and resid 25 through 31 removed outlier: 3.746A pdb=" N THRA6 31 " --> pdb=" O GLYA6 86 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'A6' and resid 124 through 126 Processing sheet with id=AO6, first strand: chain 'A6' and resid 161 through 166 Processing sheet with id=AO7, first strand: chain 'A6' and resid 238 through 239 removed outlier: 6.448A pdb=" N ALAA6 239 " --> pdb=" O TYRA6 265 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N VALA6 267 " --> pdb=" O ALAA6 239 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VALA6 264 " --> pdb=" O ARGA6 293 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEUA6 295 " --> pdb=" O VALA6 264 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLUA6 266 " --> pdb=" O LEUA6 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO7 Processing sheet with id=AO8, first strand: chain 'A6' and resid 353 through 356 Processing sheet with id=AO9, first strand: chain 'A6' and resid 453 through 457 Processing sheet with id=AP1, first strand: chain 'B6' and resid 9 through 12 Processing sheet with id=AP2, first strand: chain 'B6' and resid 25 through 31 removed outlier: 3.744A pdb=" N THRB6 31 " --> pdb=" O GLYB6 86 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'B6' and resid 124 through 126 Processing sheet with id=AP4, first strand: chain 'B6' and resid 161 through 166 Processing sheet with id=AP5, first strand: chain 'B6' and resid 238 through 239 removed outlier: 6.449A pdb=" N ALAB6 239 " --> pdb=" O TYRB6 265 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N VALB6 267 " --> pdb=" O ALAB6 239 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VALB6 264 " --> pdb=" O ARGB6 293 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEUB6 295 " --> pdb=" O VALB6 264 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLUB6 266 " --> pdb=" O LEUB6 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP5 Processing sheet with id=AP6, first strand: chain 'B6' and resid 353 through 356 Processing sheet with id=AP7, first strand: chain 'B6' and resid 453 through 457 Processing sheet with id=AP8, first strand: chain 'C6' and resid 9 through 12 Processing sheet with id=AP9, first strand: chain 'C6' and resid 25 through 31 removed outlier: 3.745A pdb=" N THRC6 31 " --> pdb=" O GLYC6 86 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'C6' and resid 124 through 126 Processing sheet with id=AQ2, first strand: chain 'C6' and resid 161 through 166 Processing sheet with id=AQ3, first strand: chain 'C6' and resid 238 through 239 removed outlier: 6.447A pdb=" N ALAC6 239 " --> pdb=" O TYRC6 265 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VALC6 267 " --> pdb=" O ALAC6 239 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VALC6 264 " --> pdb=" O ARGC6 293 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEUC6 295 " --> pdb=" O VALC6 264 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLUC6 266 " --> pdb=" O LEUC6 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ3 Processing sheet with id=AQ4, first strand: chain 'C6' and resid 353 through 356 Processing sheet with id=AQ5, first strand: chain 'C6' and resid 453 through 457 Processing sheet with id=AQ6, first strand: chain 'D6' and resid 9 through 12 Processing sheet with id=AQ7, first strand: chain 'D6' and resid 25 through 31 removed outlier: 3.745A pdb=" N THRD6 31 " --> pdb=" O GLYD6 86 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'D6' and resid 124 through 126 Processing sheet with id=AQ9, first strand: chain 'D6' and resid 161 through 166 Processing sheet with id=AR1, first strand: chain 'D6' and resid 238 through 239 removed outlier: 6.448A pdb=" N ALAD6 239 " --> pdb=" O TYRD6 265 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VALD6 267 " --> pdb=" O ALAD6 239 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VALD6 264 " --> pdb=" O ARGD6 293 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEUD6 295 " --> pdb=" O VALD6 264 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLUD6 266 " --> pdb=" O LEUD6 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR1 Processing sheet with id=AR2, first strand: chain 'D6' and resid 353 through 356 Processing sheet with id=AR3, first strand: chain 'D6' and resid 453 through 457 Processing sheet with id=AR4, first strand: chain 'E6' and resid 9 through 12 Processing sheet with id=AR5, first strand: chain 'E6' and resid 25 through 31 removed outlier: 3.744A pdb=" N THRE6 31 " --> pdb=" O GLYE6 86 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'E6' and resid 124 through 126 Processing sheet with id=AR7, first strand: chain 'E6' and resid 161 through 166 Processing sheet with id=AR8, first strand: chain 'E6' and resid 238 through 239 removed outlier: 6.448A pdb=" N ALAE6 239 " --> pdb=" O TYRE6 265 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N VALE6 267 " --> pdb=" O ALAE6 239 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VALE6 264 " --> pdb=" O ARGE6 293 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEUE6 295 " --> pdb=" O VALE6 264 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLUE6 266 " --> pdb=" O LEUE6 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR8 Processing sheet with id=AR9, first strand: chain 'E6' and resid 353 through 356 Processing sheet with id=AS1, first strand: chain 'E6' and resid 453 through 457 Processing sheet with id=AS2, first strand: chain 'F6' and resid 9 through 12 Processing sheet with id=AS3, first strand: chain 'F6' and resid 25 through 31 removed outlier: 3.745A pdb=" N THRF6 31 " --> pdb=" O GLYF6 86 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'F6' and resid 124 through 126 Processing sheet with id=AS5, first strand: chain 'F6' and resid 161 through 166 Processing sheet with id=AS6, first strand: chain 'F6' and resid 238 through 239 removed outlier: 6.447A pdb=" N ALAF6 239 " --> pdb=" O TYRF6 265 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VALF6 267 " --> pdb=" O ALAF6 239 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VALF6 264 " --> pdb=" O ARGF6 293 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEUF6 295 " --> pdb=" O VALF6 264 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLUF6 266 " --> pdb=" O LEUF6 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS6 Processing sheet with id=AS7, first strand: chain 'F6' and resid 353 through 356 Processing sheet with id=AS8, first strand: chain 'F6' and resid 453 through 457 Processing sheet with id=AS9, first strand: chain 'A7' and resid 3 through 4 removed outlier: 3.586A pdb=" N VALA7 3 " --> pdb=" O ILEA7 22 " (cutoff:3.500A) Processing sheet with id=AT1, first strand: chain 'A7' and resid 80 through 83 removed outlier: 6.590A pdb=" N ASPA7 103 " --> pdb=" O ILEA7 81 " (cutoff:3.500A) Processing sheet with id=AT2, first strand: chain 'B7' and resid 3 through 4 removed outlier: 3.587A pdb=" N VALB7 3 " --> pdb=" O ILEB7 22 " (cutoff:3.500A) Processing sheet with id=AT3, first strand: chain 'B7' and resid 80 through 83 removed outlier: 6.589A pdb=" N ASPB7 103 " --> pdb=" O ILEB7 81 " (cutoff:3.500A) Processing sheet with id=AT4, first strand: chain 'C7' and resid 3 through 4 removed outlier: 3.586A pdb=" N VALC7 3 " --> pdb=" O ILEC7 22 " (cutoff:3.500A) Processing sheet with id=AT5, first strand: chain 'C7' and resid 80 through 83 removed outlier: 6.590A pdb=" N ASPC7 103 " --> pdb=" O ILEC7 81 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'D7' and resid 3 through 4 removed outlier: 3.585A pdb=" N VALD7 3 " --> pdb=" O ILED7 22 " (cutoff:3.500A) Processing sheet with id=AT7, first strand: chain 'D7' and resid 80 through 83 removed outlier: 6.589A pdb=" N ASPD7 103 " --> pdb=" O ILED7 81 " (cutoff:3.500A) Processing sheet with id=AT8, first strand: chain 'E7' and resid 3 through 4 removed outlier: 3.586A pdb=" N VALE7 3 " --> pdb=" O ILEE7 22 " (cutoff:3.500A) Processing sheet with id=AT9, first strand: chain 'E7' and resid 80 through 83 removed outlier: 6.589A pdb=" N ASPE7 103 " --> pdb=" O ILEE7 81 " (cutoff:3.500A) Processing sheet with id=AU1, first strand: chain 'F7' and resid 3 through 4 removed outlier: 3.587A pdb=" N VALF7 3 " --> pdb=" O ILEF7 22 " (cutoff:3.500A) Processing sheet with id=AU2, first strand: chain 'F7' and resid 80 through 83 removed outlier: 6.590A pdb=" N ASPF7 103 " --> pdb=" O ILEF7 81 " (cutoff:3.500A) 3527 hydrogen bonds defined for protein. 9633 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: 56.22 Time building geometry restraints manager: 35.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 32847 1.34 - 1.46: 21492 1.46 - 1.58: 44168 1.58 - 1.70: 1 1.70 - 1.83: 402 Bond restraints: 98910 Sorted by residual: bond pdb=" CD LYSH5 321 " pdb=" CE LYSH5 321 " ideal model delta sigma weight residual 1.520 1.360 0.160 3.00e-02 1.11e+03 2.83e+01 bond pdb=" CB LYSH5 321 " pdb=" CG LYSH5 321 " ideal model delta sigma weight residual 1.520 1.372 0.148 3.00e-02 1.11e+03 2.43e+01 bond pdb=" CG ARGA5 45 " pdb=" CD ARGA5 45 " ideal model delta sigma weight residual 1.520 1.386 0.134 3.00e-02 1.11e+03 1.99e+01 bond pdb=" CD LYSL5 321 " pdb=" CE LYSL5 321 " ideal model delta sigma weight residual 1.520 1.388 0.132 3.00e-02 1.11e+03 1.94e+01 bond pdb=" CG ARGG5 45 " pdb=" CD ARGG5 45 " ideal model delta sigma weight residual 1.520 1.388 0.132 3.00e-02 1.11e+03 1.94e+01 ... (remaining 98905 not shown) Histogram of bond angle deviations from ideal: 85.83 - 95.50: 8 95.50 - 105.16: 1475 105.16 - 114.83: 60386 114.83 - 124.50: 71374 124.50 - 134.17: 1265 Bond angle restraints: 134508 Sorted by residual: angle pdb=" CB LYSH5 321 " pdb=" CG LYSH5 321 " pdb=" CD LYSH5 321 " ideal model delta sigma weight residual 111.30 85.83 25.47 2.30e+00 1.89e-01 1.23e+02 angle pdb=" CB ARGL5 45 " pdb=" CG ARGL5 45 " pdb=" CD ARGL5 45 " ideal model delta sigma weight residual 111.30 89.22 22.08 2.30e+00 1.89e-01 9.22e+01 angle pdb=" CB LYSL5 321 " pdb=" CG LYSL5 321 " pdb=" CD LYSL5 321 " ideal model delta sigma weight residual 111.30 90.33 20.97 2.30e+00 1.89e-01 8.32e+01 angle pdb=" CB LYSF5 321 " pdb=" CG LYSF5 321 " pdb=" CD LYSF5 321 " ideal model delta sigma weight residual 111.30 90.34 20.96 2.30e+00 1.89e-01 8.30e+01 angle pdb=" CA LYSE5 321 " pdb=" CB LYSE5 321 " pdb=" CG LYSE5 321 " ideal model delta sigma weight residual 114.10 96.10 18.00 2.00e+00 2.50e-01 8.10e+01 ... (remaining 134503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 53156 18.00 - 35.99: 5117 35.99 - 53.99: 820 53.99 - 71.99: 187 71.99 - 89.98: 102 Dihedral angle restraints: 59382 sinusoidal: 22980 harmonic: 36402 Sorted by residual: dihedral pdb=" CA GLNH5 320 " pdb=" C GLNH5 320 " pdb=" N LYSH5 321 " pdb=" CA LYSH5 321 " ideal model delta harmonic sigma weight residual -180.00 -136.76 -43.24 0 5.00e+00 4.00e-02 7.48e+01 dihedral pdb=" CA GLND3 103 " pdb=" C GLND3 103 " pdb=" N GLND3 104 " pdb=" CA GLND3 104 " ideal model delta harmonic sigma weight residual 180.00 147.48 32.52 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA GLNA3 103 " pdb=" C GLNA3 103 " pdb=" N GLNA3 104 " pdb=" CA GLNA3 104 " ideal model delta harmonic sigma weight residual 180.00 147.54 32.46 0 5.00e+00 4.00e-02 4.22e+01 ... (remaining 59379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 12071 0.061 - 0.121: 3180 0.121 - 0.182: 442 0.182 - 0.242: 32 0.242 - 0.303: 25 Chirality restraints: 15750 Sorted by residual: chirality pdb=" CB THRC7 34 " pdb=" CA THRC7 34 " pdb=" OG1 THRC7 34 " pdb=" CG2 THRC7 34 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB THRB7 34 " pdb=" CA THRB7 34 " pdb=" OG1 THRB7 34 " pdb=" CG2 THRB7 34 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB THRF7 34 " pdb=" CA THRF7 34 " pdb=" OG1 THRF7 34 " pdb=" CG2 THRF7 34 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 15747 not shown) Planarity restraints: 17598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRPB7 53 " -0.039 2.00e-02 2.50e+03 4.17e-02 4.34e+01 pdb=" CG TRPB7 53 " 0.105 2.00e-02 2.50e+03 pdb=" CD1 TRPB7 53 " -0.062 2.00e-02 2.50e+03 pdb=" CD2 TRPB7 53 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRPB7 53 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRPB7 53 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRPB7 53 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRPB7 53 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRPB7 53 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRPB7 53 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRPA7 53 " -0.039 2.00e-02 2.50e+03 4.17e-02 4.34e+01 pdb=" CG TRPA7 53 " 0.105 2.00e-02 2.50e+03 pdb=" CD1 TRPA7 53 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRPA7 53 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRPA7 53 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRPA7 53 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRPA7 53 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRPA7 53 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRPA7 53 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRPA7 53 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRPF7 53 " -0.039 2.00e-02 2.50e+03 4.16e-02 4.34e+01 pdb=" CG TRPF7 53 " 0.105 2.00e-02 2.50e+03 pdb=" CD1 TRPF7 53 " -0.062 2.00e-02 2.50e+03 pdb=" CD2 TRPF7 53 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRPF7 53 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRPF7 53 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRPF7 53 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRPF7 53 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRPF7 53 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRPF7 53 " -0.025 2.00e-02 2.50e+03 ... (remaining 17595 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 1679 2.59 - 3.16: 93986 3.16 - 3.74: 152459 3.74 - 4.32: 215803 4.32 - 4.90: 349371 Nonbonded interactions: 813298 Sorted by model distance: nonbonded pdb=" OE2 GLUA3 17 " pdb=" NH2 ARGF7 59 " model vdw 2.008 2.520 nonbonded pdb=" OE2 GLUF3 17 " pdb=" NH2 ARGE7 59 " model vdw 2.028 2.520 nonbonded pdb=" OE2 GLUF2 25 " pdb=" NH1 ARGK5 45 " model vdw 2.036 2.520 nonbonded pdb=" OE1 GLUB2 25 " pdb=" OH TYRD5 30 " model vdw 2.037 2.440 nonbonded pdb=" O ILED1 50 " pdb=" OG SERE3 70 " model vdw 2.037 2.440 ... (remaining 813293 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 'A1' selection = chain 'B1' selection = chain 'C1' selection = chain 'D1' selection = chain 'E1' selection = chain 'F1' } ncs_group { reference = chain 'A2' selection = chain 'B2' selection = chain 'C2' selection = chain 'D2' selection = chain 'E2' selection = chain 'F2' } ncs_group { reference = chain 'A3' selection = chain 'B3' selection = chain 'C3' selection = chain 'D3' selection = chain 'E3' selection = chain 'F3' } ncs_group { reference = chain 'A4' selection = chain 'B4' selection = chain 'C4' selection = chain 'D4' selection = chain 'E4' selection = chain 'F4' } ncs_group { reference = chain 'A5' selection = (chain 'B5' and (resid 1 through 403 or (resid 404 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'C5' selection = (chain 'D5' and (resid 1 through 403 or (resid 404 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'E5' selection = (chain 'F5' and (resid 1 through 403 or (resid 404 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G5' selection = (chain 'H5' and (resid 1 through 403 or (resid 404 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'I5' selection = (chain 'J5' and (resid 1 through 403 or (resid 404 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'K5' selection = (chain 'L5' and (resid 1 through 403 or (resid 404 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'A6' selection = chain 'B6' selection = chain 'C6' selection = chain 'D6' selection = chain 'E6' selection = chain 'F6' } ncs_group { reference = chain 'A7' selection = chain 'B7' selection = chain 'C7' selection = chain 'D7' selection = chain 'E7' selection = chain 'F7' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 216 5.16 5 C 60840 2.51 5 N 16338 2.21 5 O 19950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 12.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.100 Extract box with map and model: 32.180 Check model and map are aligned: 1.110 Convert atoms to be neutral: 0.640 Process input model: 217.350 Find NCS groups from input model: 5.290 Set up NCS constraints: 0.850 Set refine NCS operators: 0.000 Set scattering table: 0.050 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 272.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.010 0.160 98910 Z= 0.631 Angle : 0.966 25.473 134508 Z= 0.530 Chirality : 0.054 0.303 15750 Planarity : 0.006 0.072 17598 Dihedral : 14.821 89.982 35946 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 25.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.07), residues: 12480 helix: -0.61 (0.09), residues: 3264 sheet: -1.29 (0.10), residues: 2490 loop : -2.58 (0.07), residues: 6726 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2915 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 2843 time to evaluate : 8.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 24 residues processed: 2860 average time/residue: 0.8337 time to fit residues: 4146.7134 Evaluate side-chains 2414 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 2390 time to evaluate : 9.812 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.8468 time to fit residues: 46.6348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 1048 optimal weight: 8.9990 chunk 941 optimal weight: 3.9990 chunk 522 optimal weight: 1.9990 chunk 321 optimal weight: 0.0670 chunk 635 optimal weight: 0.8980 chunk 502 optimal weight: 3.9990 chunk 973 optimal weight: 0.8980 chunk 376 optimal weight: 3.9990 chunk 591 optimal weight: 0.1980 chunk 724 optimal weight: 0.9990 chunk 1127 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 80 ASN B1 80 ASN ** D1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 80 ASN E1 80 ASN ** F1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1 80 ASN ** A2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 45 ASN C2 46 ASN ** C2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2 166 GLN F2 45 ASN F2 46 ASN ** F2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 13 ASN ** B3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3 104 GLN ** D3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 104 GLN ** D3 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E3 13 ASN ** E3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 104 GLN ** F3 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 13 ASN ** A5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 222 ASN ** A5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 300 ASN A5 320 GLN ** B5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 13 ASN C5 77 GLN C5 222 ASN C5 235 ASN C5 300 ASN C5 320 GLN C5 360 ASN D5 13 ASN ** D5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 77 GLN ** E5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 300 ASN E5 320 GLN ** F5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G5 222 ASN ** G5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G5 300 ASN G5 320 GLN ** H5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I5 13 ASN ** I5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I5 77 GLN I5 222 ASN I5 235 ASN I5 250 HIS I5 300 ASN I5 320 GLN ** J5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J5 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 77 GLN ** K5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 300 ASN K5 320 GLN ** L5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 202 ASN B6 202 ASN ** B6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C6 202 ASN ** C6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 202 ASN D6 443 GLN E6 202 ASN ** E6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F6 202 ASN ** F6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F6 443 GLN ** A7 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 98910 Z= 0.211 Angle : 0.640 11.405 134508 Z= 0.341 Chirality : 0.046 0.259 15750 Planarity : 0.005 0.085 17598 Dihedral : 5.715 27.433 13506 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.07), residues: 12480 helix: 0.04 (0.09), residues: 3330 sheet: -1.18 (0.10), residues: 2634 loop : -2.16 (0.07), residues: 6516 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3112 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 2898 time to evaluate : 8.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 214 outliers final: 134 residues processed: 2971 average time/residue: 0.9102 time to fit residues: 4717.7412 Evaluate side-chains 2612 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 2478 time to evaluate : 8.424 Switching outliers to nearest non-outliers outliers start: 134 outliers final: 0 residues processed: 134 average time/residue: 0.7031 time to fit residues: 192.9024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 626 optimal weight: 9.9990 chunk 350 optimal weight: 7.9990 chunk 938 optimal weight: 2.9990 chunk 768 optimal weight: 3.9990 chunk 311 optimal weight: 4.9990 chunk 1129 optimal weight: 8.9990 chunk 1220 optimal weight: 5.9990 chunk 1006 optimal weight: 4.9990 chunk 1120 optimal weight: 2.9990 chunk 385 optimal weight: 3.9990 chunk 906 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 80 ASN B1 124 GLN C1 35 ASN C1 124 GLN ** D1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 35 ASN D1 80 ASN D1 124 GLN ** F1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1 80 ASN F1 124 GLN A2 46 ASN ** A2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 166 GLN B2 46 ASN ** B2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 45 ASN ** C2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 166 GLN ** E2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2 166 GLN F2 45 ASN ** F2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 104 GLN B3 104 GLN ** B3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 13 ASN ** D3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E3 104 GLN ** E3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 84 ASN ** C4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 84 ASN ** D4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 84 ASN ** E4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 13 ASN A5 77 GLN ** A5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 119 ASN ** A5 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 300 ASN ** B5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 135 ASN ** B5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 119 ASN ** C5 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 300 ASN D5 66 ASN ** D5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 135 ASN E5 11 GLN E5 13 ASN ** E5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 119 ASN ** E5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 300 ASN E5 364 ASN ** F5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 135 ASN G5 13 ASN G5 119 ASN ** G5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G5 300 ASN ** H5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H5 135 ASN ** H5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I5 77 GLN ** I5 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I5 300 ASN J5 66 ASN ** J5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J5 135 ASN K5 11 GLN K5 13 ASN ** K5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 119 ASN ** K5 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 300 ASN ** L5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L5 135 ASN ** B6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 443 GLN ** E6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 96 GLN ** C7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.067 98910 Z= 0.434 Angle : 0.709 11.320 134508 Z= 0.377 Chirality : 0.048 0.390 15750 Planarity : 0.005 0.090 17598 Dihedral : 5.733 25.017 13506 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer Outliers : 3.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.07), residues: 12480 helix: -0.00 (0.09), residues: 3432 sheet: -1.10 (0.10), residues: 2592 loop : -2.18 (0.07), residues: 6456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2874 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 2524 time to evaluate : 10.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 350 outliers final: 247 residues processed: 2720 average time/residue: 0.8427 time to fit residues: 3999.1471 Evaluate side-chains 2593 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 2346 time to evaluate : 8.456 Switching outliers to nearest non-outliers outliers start: 247 outliers final: 0 residues processed: 247 average time/residue: 0.6936 time to fit residues: 337.4549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 1116 optimal weight: 0.8980 chunk 849 optimal weight: 9.9990 chunk 586 optimal weight: 0.1980 chunk 125 optimal weight: 2.9990 chunk 539 optimal weight: 10.0000 chunk 758 optimal weight: 10.0000 chunk 1133 optimal weight: 4.9990 chunk 1200 optimal weight: 6.9990 chunk 592 optimal weight: 3.9990 chunk 1074 optimal weight: 0.9980 chunk 323 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 80 ASN ** D1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 46 ASN B2 69 GLN ** B2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 46 ASN ** C2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 46 ASN ** D2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2 46 ASN E2 69 GLN ** E2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 46 ASN ** F2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 104 GLN ** A3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 104 GLN ** C3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 104 GLN ** D3 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E3 104 GLN ** E3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 106 GLN ** F3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 84 ASN ** C4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4 83 ASN ** D4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 83 ASN ** E4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4 84 ASN ** F4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 300 ASN ** B5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 300 ASN ** D5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 300 ASN F5 13 ASN F5 66 ASN ** F5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G5 300 ASN H5 13 ASN ** H5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I5 77 GLN ** I5 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I5 300 ASN ** J5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 300 ASN L5 13 ASN L5 66 ASN ** L5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E6 463 GLN ** F6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 98910 Z= 0.290 Angle : 0.628 9.974 134508 Z= 0.334 Chirality : 0.046 0.208 15750 Planarity : 0.004 0.061 17598 Dihedral : 5.489 24.948 13506 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.07), residues: 12480 helix: 0.18 (0.09), residues: 3426 sheet: -1.01 (0.10), residues: 2556 loop : -2.06 (0.07), residues: 6498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2864 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 2579 time to evaluate : 8.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 285 outliers final: 148 residues processed: 2736 average time/residue: 0.8438 time to fit residues: 4024.3910 Evaluate side-chains 2525 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 2377 time to evaluate : 8.686 Switching outliers to nearest non-outliers outliers start: 148 outliers final: 0 residues processed: 148 average time/residue: 0.6815 time to fit residues: 204.8429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 999 optimal weight: 0.0970 chunk 681 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 893 optimal weight: 4.9990 chunk 495 optimal weight: 0.7980 chunk 1024 optimal weight: 5.9990 chunk 829 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 613 optimal weight: 0.0270 chunk 1077 optimal weight: 1.9990 chunk 302 optimal weight: 6.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 80 ASN C1 80 ASN ** D1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 80 ASN ** F1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 15 GLN ** A2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 166 GLN ** B2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 71 ASN ** C2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 46 ASN ** D2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2 15 GLN E2 71 ASN F2 15 GLN ** F2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 103 GLN D3 106 GLN ** D3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 83 ASN ** B4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E4 83 ASN ** F4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 83 ASN A5 13 ASN ** A5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 300 ASN B5 66 ASN ** B5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 300 ASN ** D5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 118 ASN ** E5 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 300 ASN ** F5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G5 13 ASN G5 118 ASN ** G5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G5 300 ASN H5 66 ASN ** H5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I5 38 GLN I5 157 GLN ** I5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I5 300 ASN ** J5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 13 ASN K5 38 GLN ** K5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 118 ASN K5 222 ASN ** K5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 300 ASN ** K5 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L5 320 GLN ** A6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E6 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F7 48 ASN ** F7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 98910 Z= 0.194 Angle : 0.585 11.278 134508 Z= 0.309 Chirality : 0.044 0.196 15750 Planarity : 0.004 0.056 17598 Dihedral : 5.090 26.136 13506 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.07), residues: 12480 helix: 0.28 (0.09), residues: 3438 sheet: -0.82 (0.10), residues: 2454 loop : -1.86 (0.07), residues: 6588 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2975 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 2736 time to evaluate : 8.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 239 outliers final: 118 residues processed: 2843 average time/residue: 0.8479 time to fit residues: 4191.9842 Evaluate side-chains 2599 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 2481 time to evaluate : 8.412 Switching outliers to nearest non-outliers outliers start: 118 outliers final: 0 residues processed: 118 average time/residue: 0.7041 time to fit residues: 167.6725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 403 optimal weight: 6.9990 chunk 1081 optimal weight: 5.9990 chunk 237 optimal weight: 0.9990 chunk 704 optimal weight: 9.9990 chunk 296 optimal weight: 0.9980 chunk 1201 optimal weight: 0.9980 chunk 997 optimal weight: 7.9990 chunk 556 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 397 optimal weight: 6.9990 chunk 630 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 80 ASN ** D1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 80 ASN ** F1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 71 ASN ** C2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 166 GLN ** D2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2 71 ASN ** F2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3 13 ASN ** C3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 300 ASN ** B5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 300 ASN ** D5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 11 GLN ** E5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 118 ASN ** E5 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 300 ASN ** F5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G5 118 ASN ** G5 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G5 300 ASN ** H5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I5 300 ASN ** J5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J5 250 HIS K5 11 GLN K5 13 ASN ** K5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 118 ASN ** K5 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 300 ASN ** K5 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 361 GLN ** C6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 96 GLN ** C7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E7 50 ASN ** F7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.093 98910 Z= 0.358 Angle : 0.652 11.687 134508 Z= 0.345 Chirality : 0.047 0.244 15750 Planarity : 0.005 0.071 17598 Dihedral : 5.268 24.975 13506 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.07), residues: 12480 helix: 0.27 (0.09), residues: 3456 sheet: -0.89 (0.10), residues: 2484 loop : -1.85 (0.07), residues: 6540 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2729 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 2482 time to evaluate : 8.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 247 outliers final: 169 residues processed: 2599 average time/residue: 0.8473 time to fit residues: 3828.4613 Evaluate side-chains 2546 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 2377 time to evaluate : 8.463 Switching outliers to nearest non-outliers outliers start: 169 outliers final: 0 residues processed: 169 average time/residue: 0.6887 time to fit residues: 233.3295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 1158 optimal weight: 0.4980 chunk 135 optimal weight: 0.7980 chunk 684 optimal weight: 5.9990 chunk 877 optimal weight: 10.0000 chunk 679 optimal weight: 0.4980 chunk 1011 optimal weight: 0.8980 chunk 671 optimal weight: 0.7980 chunk 1197 optimal weight: 0.8980 chunk 749 optimal weight: 8.9990 chunk 729 optimal weight: 0.6980 chunk 552 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 80 ASN ** D1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 80 ASN ** F1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 166 GLN ** D2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 69 GLN ** D2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 166 GLN ** F2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 13 ASN ** F3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 300 ASN ** B5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 13 ASN ** C5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 300 ASN ** D5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 292 ASN E5 300 ASN E5 364 ASN ** F5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G5 300 ASN ** H5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I5 13 ASN ** I5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I5 300 ASN ** J5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 300 ASN ** K5 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 327 GLN ** F6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.102 98910 Z= 0.195 Angle : 0.593 12.765 134508 Z= 0.312 Chirality : 0.044 0.211 15750 Planarity : 0.004 0.064 17598 Dihedral : 5.005 25.601 13506 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % 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: -1.45 (0.07), residues: 12480 helix: 0.37 (0.09), residues: 3444 sheet: -0.86 (0.10), residues: 2634 loop : -1.79 (0.07), residues: 6402 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2753 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 2616 time to evaluate : 10.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 137 outliers final: 74 residues processed: 2684 average time/residue: 0.8509 time to fit residues: 3977.0149 Evaluate side-chains 2508 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 2434 time to evaluate : 8.620 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 0.7059 time to fit residues: 110.2748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 740 optimal weight: 0.1980 chunk 478 optimal weight: 1.9990 chunk 714 optimal weight: 0.3980 chunk 360 optimal weight: 8.9990 chunk 235 optimal weight: 4.9990 chunk 231 optimal weight: 0.5980 chunk 761 optimal weight: 8.9990 chunk 815 optimal weight: 3.9990 chunk 591 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 940 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 80 ASN C1 80 ASN ** D1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 80 ASN ** F1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 45 ASN ** C2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 69 GLN ** C2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 69 GLN ** D2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 300 ASN ** B5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 297 GLN ** C5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 157 GLN ** C5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 300 ASN C5 364 ASN ** D5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 222 ASN ** E5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 300 ASN ** F5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 101 ASN F5 297 GLN ** G5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G5 300 ASN ** H5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H5 297 GLN ** H5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I5 300 ASN ** J5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 11 GLN K5 157 GLN ** K5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 300 ASN ** K5 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L5 101 ASN ** L5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L5 297 GLN ** L5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 327 GLN ** B6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F7 48 ASN ** F7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.122 98910 Z= 0.221 Angle : 0.604 13.554 134508 Z= 0.317 Chirality : 0.045 0.229 15750 Planarity : 0.004 0.068 17598 Dihedral : 4.939 24.480 13506 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.07), residues: 12480 helix: 0.42 (0.09), residues: 3438 sheet: -0.92 (0.10), residues: 2754 loop : -1.75 (0.07), residues: 6288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2629 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 2499 time to evaluate : 8.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 130 outliers final: 86 residues processed: 2553 average time/residue: 0.8872 time to fit residues: 3956.1050 Evaluate side-chains 2498 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 2412 time to evaluate : 8.972 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 0 residues processed: 86 average time/residue: 0.7432 time to fit residues: 134.6854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 1088 optimal weight: 10.0000 chunk 1146 optimal weight: 0.0030 chunk 1046 optimal weight: 10.0000 chunk 1115 optimal weight: 0.9980 chunk 671 optimal weight: 7.9990 chunk 485 optimal weight: 0.4980 chunk 875 optimal weight: 6.9990 chunk 342 optimal weight: 5.9990 chunk 1008 optimal weight: 5.9990 chunk 1055 optimal weight: 2.9990 chunk 1111 optimal weight: 6.9990 overall best weight: 2.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 80 ASN C1 80 ASN ** D1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 80 ASN ** F1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 69 GLN ** C2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 69 GLN C2 71 ASN ** D2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 300 ASN B5 66 ASN ** B5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 101 ASN ** B5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 300 ASN ** D5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 250 HIS ** E5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 300 ASN ** F5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G5 300 ASN ** H5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I5 300 ASN ** J5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J5 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 11 GLN ** K5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 300 ASN ** K5 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 50 ASN ** C7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F7 48 ASN ** F7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.119 98910 Z= 0.312 Angle : 0.647 13.926 134508 Z= 0.340 Chirality : 0.046 0.231 15750 Planarity : 0.004 0.055 17598 Dihedral : 5.097 27.945 13506 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.07), residues: 12480 helix: 0.37 (0.09), residues: 3450 sheet: -0.81 (0.10), residues: 2544 loop : -1.78 (0.07), residues: 6486 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2547 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 2433 time to evaluate : 8.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 74 residues processed: 2483 average time/residue: 0.8618 time to fit residues: 3719.8615 Evaluate side-chains 2449 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 2375 time to evaluate : 8.497 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 0.7152 time to fit residues: 110.4949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 732 optimal weight: 0.9990 chunk 1179 optimal weight: 0.8980 chunk 719 optimal weight: 0.9980 chunk 559 optimal weight: 0.0030 chunk 820 optimal weight: 0.8980 chunk 1237 optimal weight: 3.9990 chunk 1138 optimal weight: 4.9990 chunk 985 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 761 optimal weight: 4.9990 chunk 604 optimal weight: 2.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 80 ASN ** D1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 80 ASN ** F1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 46 ASN ** A2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 69 GLN C2 15 GLN C2 69 GLN D2 15 GLN D2 69 GLN D2 71 ASN ** F2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 300 ASN ** B5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 195 ASN ** C5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 300 ASN ** D5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 38 GLN ** E5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 300 ASN ** F5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 101 ASN ** G5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G5 300 ASN H5 13 ASN ** H5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H5 101 ASN ** H5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I5 300 ASN ** J5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J5 240 ASN ** K5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 300 ASN ** K5 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L5 101 ASN ** L5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F7 48 ASN ** F7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.118 98910 Z= 0.209 Angle : 0.614 13.733 134508 Z= 0.321 Chirality : 0.045 0.224 15750 Planarity : 0.004 0.056 17598 Dihedral : 4.928 24.816 13506 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.07), residues: 12480 helix: 0.39 (0.09), residues: 3444 sheet: -0.86 (0.10), residues: 2652 loop : -1.76 (0.07), residues: 6384 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24960 Ramachandran restraints generated. 12480 Oldfield, 0 Emsley, 12480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2511 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 2465 time to evaluate : 8.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 28 residues processed: 2489 average time/residue: 0.8717 time to fit residues: 3781.6212 Evaluate side-chains 2394 residues out of total 10902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 2366 time to evaluate : 10.179 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.7292 time to fit residues: 51.2956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 782 optimal weight: 9.9990 chunk 1049 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 908 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 273 optimal weight: 0.3980 chunk 986 optimal weight: 6.9990 chunk 413 optimal weight: 7.9990 chunk 1013 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 80 ASN C1 80 ASN ** D1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 80 ASN ** F1 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 15 GLN B2 69 GLN D2 69 GLN ** F2 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 103 GLN ** D3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 300 ASN B5 66 ASN ** B5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 101 ASN ** B5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 11 GLN ** C5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C5 300 ASN ** D5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 157 GLN ** E5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E5 300 ASN ** F5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G5 300 ASN ** H5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H5 195 ASN ** H5 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I5 11 GLN ** I5 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I5 300 ASN ** J5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J5 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J5 184 GLN ** K5 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K5 300 ASN ** K5 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C6 361 GLN ** D6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E6 463 GLN ** F6 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F6 361 GLN ** A7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D7 50 ASN ** F7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.160448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.134278 restraints weight = 146206.461| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.15 r_work: 0.3393 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.113 98910 Z= 0.307 Angle : 0.652 13.372 134508 Z= 0.342 Chirality : 0.046 0.252 15750 Planarity : 0.004 0.059 17598 Dihedral : 5.063 24.887 13506 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.07), residues: 12480 helix: 0.41 (0.09), residues: 3414 sheet: -0.80 (0.10), residues: 2496 loop : -1.77 (0.07), residues: 6570 =============================================================================== Job complete usr+sys time: 49159.35 seconds wall clock time: 850 minutes 1.90 seconds (51001.90 seconds total)