Starting phenix.real_space_refine (version: dev) on Sun Feb 26 22:02:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adz_11734/02_2023/7adz_11734.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adz_11734/02_2023/7adz_11734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adz_11734/02_2023/7adz_11734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adz_11734/02_2023/7adz_11734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adz_11734/02_2023/7adz_11734.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adz_11734/02_2023/7adz_11734.pdb" } resolution = 2.5 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= 0.000 sd= 0.007 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 Process input model Symmetric amino acids flipped Residue "0A ASP 11": "OD1" <-> "OD2" Residue "0A GLU 12": "OE1" <-> "OE2" Residue "0A ASP 24": "OD1" <-> "OD2" Residue "0A ASP 36": "OD1" <-> "OD2" Residue "0A ASP 40": "OD1" <-> "OD2" Residue "0A ARG 57": "NH1" <-> "NH2" Residue "0A GLU 71": "OE1" <-> "OE2" Residue "0A ARG 106": "NH1" <-> "NH2" Residue "0A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0A ASP 125": "OD1" <-> "OD2" Residue "0A ARG 126": "NH1" <-> "NH2" Residue "0A GLU 132": "OE1" <-> "OE2" Residue "0A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0A ASP 176": "OD1" <-> "OD2" Residue "0A ARG 177": "NH1" <-> "NH2" Residue "0A GLU 184": "OE1" <-> "OE2" Residue "0A TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0B ASP 11": "OD1" <-> "OD2" Residue "0B GLU 12": "OE1" <-> "OE2" Residue "0B ASP 24": "OD1" <-> "OD2" Residue "0B ASP 36": "OD1" <-> "OD2" Residue "0B ASP 40": "OD1" <-> "OD2" Residue "0B ARG 57": "NH1" <-> "NH2" Residue "0B GLU 71": "OE1" <-> "OE2" Residue "0B ARG 106": "NH1" <-> "NH2" Residue "0B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0B ASP 125": "OD1" <-> "OD2" Residue "0B ARG 126": "NH1" <-> "NH2" Residue "0B GLU 132": "OE1" <-> "OE2" Residue "0B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0B ASP 176": "OD1" <-> "OD2" Residue "0B ARG 177": "NH1" <-> "NH2" Residue "0B GLU 184": "OE1" <-> "OE2" Residue "0B TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0C ASP 11": "OD1" <-> "OD2" Residue "0C GLU 12": "OE1" <-> "OE2" Residue "0C ASP 24": "OD1" <-> "OD2" Residue "0C ASP 36": "OD1" <-> "OD2" Residue "0C ASP 40": "OD1" <-> "OD2" Residue "0C ARG 57": "NH1" <-> "NH2" Residue "0C GLU 71": "OE1" <-> "OE2" Residue "0C ARG 106": "NH1" <-> "NH2" Residue "0C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0C ASP 125": "OD1" <-> "OD2" Residue "0C ARG 126": "NH1" <-> "NH2" Residue "0C GLU 132": "OE1" <-> "OE2" Residue "0C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0C TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0C ASP 176": "OD1" <-> "OD2" Residue "0C ARG 177": "NH1" <-> "NH2" Residue "0C GLU 184": "OE1" <-> "OE2" Residue "0C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0D ASP 11": "OD1" <-> "OD2" Residue "0D GLU 12": "OE1" <-> "OE2" Residue "0D ASP 24": "OD1" <-> "OD2" Residue "0D ASP 36": "OD1" <-> "OD2" Residue "0D ASP 40": "OD1" <-> "OD2" Residue "0D ARG 57": "NH1" <-> "NH2" Residue "0D GLU 71": "OE1" <-> "OE2" Residue "0D ARG 106": "NH1" <-> "NH2" Residue "0D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0D ASP 125": "OD1" <-> "OD2" Residue "0D ARG 126": "NH1" <-> "NH2" Residue "0D GLU 132": "OE1" <-> "OE2" Residue "0D PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0D TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0D ASP 176": "OD1" <-> "OD2" Residue "0D ARG 177": "NH1" <-> "NH2" Residue "0D GLU 184": "OE1" <-> "OE2" Residue "0D TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0E ASP 11": "OD1" <-> "OD2" Residue "0E GLU 12": "OE1" <-> "OE2" Residue "0E ASP 24": "OD1" <-> "OD2" Residue "0E ASP 36": "OD1" <-> "OD2" Residue "0E ASP 40": "OD1" <-> "OD2" Residue "0E ARG 57": "NH1" <-> "NH2" Residue "0E GLU 71": "OE1" <-> "OE2" Residue "0E ARG 106": "NH1" <-> "NH2" Residue "0E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0E ASP 125": "OD1" <-> "OD2" Residue "0E ARG 126": "NH1" <-> "NH2" Residue "0E GLU 132": "OE1" <-> "OE2" Residue "0E PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0E PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0E TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0E ASP 176": "OD1" <-> "OD2" Residue "0E ARG 177": "NH1" <-> "NH2" Residue "0E GLU 184": "OE1" <-> "OE2" Residue "0E TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0F ASP 11": "OD1" <-> "OD2" Residue "0F GLU 12": "OE1" <-> "OE2" Residue "0F ASP 24": "OD1" <-> "OD2" Residue "0F ASP 36": "OD1" <-> "OD2" Residue "0F ASP 40": "OD1" <-> "OD2" Residue "0F ARG 57": "NH1" <-> "NH2" Residue "0F GLU 71": "OE1" <-> "OE2" Residue "0F ARG 106": "NH1" <-> "NH2" Residue "0F PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0F ASP 125": "OD1" <-> "OD2" Residue "0F ARG 126": "NH1" <-> "NH2" Residue "0F GLU 132": "OE1" <-> "OE2" Residue "0F PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0F PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0F TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0F ASP 176": "OD1" <-> "OD2" Residue "0F ARG 177": "NH1" <-> "NH2" Residue "0F GLU 184": "OE1" <-> "OE2" Residue "0F TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A GLU 97": "OE1" <-> "OE2" Residue "1A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B GLU 97": "OE1" <-> "OE2" Residue "1B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C GLU 97": "OE1" <-> "OE2" Residue "1C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D GLU 97": "OE1" <-> "OE2" Residue "1D PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E GLU 97": "OE1" <-> "OE2" Residue "1E PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F GLU 97": "OE1" <-> "OE2" Residue "1F PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1a GLU 23": "OE1" <-> "OE2" Residue "1a TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1a PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1a TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1a GLU 95": "OE1" <-> "OE2" Residue "1a ASP 117": "OD1" <-> "OD2" Residue "1a ASP 121": "OD1" <-> "OD2" Residue "1a GLU 124": "OE1" <-> "OE2" Residue "1a GLU 131": "OE1" <-> "OE2" Residue "1a GLU 142": "OE1" <-> "OE2" Residue "1b GLU 23": "OE1" <-> "OE2" Residue "1b TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1b PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1b TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1b GLU 95": "OE1" <-> "OE2" Residue "1b ASP 117": "OD1" <-> "OD2" Residue "1b ASP 121": "OD1" <-> "OD2" Residue "1b GLU 124": "OE1" <-> "OE2" Residue "1b GLU 131": "OE1" <-> "OE2" Residue "1b GLU 142": "OE1" <-> "OE2" Residue "1c GLU 23": "OE1" <-> "OE2" Residue "1c TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1c PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1c TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1c GLU 95": "OE1" <-> "OE2" Residue "1c ASP 117": "OD1" <-> "OD2" Residue "1c ASP 121": "OD1" <-> "OD2" Residue "1c GLU 124": "OE1" <-> "OE2" Residue "1c GLU 131": "OE1" <-> "OE2" Residue "1c GLU 142": "OE1" <-> "OE2" Residue "1d GLU 23": "OE1" <-> "OE2" Residue "1d TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1d PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1d TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1d GLU 95": "OE1" <-> "OE2" Residue "1d ASP 117": "OD1" <-> "OD2" Residue "1d ASP 121": "OD1" <-> "OD2" Residue "1d GLU 124": "OE1" <-> "OE2" Residue "1d GLU 131": "OE1" <-> "OE2" Residue "1d GLU 142": "OE1" <-> "OE2" Residue "1e GLU 23": "OE1" <-> "OE2" Residue "1e TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1e PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1e TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1e GLU 95": "OE1" <-> "OE2" Residue "1e ASP 117": "OD1" <-> "OD2" Residue "1e ASP 121": "OD1" <-> "OD2" Residue "1e GLU 124": "OE1" <-> "OE2" Residue "1e GLU 131": "OE1" <-> "OE2" Residue "1e GLU 142": "OE1" <-> "OE2" Residue "1f GLU 23": "OE1" <-> "OE2" Residue "1f TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1f PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1f TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1f GLU 95": "OE1" <-> "OE2" Residue "1f ASP 117": "OD1" <-> "OD2" Residue "1f ASP 121": "OD1" <-> "OD2" Residue "1f GLU 124": "OE1" <-> "OE2" Residue "1f GLU 131": "OE1" <-> "OE2" Residue "1f GLU 142": "OE1" <-> "OE2" Residue "2A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A GLU 426": "OE1" <-> "OE2" Residue "2A TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B GLU 426": "OE1" <-> "OE2" Residue "2B TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C GLU 426": "OE1" <-> "OE2" Residue "2C TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D GLU 426": "OE1" <-> "OE2" Residue "2D TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E GLU 426": "OE1" <-> "OE2" Residue "2E TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F GLU 426": "OE1" <-> "OE2" Residue "2F TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2a PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2a TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2a PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2a TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2a GLU 84": "OE1" <-> "OE2" Residue "2b PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2b TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2b PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2b TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2b GLU 84": "OE1" <-> "OE2" Residue "2c PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2c TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2c PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2c TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2c GLU 84": "OE1" <-> "OE2" Residue "2d PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2d TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2d PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2d TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2d GLU 84": "OE1" <-> "OE2" Residue "2e PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2e TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2e PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2e TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2e GLU 84": "OE1" <-> "OE2" Residue "2f PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2f TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2f PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2f TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2f GLU 84": "OE1" <-> "OE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 67794 Number of models: 1 Model: "" Number of chains: 30 Chain: "0A" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1615 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "0B" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1615 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "0C" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1615 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "0D" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1615 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "0E" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1615 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "0F" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1615 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "1A" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2337 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "1B" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2337 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "1C" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2337 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "1D" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2337 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "1E" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2337 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "1F" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2337 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "1a" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "1b" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "1c" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "1d" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "1e" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "1f" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "2A" Number of atoms: 5057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 5057 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 625} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "2B" Number of atoms: 5057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 5057 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 625} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "2C" Number of atoms: 5057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 5057 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 625} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "2D" Number of atoms: 5057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 5057 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 625} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "2E" Number of atoms: 5057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 5057 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 625} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "2F" Number of atoms: 5057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 5057 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 625} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "2a" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "2b" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "2c" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "2d" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "2e" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "2f" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1145 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Time building chain proxies: 28.42, per 1000 atoms: 0.42 Number of scatterers: 67794 At special positions: 0 Unit cell: (232.1, 232.1, 156.2, 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 186 16.00 O 13260 8.00 N 11100 7.00 C 43248 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: 21.10 Conformation dependent library (CDL) restraints added in 7.8 seconds 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16092 Finding SS restraints... Secondary structure from input PDB file: 282 helices and 96 sheets defined 33.4% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain '0A' and resid 1 through 20 Processing helix chain '0A' and resid 31 through 35 removed outlier: 3.647A pdb=" N LEU0A 34 " --> pdb=" O ASN0A 31 " (cutoff:3.500A) Processing helix chain '0A' and resid 41 through 46 removed outlier: 3.728A pdb=" N LEU0A 45 " --> pdb=" O VAL0A 41 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN0A 46 " --> pdb=" O ALA0A 42 " (cutoff:3.500A) No H-bonds generated for 'chain '0A' and resid 41 through 46' Processing helix chain '0A' and resid 96 through 114 removed outlier: 3.586A pdb=" N SER0A 105 " --> pdb=" O LEU0A 101 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS0A 113 " --> pdb=" O GLU0A 109 " (cutoff:3.500A) Processing helix chain '0A' and resid 128 through 132 removed outlier: 3.592A pdb=" N GLU0A 132 " --> pdb=" O GLU0A 129 " (cutoff:3.500A) Processing helix chain '0A' and resid 147 through 157 removed outlier: 3.690A pdb=" N THR0A 157 " --> pdb=" O TYR0A 153 " (cutoff:3.500A) Processing helix chain '0B' and resid 2 through 20 Processing helix chain '0B' and resid 31 through 35 removed outlier: 3.648A pdb=" N LEU0B 34 " --> pdb=" O ASN0B 31 " (cutoff:3.500A) Processing helix chain '0B' and resid 41 through 46 removed outlier: 3.728A pdb=" N LEU0B 45 " --> pdb=" O VAL0B 41 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN0B 46 " --> pdb=" O ALA0B 42 " (cutoff:3.500A) No H-bonds generated for 'chain '0B' and resid 41 through 46' Processing helix chain '0B' and resid 96 through 114 removed outlier: 3.587A pdb=" N SER0B 105 " --> pdb=" O LEU0B 101 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS0B 113 " --> pdb=" O GLU0B 109 " (cutoff:3.500A) Processing helix chain '0B' and resid 128 through 132 removed outlier: 3.592A pdb=" N GLU0B 132 " --> pdb=" O GLU0B 129 " (cutoff:3.500A) Processing helix chain '0B' and resid 147 through 157 removed outlier: 3.691A pdb=" N THR0B 157 " --> pdb=" O TYR0B 153 " (cutoff:3.500A) Processing helix chain '0C' and resid 2 through 20 Processing helix chain '0C' and resid 31 through 35 removed outlier: 3.648A pdb=" N LEU0C 34 " --> pdb=" O ASN0C 31 " (cutoff:3.500A) Processing helix chain '0C' and resid 41 through 46 removed outlier: 3.727A pdb=" N LEU0C 45 " --> pdb=" O VAL0C 41 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN0C 46 " --> pdb=" O ALA0C 42 " (cutoff:3.500A) No H-bonds generated for 'chain '0C' and resid 41 through 46' Processing helix chain '0C' and resid 96 through 114 removed outlier: 3.586A pdb=" N SER0C 105 " --> pdb=" O LEU0C 101 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS0C 113 " --> pdb=" O GLU0C 109 " (cutoff:3.500A) Processing helix chain '0C' and resid 128 through 132 removed outlier: 3.591A pdb=" N GLU0C 132 " --> pdb=" O GLU0C 129 " (cutoff:3.500A) Processing helix chain '0C' and resid 147 through 157 removed outlier: 3.690A pdb=" N THR0C 157 " --> pdb=" O TYR0C 153 " (cutoff:3.500A) Processing helix chain '0D' and resid 2 through 20 Processing helix chain '0D' and resid 31 through 35 removed outlier: 3.647A pdb=" N LEU0D 34 " --> pdb=" O ASN0D 31 " (cutoff:3.500A) Processing helix chain '0D' and resid 41 through 46 removed outlier: 3.728A pdb=" N LEU0D 45 " --> pdb=" O VAL0D 41 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN0D 46 " --> pdb=" O ALA0D 42 " (cutoff:3.500A) No H-bonds generated for 'chain '0D' and resid 41 through 46' Processing helix chain '0D' and resid 96 through 114 removed outlier: 3.586A pdb=" N SER0D 105 " --> pdb=" O LEU0D 101 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS0D 113 " --> pdb=" O GLU0D 109 " (cutoff:3.500A) Processing helix chain '0D' and resid 128 through 132 removed outlier: 3.591A pdb=" N GLU0D 132 " --> pdb=" O GLU0D 129 " (cutoff:3.500A) Processing helix chain '0D' and resid 147 through 157 removed outlier: 3.690A pdb=" N THR0D 157 " --> pdb=" O TYR0D 153 " (cutoff:3.500A) Processing helix chain '0E' and resid 2 through 20 Processing helix chain '0E' and resid 31 through 35 removed outlier: 3.647A pdb=" N LEU0E 34 " --> pdb=" O ASN0E 31 " (cutoff:3.500A) Processing helix chain '0E' and resid 41 through 46 removed outlier: 3.729A pdb=" N LEU0E 45 " --> pdb=" O VAL0E 41 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN0E 46 " --> pdb=" O ALA0E 42 " (cutoff:3.500A) No H-bonds generated for 'chain '0E' and resid 41 through 46' Processing helix chain '0E' and resid 96 through 114 removed outlier: 3.587A pdb=" N SER0E 105 " --> pdb=" O LEU0E 101 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS0E 113 " --> pdb=" O GLU0E 109 " (cutoff:3.500A) Processing helix chain '0E' and resid 128 through 132 removed outlier: 3.592A pdb=" N GLU0E 132 " --> pdb=" O GLU0E 129 " (cutoff:3.500A) Processing helix chain '0E' and resid 147 through 157 removed outlier: 3.691A pdb=" N THR0E 157 " --> pdb=" O TYR0E 153 " (cutoff:3.500A) Processing helix chain '0F' and resid 2 through 20 Processing helix chain '0F' and resid 31 through 35 removed outlier: 3.648A pdb=" N LEU0F 34 " --> pdb=" O ASN0F 31 " (cutoff:3.500A) Processing helix chain '0F' and resid 41 through 46 removed outlier: 3.727A pdb=" N LEU0F 45 " --> pdb=" O VAL0F 41 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN0F 46 " --> pdb=" O ALA0F 42 " (cutoff:3.500A) No H-bonds generated for 'chain '0F' and resid 41 through 46' Processing helix chain '0F' and resid 96 through 114 removed outlier: 3.587A pdb=" N SER0F 105 " --> pdb=" O LEU0F 101 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS0F 113 " --> pdb=" O GLU0F 109 " (cutoff:3.500A) Processing helix chain '0F' and resid 128 through 132 removed outlier: 3.591A pdb=" N GLU0F 132 " --> pdb=" O GLU0F 129 " (cutoff:3.500A) Processing helix chain '0F' and resid 147 through 157 removed outlier: 3.691A pdb=" N THR0F 157 " --> pdb=" O TYR0F 153 " (cutoff:3.500A) Processing helix chain '1A' and resid 18 through 22 Processing helix chain '1A' and resid 27 through 31 Processing helix chain '1A' and resid 32 through 41 Processing helix chain '1A' and resid 42 through 43 No H-bonds generated for 'chain '1A' and resid 42 through 43' Processing helix chain '1A' and resid 44 through 47 Processing helix chain '1A' and resid 54 through 65 Processing helix chain '1A' and resid 109 through 114 Processing helix chain '1A' and resid 151 through 153 No H-bonds generated for 'chain '1A' and resid 151 through 153' Processing helix chain '1A' and resid 157 through 168 Processing helix chain '1A' and resid 188 through 192 Processing helix chain '1A' and resid 247 through 249 No H-bonds generated for 'chain '1A' and resid 247 through 249' Processing helix chain '1A' and resid 257 through 261 Processing helix chain '1B' and resid 18 through 22 Processing helix chain '1B' and resid 27 through 31 Processing helix chain '1B' and resid 32 through 41 Processing helix chain '1B' and resid 42 through 43 No H-bonds generated for 'chain '1B' and resid 42 through 43' Processing helix chain '1B' and resid 44 through 47 Processing helix chain '1B' and resid 54 through 65 Processing helix chain '1B' and resid 109 through 114 Processing helix chain '1B' and resid 151 through 153 No H-bonds generated for 'chain '1B' and resid 151 through 153' Processing helix chain '1B' and resid 157 through 168 Processing helix chain '1B' and resid 188 through 192 Processing helix chain '1B' and resid 247 through 249 No H-bonds generated for 'chain '1B' and resid 247 through 249' Processing helix chain '1B' and resid 257 through 261 Processing helix chain '1C' and resid 18 through 22 Processing helix chain '1C' and resid 27 through 31 Processing helix chain '1C' and resid 32 through 41 Processing helix chain '1C' and resid 42 through 43 No H-bonds generated for 'chain '1C' and resid 42 through 43' Processing helix chain '1C' and resid 44 through 47 Processing helix chain '1C' and resid 54 through 65 Processing helix chain '1C' and resid 109 through 114 Processing helix chain '1C' and resid 151 through 153 No H-bonds generated for 'chain '1C' and resid 151 through 153' Processing helix chain '1C' and resid 157 through 168 Processing helix chain '1C' and resid 188 through 192 Processing helix chain '1C' and resid 247 through 249 No H-bonds generated for 'chain '1C' and resid 247 through 249' Processing helix chain '1C' and resid 257 through 261 Processing helix chain '1D' and resid 18 through 22 Processing helix chain '1D' and resid 27 through 31 Processing helix chain '1D' and resid 32 through 41 Processing helix chain '1D' and resid 42 through 43 No H-bonds generated for 'chain '1D' and resid 42 through 43' Processing helix chain '1D' and resid 44 through 47 Processing helix chain '1D' and resid 54 through 65 Processing helix chain '1D' and resid 109 through 114 Processing helix chain '1D' and resid 151 through 153 No H-bonds generated for 'chain '1D' and resid 151 through 153' Processing helix chain '1D' and resid 157 through 168 Processing helix chain '1D' and resid 188 through 192 Processing helix chain '1D' and resid 247 through 249 No H-bonds generated for 'chain '1D' and resid 247 through 249' Processing helix chain '1D' and resid 257 through 261 Processing helix chain '1E' and resid 18 through 22 Processing helix chain '1E' and resid 27 through 31 Processing helix chain '1E' and resid 32 through 41 Processing helix chain '1E' and resid 42 through 43 No H-bonds generated for 'chain '1E' and resid 42 through 43' Processing helix chain '1E' and resid 44 through 47 Processing helix chain '1E' and resid 54 through 65 Processing helix chain '1E' and resid 109 through 114 Processing helix chain '1E' and resid 151 through 153 No H-bonds generated for 'chain '1E' and resid 151 through 153' Processing helix chain '1E' and resid 157 through 168 Processing helix chain '1E' and resid 188 through 192 Processing helix chain '1E' and resid 247 through 249 No H-bonds generated for 'chain '1E' and resid 247 through 249' Processing helix chain '1E' and resid 257 through 261 Processing helix chain '1F' and resid 18 through 22 Processing helix chain '1F' and resid 27 through 31 Processing helix chain '1F' and resid 32 through 41 Processing helix chain '1F' and resid 42 through 43 No H-bonds generated for 'chain '1F' and resid 42 through 43' Processing helix chain '1F' and resid 44 through 47 Processing helix chain '1F' and resid 54 through 65 Processing helix chain '1F' and resid 109 through 114 Processing helix chain '1F' and resid 151 through 153 No H-bonds generated for 'chain '1F' and resid 151 through 153' Processing helix chain '1F' and resid 157 through 168 Processing helix chain '1F' and resid 188 through 192 Processing helix chain '1F' and resid 247 through 249 No H-bonds generated for 'chain '1F' and resid 247 through 249' Processing helix chain '1F' and resid 257 through 261 Processing helix chain '1a' and resid 69 through 76 Processing helix chain '1b' and resid 69 through 76 Processing helix chain '1c' and resid 69 through 76 Processing helix chain '1d' and resid 69 through 76 Processing helix chain '1e' and resid 69 through 76 Processing helix chain '1f' and resid 69 through 76 Processing helix chain '2A' and resid 58 through 66 removed outlier: 3.930A pdb=" N THR2A 64 " --> pdb=" O LEU2A 60 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR2A 65 " --> pdb=" O ASP2A 61 " (cutoff:3.500A) Processing helix chain '2A' and resid 104 through 115 Processing helix chain '2A' and resid 141 through 153 removed outlier: 3.709A pdb=" N LEU2A 145 " --> pdb=" O ASN2A 141 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG2A 153 " --> pdb=" O LEU2A 149 " (cutoff:3.500A) Processing helix chain '2A' and resid 165 through 169 Processing helix chain '2A' and resid 171 through 190 Processing helix chain '2A' and resid 212 through 221 Processing helix chain '2A' and resid 224 through 229 Processing helix chain '2A' and resid 247 through 251 Processing helix chain '2A' and resid 261 through 274 Processing helix chain '2A' and resid 279 through 287 Processing helix chain '2A' and resid 322 through 360 removed outlier: 3.886A pdb=" N SER2A 355 " --> pdb=" O LYS2A 351 " (cutoff:3.500A) Processing helix chain '2A' and resid 363 through 379 removed outlier: 3.592A pdb=" N LYS2A 367 " --> pdb=" O ASP2A 363 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU2A 379 " --> pdb=" O ASP2A 375 " (cutoff:3.500A) Processing helix chain '2A' and resid 380 through 381 No H-bonds generated for 'chain '2A' and resid 380 through 381' Processing helix chain '2A' and resid 382 through 385 Processing helix chain '2A' and resid 386 through 405 removed outlier: 4.140A pdb=" N ASP2A 405 " --> pdb=" O ILE2A 401 " (cutoff:3.500A) Processing helix chain '2A' and resid 410 through 418 removed outlier: 5.286A pdb=" N ILE2A 416 " --> pdb=" O ASN2A 412 " (cutoff:3.500A) Processing helix chain '2A' and resid 420 through 427 removed outlier: 3.746A pdb=" N LYS2A 427 " --> pdb=" O ALA2A 423 " (cutoff:3.500A) Processing helix chain '2A' and resid 431 through 435 Processing helix chain '2A' and resid 448 through 462 Processing helix chain '2A' and resid 477 through 481 Processing helix chain '2A' and resid 485 through 497 Processing helix chain '2A' and resid 505 through 520 Processing helix chain '2A' and resid 542 through 551 removed outlier: 3.858A pdb=" N GLU2A 547 " --> pdb=" O HIS2A 543 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N SER2A 548 " --> pdb=" O GLU2A 544 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET2A 549 " --> pdb=" O GLU2A 545 " (cutoff:3.500A) Processing helix chain '2A' and resid 586 through 606 removed outlier: 3.853A pdb=" N GLN2A 606 " --> pdb=" O LYS2A 602 " (cutoff:3.500A) Processing helix chain '2A' and resid 613 through 634 Processing helix chain '2A' and resid 641 through 644 Processing helix chain '2A' and resid 657 through 664 Processing helix chain '2B' and resid 58 through 66 removed outlier: 3.930A pdb=" N THR2B 64 " --> pdb=" O LEU2B 60 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR2B 65 " --> pdb=" O ASP2B 61 " (cutoff:3.500A) Processing helix chain '2B' and resid 104 through 115 Processing helix chain '2B' and resid 141 through 153 removed outlier: 3.709A pdb=" N LEU2B 145 " --> pdb=" O ASN2B 141 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG2B 153 " --> pdb=" O LEU2B 149 " (cutoff:3.500A) Processing helix chain '2B' and resid 165 through 169 Processing helix chain '2B' and resid 171 through 190 Processing helix chain '2B' and resid 212 through 221 Processing helix chain '2B' and resid 224 through 229 Processing helix chain '2B' and resid 247 through 251 Processing helix chain '2B' and resid 261 through 274 Processing helix chain '2B' and resid 279 through 287 Processing helix chain '2B' and resid 322 through 360 removed outlier: 3.887A pdb=" N SER2B 355 " --> pdb=" O LYS2B 351 " (cutoff:3.500A) Processing helix chain '2B' and resid 363 through 379 removed outlier: 3.591A pdb=" N LYS2B 367 " --> pdb=" O ASP2B 363 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU2B 379 " --> pdb=" O ASP2B 375 " (cutoff:3.500A) Processing helix chain '2B' and resid 380 through 381 No H-bonds generated for 'chain '2B' and resid 380 through 381' Processing helix chain '2B' and resid 382 through 385 Processing helix chain '2B' and resid 386 through 405 removed outlier: 4.140A pdb=" N ASP2B 405 " --> pdb=" O ILE2B 401 " (cutoff:3.500A) Processing helix chain '2B' and resid 410 through 418 removed outlier: 5.285A pdb=" N ILE2B 416 " --> pdb=" O ASN2B 412 " (cutoff:3.500A) Processing helix chain '2B' and resid 420 through 427 removed outlier: 3.746A pdb=" N LYS2B 427 " --> pdb=" O ALA2B 423 " (cutoff:3.500A) Processing helix chain '2B' and resid 431 through 435 Processing helix chain '2B' and resid 448 through 462 Processing helix chain '2B' and resid 477 through 481 Processing helix chain '2B' and resid 485 through 497 Processing helix chain '2B' and resid 505 through 520 Processing helix chain '2B' and resid 542 through 551 removed outlier: 3.858A pdb=" N GLU2B 547 " --> pdb=" O HIS2B 543 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N SER2B 548 " --> pdb=" O GLU2B 544 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET2B 549 " --> pdb=" O GLU2B 545 " (cutoff:3.500A) Processing helix chain '2B' and resid 586 through 606 removed outlier: 3.853A pdb=" N GLN2B 606 " --> pdb=" O LYS2B 602 " (cutoff:3.500A) Processing helix chain '2B' and resid 613 through 634 Processing helix chain '2B' and resid 641 through 644 Processing helix chain '2B' and resid 657 through 664 Processing helix chain '2C' and resid 58 through 66 removed outlier: 3.930A pdb=" N THR2C 64 " --> pdb=" O LEU2C 60 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR2C 65 " --> pdb=" O ASP2C 61 " (cutoff:3.500A) Processing helix chain '2C' and resid 104 through 115 Processing helix chain '2C' and resid 141 through 153 removed outlier: 3.710A pdb=" N LEU2C 145 " --> pdb=" O ASN2C 141 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG2C 153 " --> pdb=" O LEU2C 149 " (cutoff:3.500A) Processing helix chain '2C' and resid 165 through 169 Processing helix chain '2C' and resid 171 through 190 Processing helix chain '2C' and resid 212 through 221 Processing helix chain '2C' and resid 224 through 229 Processing helix chain '2C' and resid 247 through 251 Processing helix chain '2C' and resid 261 through 274 Processing helix chain '2C' and resid 279 through 287 Processing helix chain '2C' and resid 322 through 360 removed outlier: 3.886A pdb=" N SER2C 355 " --> pdb=" O LYS2C 351 " (cutoff:3.500A) Processing helix chain '2C' and resid 363 through 379 removed outlier: 3.593A pdb=" N LYS2C 367 " --> pdb=" O ASP2C 363 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU2C 379 " --> pdb=" O ASP2C 375 " (cutoff:3.500A) Processing helix chain '2C' and resid 380 through 381 No H-bonds generated for 'chain '2C' and resid 380 through 381' Processing helix chain '2C' and resid 382 through 385 Processing helix chain '2C' and resid 386 through 405 removed outlier: 4.140A pdb=" N ASP2C 405 " --> pdb=" O ILE2C 401 " (cutoff:3.500A) Processing helix chain '2C' and resid 410 through 418 removed outlier: 5.285A pdb=" N ILE2C 416 " --> pdb=" O ASN2C 412 " (cutoff:3.500A) Processing helix chain '2C' and resid 420 through 427 removed outlier: 3.746A pdb=" N LYS2C 427 " --> pdb=" O ALA2C 423 " (cutoff:3.500A) Processing helix chain '2C' and resid 431 through 435 Processing helix chain '2C' and resid 448 through 462 Processing helix chain '2C' and resid 477 through 481 Processing helix chain '2C' and resid 485 through 497 Processing helix chain '2C' and resid 505 through 520 Processing helix chain '2C' and resid 542 through 551 removed outlier: 3.858A pdb=" N GLU2C 547 " --> pdb=" O HIS2C 543 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N SER2C 548 " --> pdb=" O GLU2C 544 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET2C 549 " --> pdb=" O GLU2C 545 " (cutoff:3.500A) Processing helix chain '2C' and resid 586 through 606 removed outlier: 3.853A pdb=" N GLN2C 606 " --> pdb=" O LYS2C 602 " (cutoff:3.500A) Processing helix chain '2C' and resid 613 through 634 Processing helix chain '2C' and resid 641 through 644 Processing helix chain '2C' and resid 657 through 664 Processing helix chain '2D' and resid 58 through 66 removed outlier: 3.930A pdb=" N THR2D 64 " --> pdb=" O LEU2D 60 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR2D 65 " --> pdb=" O ASP2D 61 " (cutoff:3.500A) Processing helix chain '2D' and resid 104 through 115 Processing helix chain '2D' and resid 141 through 153 removed outlier: 3.710A pdb=" N LEU2D 145 " --> pdb=" O ASN2D 141 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG2D 153 " --> pdb=" O LEU2D 149 " (cutoff:3.500A) Processing helix chain '2D' and resid 165 through 169 Processing helix chain '2D' and resid 171 through 190 Processing helix chain '2D' and resid 212 through 221 Processing helix chain '2D' and resid 224 through 229 Processing helix chain '2D' and resid 247 through 251 Processing helix chain '2D' and resid 261 through 274 Processing helix chain '2D' and resid 279 through 287 Processing helix chain '2D' and resid 322 through 360 removed outlier: 3.886A pdb=" N SER2D 355 " --> pdb=" O LYS2D 351 " (cutoff:3.500A) Processing helix chain '2D' and resid 363 through 379 removed outlier: 3.590A pdb=" N LYS2D 367 " --> pdb=" O ASP2D 363 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU2D 379 " --> pdb=" O ASP2D 375 " (cutoff:3.500A) Processing helix chain '2D' and resid 380 through 381 No H-bonds generated for 'chain '2D' and resid 380 through 381' Processing helix chain '2D' and resid 382 through 385 Processing helix chain '2D' and resid 386 through 405 removed outlier: 4.141A pdb=" N ASP2D 405 " --> pdb=" O ILE2D 401 " (cutoff:3.500A) Processing helix chain '2D' and resid 410 through 418 removed outlier: 5.286A pdb=" N ILE2D 416 " --> pdb=" O ASN2D 412 " (cutoff:3.500A) Processing helix chain '2D' and resid 420 through 427 removed outlier: 3.747A pdb=" N LYS2D 427 " --> pdb=" O ALA2D 423 " (cutoff:3.500A) Processing helix chain '2D' and resid 431 through 435 Processing helix chain '2D' and resid 448 through 462 Processing helix chain '2D' and resid 477 through 481 Processing helix chain '2D' and resid 485 through 497 Processing helix chain '2D' and resid 505 through 520 Processing helix chain '2D' and resid 542 through 551 removed outlier: 3.858A pdb=" N GLU2D 547 " --> pdb=" O HIS2D 543 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N SER2D 548 " --> pdb=" O GLU2D 544 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET2D 549 " --> pdb=" O GLU2D 545 " (cutoff:3.500A) Processing helix chain '2D' and resid 586 through 606 removed outlier: 3.853A pdb=" N GLN2D 606 " --> pdb=" O LYS2D 602 " (cutoff:3.500A) Processing helix chain '2D' and resid 613 through 634 Processing helix chain '2D' and resid 641 through 644 Processing helix chain '2D' and resid 657 through 664 Processing helix chain '2E' and resid 58 through 66 removed outlier: 3.931A pdb=" N THR2E 64 " --> pdb=" O LEU2E 60 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR2E 65 " --> pdb=" O ASP2E 61 " (cutoff:3.500A) Processing helix chain '2E' and resid 104 through 115 Processing helix chain '2E' and resid 141 through 153 removed outlier: 3.709A pdb=" N LEU2E 145 " --> pdb=" O ASN2E 141 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG2E 153 " --> pdb=" O LEU2E 149 " (cutoff:3.500A) Processing helix chain '2E' and resid 165 through 169 Processing helix chain '2E' and resid 171 through 190 Processing helix chain '2E' and resid 212 through 221 Processing helix chain '2E' and resid 224 through 229 Processing helix chain '2E' and resid 247 through 251 Processing helix chain '2E' and resid 261 through 274 Processing helix chain '2E' and resid 279 through 287 Processing helix chain '2E' and resid 322 through 360 removed outlier: 3.887A pdb=" N SER2E 355 " --> pdb=" O LYS2E 351 " (cutoff:3.500A) Processing helix chain '2E' and resid 363 through 379 removed outlier: 3.591A pdb=" N LYS2E 367 " --> pdb=" O ASP2E 363 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU2E 379 " --> pdb=" O ASP2E 375 " (cutoff:3.500A) Processing helix chain '2E' and resid 380 through 381 No H-bonds generated for 'chain '2E' and resid 380 through 381' Processing helix chain '2E' and resid 382 through 385 Processing helix chain '2E' and resid 386 through 405 removed outlier: 4.141A pdb=" N ASP2E 405 " --> pdb=" O ILE2E 401 " (cutoff:3.500A) Processing helix chain '2E' and resid 410 through 418 removed outlier: 5.285A pdb=" N ILE2E 416 " --> pdb=" O ASN2E 412 " (cutoff:3.500A) Processing helix chain '2E' and resid 420 through 427 removed outlier: 3.746A pdb=" N LYS2E 427 " --> pdb=" O ALA2E 423 " (cutoff:3.500A) Processing helix chain '2E' and resid 431 through 435 Processing helix chain '2E' and resid 448 through 462 Processing helix chain '2E' and resid 477 through 481 Processing helix chain '2E' and resid 485 through 497 Processing helix chain '2E' and resid 505 through 520 Processing helix chain '2E' and resid 542 through 551 removed outlier: 3.858A pdb=" N GLU2E 547 " --> pdb=" O HIS2E 543 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N SER2E 548 " --> pdb=" O GLU2E 544 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET2E 549 " --> pdb=" O GLU2E 545 " (cutoff:3.500A) Processing helix chain '2E' and resid 586 through 606 removed outlier: 3.853A pdb=" N GLN2E 606 " --> pdb=" O LYS2E 602 " (cutoff:3.500A) Processing helix chain '2E' and resid 613 through 634 Processing helix chain '2E' and resid 641 through 644 Processing helix chain '2E' and resid 657 through 664 Processing helix chain '2F' and resid 58 through 66 removed outlier: 3.930A pdb=" N THR2F 64 " --> pdb=" O LEU2F 60 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR2F 65 " --> pdb=" O ASP2F 61 " (cutoff:3.500A) Processing helix chain '2F' and resid 104 through 115 Processing helix chain '2F' and resid 141 through 153 removed outlier: 3.710A pdb=" N LEU2F 145 " --> pdb=" O ASN2F 141 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG2F 153 " --> pdb=" O LEU2F 149 " (cutoff:3.500A) Processing helix chain '2F' and resid 165 through 169 Processing helix chain '2F' and resid 171 through 190 Processing helix chain '2F' and resid 212 through 221 Processing helix chain '2F' and resid 224 through 229 Processing helix chain '2F' and resid 247 through 251 Processing helix chain '2F' and resid 261 through 274 Processing helix chain '2F' and resid 279 through 287 Processing helix chain '2F' and resid 322 through 360 removed outlier: 3.887A pdb=" N SER2F 355 " --> pdb=" O LYS2F 351 " (cutoff:3.500A) Processing helix chain '2F' and resid 363 through 379 removed outlier: 3.592A pdb=" N LYS2F 367 " --> pdb=" O ASP2F 363 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU2F 379 " --> pdb=" O ASP2F 375 " (cutoff:3.500A) Processing helix chain '2F' and resid 380 through 381 No H-bonds generated for 'chain '2F' and resid 380 through 381' Processing helix chain '2F' and resid 382 through 385 Processing helix chain '2F' and resid 386 through 405 removed outlier: 4.141A pdb=" N ASP2F 405 " --> pdb=" O ILE2F 401 " (cutoff:3.500A) Processing helix chain '2F' and resid 410 through 418 removed outlier: 5.286A pdb=" N ILE2F 416 " --> pdb=" O ASN2F 412 " (cutoff:3.500A) Processing helix chain '2F' and resid 420 through 427 removed outlier: 3.747A pdb=" N LYS2F 427 " --> pdb=" O ALA2F 423 " (cutoff:3.500A) Processing helix chain '2F' and resid 431 through 435 Processing helix chain '2F' and resid 448 through 462 Processing helix chain '2F' and resid 477 through 481 Processing helix chain '2F' and resid 485 through 497 Processing helix chain '2F' and resid 505 through 520 Processing helix chain '2F' and resid 542 through 551 removed outlier: 3.858A pdb=" N GLU2F 547 " --> pdb=" O HIS2F 543 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N SER2F 548 " --> pdb=" O GLU2F 544 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET2F 549 " --> pdb=" O GLU2F 545 " (cutoff:3.500A) Processing helix chain '2F' and resid 586 through 606 removed outlier: 3.853A pdb=" N GLN2F 606 " --> pdb=" O LYS2F 602 " (cutoff:3.500A) Processing helix chain '2F' and resid 613 through 634 Processing helix chain '2F' and resid 641 through 644 Processing helix chain '2F' and resid 657 through 664 Processing helix chain '2a' and resid 69 through 76 Processing helix chain '2b' and resid 69 through 76 Processing helix chain '2c' and resid 69 through 76 Processing helix chain '2d' and resid 69 through 76 Processing helix chain '2e' and resid 69 through 76 Processing helix chain '2f' and resid 69 through 76 Processing sheet with id=AA1, first strand: chain '0A' and resid 27 through 29 removed outlier: 6.438A pdb=" N VAL0A 28 " --> pdb=" O LEU0A 51 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N MET0A 53 " --> pdb=" O VAL0A 28 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE0A 87 " --> pdb=" O ILE0A 54 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU0A 56 " --> pdb=" O ASN0A 85 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN0A 85 " --> pdb=" O LEU0A 56 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU0A 58 " --> pdb=" O ASN0A 83 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASN0A 83 " --> pdb=" O GLU0A 58 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU0A 82 " --> pdb=" O VAL0A 174 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N VAL0A 174 " --> pdb=" O LEU0A 82 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE0A 84 " --> pdb=" O LEU0A 172 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE0A 167 " --> pdb=" O PHE0A 144 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR0A 140 " --> pdb=" O ASN0A 171 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE0A 173 " --> pdb=" O ARG0A 138 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N ARG0A 138 " --> pdb=" O ILE0A 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0A' and resid 69 through 71 removed outlier: 3.916A pdb=" N SER0A 182 " --> pdb=" O TYR0A 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1A' and resid 66 through 71 removed outlier: 6.816A pdb=" N ILE1A 75 " --> pdb=" O LYS1A 12 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS1A 12 " --> pdb=" O ILE1A 75 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU1A 77 " --> pdb=" O PHE1A 10 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1A' and resid 66 through 71 removed outlier: 6.816A pdb=" N ILE1A 75 " --> pdb=" O LYS1A 12 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS1A 12 " --> pdb=" O ILE1A 75 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU1A 77 " --> pdb=" O PHE1A 10 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE0A 190 " --> pdb=" O SER1A 5 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN0A 189 " --> pdb=" O MET2A 666 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL2A 668 " --> pdb=" O ASN0A 189 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N HIS0A 191 " --> pdb=" O VAL2A 668 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE2A 670 " --> pdb=" O HIS0A 191 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASN0A 193 " --> pdb=" O ILE2A 670 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU2A 672 " --> pdb=" O ASN0A 193 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU0A 195 " --> pdb=" O LEU2A 672 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '0B' and resid 27 through 29 removed outlier: 6.438A pdb=" N VAL0B 28 " --> pdb=" O LEU0B 51 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N MET0B 53 " --> pdb=" O VAL0B 28 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE0B 87 " --> pdb=" O ILE0B 54 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU0B 56 " --> pdb=" O ASN0B 85 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN0B 85 " --> pdb=" O LEU0B 56 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU0B 58 " --> pdb=" O ASN0B 83 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASN0B 83 " --> pdb=" O GLU0B 58 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU0B 82 " --> pdb=" O VAL0B 174 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL0B 174 " --> pdb=" O LEU0B 82 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE0B 84 " --> pdb=" O LEU0B 172 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE0B 167 " --> pdb=" O PHE0B 144 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR0B 140 " --> pdb=" O ASN0B 171 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE0B 173 " --> pdb=" O ARG0B 138 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N ARG0B 138 " --> pdb=" O ILE0B 173 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '0B' and resid 69 through 71 removed outlier: 3.915A pdb=" N SER0B 182 " --> pdb=" O TYR0B 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1F' and resid 66 through 71 removed outlier: 6.816A pdb=" N ILE1F 75 " --> pdb=" O LYS1F 12 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS1F 12 " --> pdb=" O ILE1F 75 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU1F 77 " --> pdb=" O PHE1F 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '1F' and resid 66 through 71 removed outlier: 6.816A pdb=" N ILE1F 75 " --> pdb=" O LYS1F 12 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS1F 12 " --> pdb=" O ILE1F 75 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU1F 77 " --> pdb=" O PHE1F 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE0B 190 " --> pdb=" O SER1F 5 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN0B 189 " --> pdb=" O MET2F 666 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL2F 668 " --> pdb=" O ASN0B 189 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N HIS0B 191 " --> pdb=" O VAL2F 668 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE2F 670 " --> pdb=" O HIS0B 191 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN0B 193 " --> pdb=" O ILE2F 670 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N LEU2F 672 " --> pdb=" O ASN0B 193 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU0B 195 " --> pdb=" O LEU2F 672 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '0C' and resid 27 through 29 removed outlier: 6.438A pdb=" N VAL0C 28 " --> pdb=" O LEU0C 51 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N MET0C 53 " --> pdb=" O VAL0C 28 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE0C 87 " --> pdb=" O ILE0C 54 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU0C 56 " --> pdb=" O ASN0C 85 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN0C 85 " --> pdb=" O LEU0C 56 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU0C 58 " --> pdb=" O ASN0C 83 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN0C 83 " --> pdb=" O GLU0C 58 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU0C 82 " --> pdb=" O VAL0C 174 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N VAL0C 174 " --> pdb=" O LEU0C 82 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE0C 84 " --> pdb=" O LEU0C 172 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE0C 167 " --> pdb=" O PHE0C 144 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR0C 140 " --> pdb=" O ASN0C 171 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE0C 173 " --> pdb=" O ARG0C 138 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N ARG0C 138 " --> pdb=" O ILE0C 173 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '0C' and resid 69 through 71 removed outlier: 3.915A pdb=" N SER0C 182 " --> pdb=" O TYR0C 77 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '1E' and resid 66 through 71 removed outlier: 6.817A pdb=" N ILE1E 75 " --> pdb=" O LYS1E 12 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS1E 12 " --> pdb=" O ILE1E 75 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU1E 77 " --> pdb=" O PHE1E 10 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '1E' and resid 66 through 71 removed outlier: 6.817A pdb=" N ILE1E 75 " --> pdb=" O LYS1E 12 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS1E 12 " --> pdb=" O ILE1E 75 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU1E 77 " --> pdb=" O PHE1E 10 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE0C 190 " --> pdb=" O SER1E 5 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN0C 189 " --> pdb=" O MET2E 666 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL2E 668 " --> pdb=" O ASN0C 189 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N HIS0C 191 " --> pdb=" O VAL2E 668 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE2E 670 " --> pdb=" O HIS0C 191 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASN0C 193 " --> pdb=" O ILE2E 670 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU2E 672 " --> pdb=" O ASN0C 193 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLU0C 195 " --> pdb=" O LEU2E 672 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '0D' and resid 27 through 29 removed outlier: 6.439A pdb=" N VAL0D 28 " --> pdb=" O LEU0D 51 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N MET0D 53 " --> pdb=" O VAL0D 28 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE0D 87 " --> pdb=" O ILE0D 54 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU0D 56 " --> pdb=" O ASN0D 85 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN0D 85 " --> pdb=" O LEU0D 56 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU0D 58 " --> pdb=" O ASN0D 83 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASN0D 83 " --> pdb=" O GLU0D 58 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU0D 82 " --> pdb=" O VAL0D 174 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL0D 174 " --> pdb=" O LEU0D 82 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE0D 84 " --> pdb=" O LEU0D 172 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE0D 167 " --> pdb=" O PHE0D 144 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR0D 140 " --> pdb=" O ASN0D 171 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE0D 173 " --> pdb=" O ARG0D 138 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N ARG0D 138 " --> pdb=" O ILE0D 173 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '0D' and resid 69 through 71 removed outlier: 3.916A pdb=" N SER0D 182 " --> pdb=" O TYR0D 77 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '1D' and resid 66 through 71 removed outlier: 6.817A pdb=" N ILE1D 75 " --> pdb=" O LYS1D 12 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS1D 12 " --> pdb=" O ILE1D 75 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU1D 77 " --> pdb=" O PHE1D 10 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '1D' and resid 66 through 71 removed outlier: 6.817A pdb=" N ILE1D 75 " --> pdb=" O LYS1D 12 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS1D 12 " --> pdb=" O ILE1D 75 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU1D 77 " --> pdb=" O PHE1D 10 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE0D 190 " --> pdb=" O SER1D 5 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN0D 189 " --> pdb=" O MET2D 666 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL2D 668 " --> pdb=" O ASN0D 189 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N HIS0D 191 " --> pdb=" O VAL2D 668 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE2D 670 " --> pdb=" O HIS0D 191 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN0D 193 " --> pdb=" O ILE2D 670 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N LEU2D 672 " --> pdb=" O ASN0D 193 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU0D 195 " --> pdb=" O LEU2D 672 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '0E' and resid 27 through 29 removed outlier: 6.439A pdb=" N VAL0E 28 " --> pdb=" O LEU0E 51 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N MET0E 53 " --> pdb=" O VAL0E 28 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE0E 87 " --> pdb=" O ILE0E 54 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU0E 56 " --> pdb=" O ASN0E 85 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN0E 85 " --> pdb=" O LEU0E 56 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU0E 58 " --> pdb=" O ASN0E 83 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASN0E 83 " --> pdb=" O GLU0E 58 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU0E 82 " --> pdb=" O VAL0E 174 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N VAL0E 174 " --> pdb=" O LEU0E 82 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE0E 84 " --> pdb=" O LEU0E 172 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE0E 167 " --> pdb=" O PHE0E 144 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR0E 140 " --> pdb=" O ASN0E 171 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE0E 173 " --> pdb=" O ARG0E 138 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N ARG0E 138 " --> pdb=" O ILE0E 173 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '0E' and resid 69 through 71 removed outlier: 3.915A pdb=" N SER0E 182 " --> pdb=" O TYR0E 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '1C' and resid 66 through 71 removed outlier: 6.817A pdb=" N ILE1C 75 " --> pdb=" O LYS1C 12 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS1C 12 " --> pdb=" O ILE1C 75 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU1C 77 " --> pdb=" O PHE1C 10 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '1C' and resid 66 through 71 removed outlier: 6.817A pdb=" N ILE1C 75 " --> pdb=" O LYS1C 12 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS1C 12 " --> pdb=" O ILE1C 75 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU1C 77 " --> pdb=" O PHE1C 10 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE0E 190 " --> pdb=" O SER1C 5 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN0E 189 " --> pdb=" O MET2C 666 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N VAL2C 668 " --> pdb=" O ASN0E 189 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N HIS0E 191 " --> pdb=" O VAL2C 668 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE2C 670 " --> pdb=" O HIS0E 191 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASN0E 193 " --> pdb=" O ILE2C 670 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N LEU2C 672 " --> pdb=" O ASN0E 193 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU0E 195 " --> pdb=" O LEU2C 672 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '0F' and resid 27 through 29 removed outlier: 6.439A pdb=" N VAL0F 28 " --> pdb=" O LEU0F 51 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N MET0F 53 " --> pdb=" O VAL0F 28 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE0F 87 " --> pdb=" O ILE0F 54 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU0F 56 " --> pdb=" O ASN0F 85 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN0F 85 " --> pdb=" O LEU0F 56 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU0F 58 " --> pdb=" O ASN0F 83 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN0F 83 " --> pdb=" O GLU0F 58 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU0F 82 " --> pdb=" O VAL0F 174 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL0F 174 " --> pdb=" O LEU0F 82 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE0F 84 " --> pdb=" O LEU0F 172 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE0F 167 " --> pdb=" O PHE0F 144 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR0F 140 " --> pdb=" O ASN0F 171 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE0F 173 " --> pdb=" O ARG0F 138 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N ARG0F 138 " --> pdb=" O ILE0F 173 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '0F' and resid 69 through 71 removed outlier: 3.916A pdb=" N SER0F 182 " --> pdb=" O TYR0F 77 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '1B' and resid 66 through 71 removed outlier: 6.816A pdb=" N ILE1B 75 " --> pdb=" O LYS1B 12 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS1B 12 " --> pdb=" O ILE1B 75 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU1B 77 " --> pdb=" O PHE1B 10 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '1B' and resid 66 through 71 removed outlier: 6.816A pdb=" N ILE1B 75 " --> pdb=" O LYS1B 12 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS1B 12 " --> pdb=" O ILE1B 75 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU1B 77 " --> pdb=" O PHE1B 10 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE0F 190 " --> pdb=" O SER1B 5 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN0F 189 " --> pdb=" O MET2B 666 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL2B 668 " --> pdb=" O ASN0F 189 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS0F 191 " --> pdb=" O VAL2B 668 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE2B 670 " --> pdb=" O HIS0F 191 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASN0F 193 " --> pdb=" O ILE2B 670 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU2B 672 " --> pdb=" O ASN0F 193 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU0F 195 " --> pdb=" O LEU2B 672 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '1A' and resid 49 through 53 removed outlier: 6.732A pdb=" N LEU1A 123 " --> pdb=" O ILE1A 179 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N GLN1A 181 " --> pdb=" O LEU1A 123 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N PHE1A 125 " --> pdb=" O GLN1A 181 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N TYR1A 183 " --> pdb=" O PHE1A 125 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '1A' and resid 235 through 236 removed outlier: 5.487A pdb=" N TRP1A 218 " --> pdb=" O THR1A 231 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU1A 230 " --> pdb=" O ILE1A 252 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '1A' and resid 235 through 236 removed outlier: 7.788A pdb=" N LYS1A 215 " --> pdb=" O ASN1A 278 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N SER1A 280 " --> pdb=" O LYS1A 215 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR1A 217 " --> pdb=" O SER1A 280 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE1A 282 " --> pdb=" O THR1A 217 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYS1A 219 " --> pdb=" O ILE1A 282 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '1B' and resid 49 through 53 removed outlier: 6.732A pdb=" N LEU1B 123 " --> pdb=" O ILE1B 179 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N GLN1B 181 " --> pdb=" O LEU1B 123 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE1B 125 " --> pdb=" O GLN1B 181 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N TYR1B 183 " --> pdb=" O PHE1B 125 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '1B' and resid 235 through 236 removed outlier: 5.486A pdb=" N TRP1B 218 " --> pdb=" O THR1B 231 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU1B 230 " --> pdb=" O ILE1B 252 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '1B' and resid 235 through 236 removed outlier: 7.787A pdb=" N LYS1B 215 " --> pdb=" O ASN1B 278 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N SER1B 280 " --> pdb=" O LYS1B 215 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR1B 217 " --> pdb=" O SER1B 280 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE1B 282 " --> pdb=" O THR1B 217 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS1B 219 " --> pdb=" O ILE1B 282 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '1C' and resid 49 through 53 removed outlier: 6.733A pdb=" N LEU1C 123 " --> pdb=" O ILE1C 179 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLN1C 181 " --> pdb=" O LEU1C 123 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N PHE1C 125 " --> pdb=" O GLN1C 181 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TYR1C 183 " --> pdb=" O PHE1C 125 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '1C' and resid 235 through 236 removed outlier: 5.487A pdb=" N TRP1C 218 " --> pdb=" O THR1C 231 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU1C 230 " --> pdb=" O ILE1C 252 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '1C' and resid 235 through 236 removed outlier: 7.788A pdb=" N LYS1C 215 " --> pdb=" O ASN1C 278 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N SER1C 280 " --> pdb=" O LYS1C 215 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR1C 217 " --> pdb=" O SER1C 280 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE1C 282 " --> pdb=" O THR1C 217 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYS1C 219 " --> pdb=" O ILE1C 282 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '1D' and resid 49 through 53 removed outlier: 6.732A pdb=" N LEU1D 123 " --> pdb=" O ILE1D 179 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N GLN1D 181 " --> pdb=" O LEU1D 123 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE1D 125 " --> pdb=" O GLN1D 181 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TYR1D 183 " --> pdb=" O PHE1D 125 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '1D' and resid 235 through 236 removed outlier: 5.488A pdb=" N TRP1D 218 " --> pdb=" O THR1D 231 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU1D 230 " --> pdb=" O ILE1D 252 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '1D' and resid 235 through 236 removed outlier: 7.788A pdb=" N LYS1D 215 " --> pdb=" O ASN1D 278 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N SER1D 280 " --> pdb=" O LYS1D 215 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR1D 217 " --> pdb=" O SER1D 280 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE1D 282 " --> pdb=" O THR1D 217 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LYS1D 219 " --> pdb=" O ILE1D 282 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '1E' and resid 49 through 53 removed outlier: 6.733A pdb=" N LEU1E 123 " --> pdb=" O ILE1E 179 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N GLN1E 181 " --> pdb=" O LEU1E 123 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N PHE1E 125 " --> pdb=" O GLN1E 181 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TYR1E 183 " --> pdb=" O PHE1E 125 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '1E' and resid 235 through 236 removed outlier: 5.486A pdb=" N TRP1E 218 " --> pdb=" O THR1E 231 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU1E 230 " --> pdb=" O ILE1E 252 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '1E' and resid 235 through 236 removed outlier: 7.788A pdb=" N LYS1E 215 " --> pdb=" O ASN1E 278 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N SER1E 280 " --> pdb=" O LYS1E 215 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR1E 217 " --> pdb=" O SER1E 280 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE1E 282 " --> pdb=" O THR1E 217 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYS1E 219 " --> pdb=" O ILE1E 282 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '1F' and resid 49 through 53 removed outlier: 6.733A pdb=" N LEU1F 123 " --> pdb=" O ILE1F 179 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N GLN1F 181 " --> pdb=" O LEU1F 123 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE1F 125 " --> pdb=" O GLN1F 181 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N TYR1F 183 " --> pdb=" O PHE1F 125 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '1F' and resid 235 through 236 removed outlier: 5.486A pdb=" N TRP1F 218 " --> pdb=" O THR1F 231 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU1F 230 " --> pdb=" O ILE1F 252 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '1F' and resid 235 through 236 removed outlier: 7.789A pdb=" N LYS1F 215 " --> pdb=" O ASN1F 278 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N SER1F 280 " --> pdb=" O LYS1F 215 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR1F 217 " --> pdb=" O SER1F 280 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE1F 282 " --> pdb=" O THR1F 217 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYS1F 219 " --> pdb=" O ILE1F 282 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '1a' and resid 10 through 13 removed outlier: 5.645A pdb=" N ARG1a 86 " --> pdb=" O ASN1a 107 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN1a 107 " --> pdb=" O ARG1a 86 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL1a 101 " --> pdb=" O LEU1a 92 " (cutoff:3.500A) removed outlier: 16.775A pdb=" N ASN1a 107 " --> pdb=" O GLU1b 35 " (cutoff:3.500A) removed outlier: 12.584A pdb=" N GLU1b 35 " --> pdb=" O ASN1a 107 " (cutoff:3.500A) removed outlier: 13.480A pdb=" N TRP1a 109 " --> pdb=" O ILE1b 33 " (cutoff:3.500A) removed outlier: 10.276A pdb=" N ILE1b 33 " --> pdb=" O TRP1a 109 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU1a 111 " --> pdb=" O THR1b 31 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU1b 30 " --> pdb=" O LYS1b 54 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N MET1b 52 " --> pdb=" O GLU1b 32 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE1b 34 " --> pdb=" O PRO1b 50 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N TYR1b 36 " --> pdb=" O LYS1b 48 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LYS1b 48 " --> pdb=" O TYR1b 36 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '1a' and resid 137 through 140 removed outlier: 6.236A pdb=" N ALA1a 133 " --> pdb=" O PRO1a 110 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS1a 112 " --> pdb=" O GLU1a 131 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU1a 23 " --> pdb=" O LYS1a 61 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '1a' and resid 47 through 54 removed outlier: 5.762A pdb=" N LYS1a 48 " --> pdb=" O TYR1a 36 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N TYR1a 36 " --> pdb=" O LYS1a 48 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE1a 34 " --> pdb=" O PRO1a 50 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N MET1a 52 " --> pdb=" O GLU1a 32 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU1a 30 " --> pdb=" O LYS1a 54 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU1f 111 " --> pdb=" O THR1a 31 " (cutoff:3.500A) removed outlier: 10.301A pdb=" N ILE1a 33 " --> pdb=" O TRP1f 109 " (cutoff:3.500A) removed outlier: 13.503A pdb=" N TRP1f 109 " --> pdb=" O ILE1a 33 " (cutoff:3.500A) removed outlier: 12.607A pdb=" N GLU1a 35 " --> pdb=" O ASN1f 107 " (cutoff:3.500A) removed outlier: 16.798A pdb=" N ASN1f 107 " --> pdb=" O GLU1a 35 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL1f 101 " --> pdb=" O LEU1f 92 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN1f 107 " --> pdb=" O ARG1f 86 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ARG1f 86 " --> pdb=" O ASN1f 107 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '1e' and resid 118 through 119 removed outlier: 3.598A pdb=" N GLU1f 23 " --> pdb=" O LYS1f 61 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS1f 112 " --> pdb=" O GLU1f 131 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA1f 133 " --> pdb=" O PRO1f 110 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '1a' and resid 118 through 119 removed outlier: 3.598A pdb=" N GLU1b 23 " --> pdb=" O LYS1b 61 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS1b 112 " --> pdb=" O GLU1b 131 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA1b 133 " --> pdb=" O PRO1b 110 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '1b' and resid 10 through 13 removed outlier: 5.644A pdb=" N ARG1b 86 " --> pdb=" O ASN1b 107 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN1b 107 " --> pdb=" O ARG1b 86 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL1b 101 " --> pdb=" O LEU1b 92 " (cutoff:3.500A) removed outlier: 16.800A pdb=" N ASN1b 107 " --> pdb=" O GLU1c 35 " (cutoff:3.500A) removed outlier: 12.608A pdb=" N GLU1c 35 " --> pdb=" O ASN1b 107 " (cutoff:3.500A) removed outlier: 13.502A pdb=" N TRP1b 109 " --> pdb=" O ILE1c 33 " (cutoff:3.500A) removed outlier: 10.297A pdb=" N ILE1c 33 " --> pdb=" O TRP1b 109 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU1b 111 " --> pdb=" O THR1c 31 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU1c 30 " --> pdb=" O LYS1c 54 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET1c 52 " --> pdb=" O GLU1c 32 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE1c 34 " --> pdb=" O PRO1c 50 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N TYR1c 36 " --> pdb=" O LYS1c 48 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS1c 48 " --> pdb=" O TYR1c 36 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '1b' and resid 118 through 119 removed outlier: 3.598A pdb=" N GLU1c 23 " --> pdb=" O LYS1c 61 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS1c 112 " --> pdb=" O GLU1c 131 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA1c 133 " --> pdb=" O PRO1c 110 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain '1c' and resid 10 through 13 removed outlier: 5.644A pdb=" N ARG1c 86 " --> pdb=" O ASN1c 107 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN1c 107 " --> pdb=" O ARG1c 86 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL1c 101 " --> pdb=" O LEU1c 92 " (cutoff:3.500A) removed outlier: 16.790A pdb=" N ASN1c 107 " --> pdb=" O GLU1d 35 " (cutoff:3.500A) removed outlier: 12.598A pdb=" N GLU1d 35 " --> pdb=" O ASN1c 107 " (cutoff:3.500A) removed outlier: 13.492A pdb=" N TRP1c 109 " --> pdb=" O ILE1d 33 " (cutoff:3.500A) removed outlier: 10.290A pdb=" N ILE1d 33 " --> pdb=" O TRP1c 109 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU1c 111 " --> pdb=" O THR1d 31 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU1d 30 " --> pdb=" O LYS1d 54 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N MET1d 52 " --> pdb=" O GLU1d 32 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE1d 34 " --> pdb=" O PRO1d 50 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N TYR1d 36 " --> pdb=" O LYS1d 48 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LYS1d 48 " --> pdb=" O TYR1d 36 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '1c' and resid 118 through 119 removed outlier: 3.597A pdb=" N GLU1d 23 " --> pdb=" O LYS1d 61 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS1d 112 " --> pdb=" O GLU1d 131 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA1d 133 " --> pdb=" O PRO1d 110 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain '1d' and resid 10 through 13 removed outlier: 5.644A pdb=" N ARG1d 86 " --> pdb=" O ASN1d 107 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN1d 107 " --> pdb=" O ARG1d 86 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL1d 101 " --> pdb=" O LEU1d 92 " (cutoff:3.500A) removed outlier: 16.803A pdb=" N ASN1d 107 " --> pdb=" O GLU1e 35 " (cutoff:3.500A) removed outlier: 12.612A pdb=" N GLU1e 35 " --> pdb=" O ASN1d 107 " (cutoff:3.500A) removed outlier: 13.506A pdb=" N TRP1d 109 " --> pdb=" O ILE1e 33 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N ILE1e 33 " --> pdb=" O TRP1d 109 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU1d 111 " --> pdb=" O THR1e 31 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU1e 30 " --> pdb=" O LYS1e 54 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N MET1e 52 " --> pdb=" O GLU1e 32 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE1e 34 " --> pdb=" O PRO1e 50 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N TYR1e 36 " --> pdb=" O LYS1e 48 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LYS1e 48 " --> pdb=" O TYR1e 36 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain '1d' and resid 118 through 119 removed outlier: 3.598A pdb=" N GLU1e 23 " --> pdb=" O LYS1e 61 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS1e 112 " --> pdb=" O GLU1e 131 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA1e 133 " --> pdb=" O PRO1e 110 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain '1e' and resid 10 through 13 removed outlier: 5.645A pdb=" N ARG1e 86 " --> pdb=" O ASN1e 107 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN1e 107 " --> pdb=" O ARG1e 86 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL1e 101 " --> pdb=" O LEU1e 92 " (cutoff:3.500A) removed outlier: 16.800A pdb=" N ASN1e 107 " --> pdb=" O GLU1f 35 " (cutoff:3.500A) removed outlier: 12.608A pdb=" N GLU1f 35 " --> pdb=" O ASN1e 107 " (cutoff:3.500A) removed outlier: 13.502A pdb=" N TRP1e 109 " --> pdb=" O ILE1f 33 " (cutoff:3.500A) removed outlier: 10.297A pdb=" N ILE1f 33 " --> pdb=" O TRP1e 109 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU1e 111 " --> pdb=" O THR1f 31 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU1f 30 " --> pdb=" O LYS1f 54 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET1f 52 " --> pdb=" O GLU1f 32 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE1f 34 " --> pdb=" O PRO1f 50 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N TYR1f 36 " --> pdb=" O LYS1f 48 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LYS1f 48 " --> pdb=" O TYR1f 36 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain '2A' and resid 8 through 13 removed outlier: 6.425A pdb=" N GLY2A 8 " --> pdb=" O ILE2B 681 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU2B 683 " --> pdb=" O GLY2A 8 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR2A 10 " --> pdb=" O LEU2B 683 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE2B 685 " --> pdb=" O TYR2A 10 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU2A 12 " --> pdb=" O PHE2B 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain '2A' and resid 54 through 56 removed outlier: 7.425A pdb=" N THR2A 35 " --> pdb=" O THR2A 125 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL2A 127 " --> pdb=" O THR2A 35 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE2A 195 " --> pdb=" O LEU2A 161 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ASN2A 559 " --> pdb=" O GLY2A 231 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA2A 233 " --> pdb=" O ASN2A 559 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE2A 561 " --> pdb=" O ALA2A 233 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR2A 235 " --> pdb=" O ILE2A 561 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N SER2A 563 " --> pdb=" O TYR2A 235 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain '2A' and resid 87 through 93 Processing sheet with id=AG4, first strand: chain '2A' and resid 204 through 205 Processing sheet with id=AG5, first strand: chain '2A' and resid 502 through 503 removed outlier: 3.605A pdb=" N LYS2A 536 " --> pdb=" O GLN2A 239 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain '2A' and resid 680 through 685 Processing sheet with id=AG7, first strand: chain '2B' and resid 8 through 13 removed outlier: 6.414A pdb=" N GLY2B 8 " --> pdb=" O ILE2C 681 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU2C 683 " --> pdb=" O GLY2B 8 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TYR2B 10 " --> pdb=" O LEU2C 683 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N PHE2C 685 " --> pdb=" O TYR2B 10 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU2B 12 " --> pdb=" O PHE2C 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain '2B' and resid 54 through 56 removed outlier: 7.425A pdb=" N THR2B 35 " --> pdb=" O THR2B 125 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL2B 127 " --> pdb=" O THR2B 35 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE2B 195 " --> pdb=" O LEU2B 161 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N ASN2B 559 " --> pdb=" O GLY2B 231 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA2B 233 " --> pdb=" O ASN2B 559 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE2B 561 " --> pdb=" O ALA2B 233 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR2B 235 " --> pdb=" O ILE2B 561 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N SER2B 563 " --> pdb=" O TYR2B 235 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '2B' and resid 87 through 93 Processing sheet with id=AH1, first strand: chain '2B' and resid 204 through 205 Processing sheet with id=AH2, first strand: chain '2B' and resid 502 through 503 removed outlier: 3.605A pdb=" N LYS2B 536 " --> pdb=" O GLN2B 239 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '2C' and resid 8 through 13 removed outlier: 6.430A pdb=" N GLY2C 8 " --> pdb=" O ILE2D 681 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU2D 683 " --> pdb=" O GLY2C 8 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR2C 10 " --> pdb=" O LEU2D 683 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N PHE2D 685 " --> pdb=" O TYR2C 10 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU2C 12 " --> pdb=" O PHE2D 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain '2C' and resid 54 through 56 removed outlier: 7.425A pdb=" N THR2C 35 " --> pdb=" O THR2C 125 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL2C 127 " --> pdb=" O THR2C 35 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE2C 195 " --> pdb=" O LEU2C 161 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ASN2C 559 " --> pdb=" O GLY2C 231 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA2C 233 " --> pdb=" O ASN2C 559 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE2C 561 " --> pdb=" O ALA2C 233 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR2C 235 " --> pdb=" O ILE2C 561 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N SER2C 563 " --> pdb=" O TYR2C 235 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '2C' and resid 87 through 93 Processing sheet with id=AH6, first strand: chain '2C' and resid 204 through 205 Processing sheet with id=AH7, first strand: chain '2C' and resid 502 through 503 removed outlier: 3.605A pdb=" N LYS2C 536 " --> pdb=" O GLN2C 239 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain '2D' and resid 8 through 13 removed outlier: 6.422A pdb=" N GLY2D 8 " --> pdb=" O ILE2E 681 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU2E 683 " --> pdb=" O GLY2D 8 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR2D 10 " --> pdb=" O LEU2E 683 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE2E 685 " --> pdb=" O TYR2D 10 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU2D 12 " --> pdb=" O PHE2E 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain '2D' and resid 54 through 56 removed outlier: 7.426A pdb=" N THR2D 35 " --> pdb=" O THR2D 125 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL2D 127 " --> pdb=" O THR2D 35 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE2D 195 " --> pdb=" O LEU2D 161 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ASN2D 559 " --> pdb=" O GLY2D 231 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA2D 233 " --> pdb=" O ASN2D 559 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE2D 561 " --> pdb=" O ALA2D 233 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR2D 235 " --> pdb=" O ILE2D 561 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N SER2D 563 " --> pdb=" O TYR2D 235 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain '2D' and resid 87 through 93 Processing sheet with id=AI2, first strand: chain '2D' and resid 204 through 205 Processing sheet with id=AI3, first strand: chain '2D' and resid 502 through 503 removed outlier: 3.605A pdb=" N LYS2D 536 " --> pdb=" O GLN2D 239 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain '2E' and resid 8 through 13 removed outlier: 6.417A pdb=" N GLY2E 8 " --> pdb=" O ILE2F 681 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU2F 683 " --> pdb=" O GLY2E 8 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR2E 10 " --> pdb=" O LEU2F 683 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE2F 685 " --> pdb=" O TYR2E 10 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU2E 12 " --> pdb=" O PHE2F 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain '2E' and resid 54 through 56 removed outlier: 7.425A pdb=" N THR2E 35 " --> pdb=" O THR2E 125 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL2E 127 " --> pdb=" O THR2E 35 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE2E 195 " --> pdb=" O LEU2E 161 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N ASN2E 559 " --> pdb=" O GLY2E 231 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA2E 233 " --> pdb=" O ASN2E 559 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE2E 561 " --> pdb=" O ALA2E 233 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR2E 235 " --> pdb=" O ILE2E 561 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N SER2E 563 " --> pdb=" O TYR2E 235 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain '2E' and resid 87 through 93 Processing sheet with id=AI7, first strand: chain '2E' and resid 204 through 205 Processing sheet with id=AI8, first strand: chain '2E' and resid 502 through 503 removed outlier: 3.605A pdb=" N LYS2E 536 " --> pdb=" O GLN2E 239 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain '2F' and resid 54 through 56 removed outlier: 7.424A pdb=" N THR2F 35 " --> pdb=" O THR2F 125 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL2F 127 " --> pdb=" O THR2F 35 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE2F 195 " --> pdb=" O LEU2F 161 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ASN2F 559 " --> pdb=" O GLY2F 231 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA2F 233 " --> pdb=" O ASN2F 559 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE2F 561 " --> pdb=" O ALA2F 233 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR2F 235 " --> pdb=" O ILE2F 561 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N SER2F 563 " --> pdb=" O TYR2F 235 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain '2F' and resid 87 through 93 Processing sheet with id=AJ2, first strand: chain '2F' and resid 204 through 205 Processing sheet with id=AJ3, first strand: chain '2F' and resid 502 through 503 removed outlier: 3.606A pdb=" N LYS2F 536 " --> pdb=" O GLN2F 239 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain '2a' and resid 10 through 13 removed outlier: 5.178A pdb=" N ARG2a 86 " --> pdb=" O ASN2a 107 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN2a 107 " --> pdb=" O ARG2a 86 " (cutoff:3.500A) removed outlier: 16.696A pdb=" N ASN2a 107 " --> pdb=" O GLU2b 35 " (cutoff:3.500A) removed outlier: 12.747A pdb=" N GLU2b 35 " --> pdb=" O ASN2a 107 " (cutoff:3.500A) removed outlier: 13.092A pdb=" N TRP2a 109 " --> pdb=" O ILE2b 33 " (cutoff:3.500A) removed outlier: 9.770A pdb=" N ILE2b 33 " --> pdb=" O TRP2a 109 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU2a 111 " --> pdb=" O THR2b 31 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASP2b 28 " --> pdb=" O PHE2b 55 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE2b 55 " --> pdb=" O ASP2b 28 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU2b 30 " --> pdb=" O GLN2b 53 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLN2b 53 " --> pdb=" O GLU2b 30 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLU2b 32 " --> pdb=" O GLY2b 51 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain '2a' and resid 137 through 140 removed outlier: 6.860A pdb=" N GLU2a 131 " --> pdb=" O LEU2a 111 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL2a 113 " --> pdb=" O SER2a 129 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER2a 129 " --> pdb=" O VAL2a 113 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain '2a' and resid 47 through 55 removed outlier: 4.924A pdb=" N GLU2a 32 " --> pdb=" O GLY2a 51 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLN2a 53 " --> pdb=" O GLU2a 30 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLU2a 30 " --> pdb=" O GLN2a 53 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE2a 55 " --> pdb=" O ASP2a 28 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASP2a 28 " --> pdb=" O PHE2a 55 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU2f 111 " --> pdb=" O THR2a 31 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N ILE2a 33 " --> pdb=" O TRP2f 109 " (cutoff:3.500A) removed outlier: 13.075A pdb=" N TRP2f 109 " --> pdb=" O ILE2a 33 " (cutoff:3.500A) removed outlier: 12.731A pdb=" N GLU2a 35 " --> pdb=" O ASN2f 107 " (cutoff:3.500A) removed outlier: 16.679A pdb=" N ASN2f 107 " --> pdb=" O GLU2a 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN2f 107 " --> pdb=" O ARG2f 86 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ARG2f 86 " --> pdb=" O ASN2f 107 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain '2e' and resid 118 through 119 removed outlier: 6.868A pdb=" N SER2f 129 " --> pdb=" O VAL2f 113 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL2f 113 " --> pdb=" O SER2f 129 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU2f 131 " --> pdb=" O LEU2f 111 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain '2a' and resid 118 through 119 removed outlier: 6.867A pdb=" N SER2b 129 " --> pdb=" O VAL2b 113 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL2b 113 " --> pdb=" O SER2b 129 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU2b 131 " --> pdb=" O LEU2b 111 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain '2b' and resid 10 through 13 removed outlier: 5.177A pdb=" N ARG2b 86 " --> pdb=" O ASN2b 107 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN2b 107 " --> pdb=" O ARG2b 86 " (cutoff:3.500A) removed outlier: 16.683A pdb=" N ASN2b 107 " --> pdb=" O GLU2c 35 " (cutoff:3.500A) removed outlier: 12.735A pdb=" N GLU2c 35 " --> pdb=" O ASN2b 107 " (cutoff:3.500A) removed outlier: 13.082A pdb=" N TRP2b 109 " --> pdb=" O ILE2c 33 " (cutoff:3.500A) removed outlier: 9.762A pdb=" N ILE2c 33 " --> pdb=" O TRP2b 109 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU2b 111 " --> pdb=" O THR2c 31 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASP2c 28 " --> pdb=" O PHE2c 55 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE2c 55 " --> pdb=" O ASP2c 28 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU2c 30 " --> pdb=" O GLN2c 53 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLN2c 53 " --> pdb=" O GLU2c 30 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU2c 32 " --> pdb=" O GLY2c 51 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain '2b' and resid 118 through 119 removed outlier: 6.869A pdb=" N SER2c 129 " --> pdb=" O VAL2c 113 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL2c 113 " --> pdb=" O SER2c 129 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU2c 131 " --> pdb=" O LEU2c 111 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain '2c' and resid 10 through 13 removed outlier: 5.177A pdb=" N ARG2c 86 " --> pdb=" O ASN2c 107 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN2c 107 " --> pdb=" O ARG2c 86 " (cutoff:3.500A) removed outlier: 16.695A pdb=" N ASN2c 107 " --> pdb=" O GLU2d 35 " (cutoff:3.500A) removed outlier: 12.747A pdb=" N GLU2d 35 " --> pdb=" O ASN2c 107 " (cutoff:3.500A) removed outlier: 13.092A pdb=" N TRP2c 109 " --> pdb=" O ILE2d 33 " (cutoff:3.500A) removed outlier: 9.769A pdb=" N ILE2d 33 " --> pdb=" O TRP2c 109 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU2c 111 " --> pdb=" O THR2d 31 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASP2d 28 " --> pdb=" O PHE2d 55 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N PHE2d 55 " --> pdb=" O ASP2d 28 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU2d 30 " --> pdb=" O GLN2d 53 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLN2d 53 " --> pdb=" O GLU2d 30 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLU2d 32 " --> pdb=" O GLY2d 51 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain '2c' and resid 118 through 119 removed outlier: 6.867A pdb=" N SER2d 129 " --> pdb=" O VAL2d 113 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL2d 113 " --> pdb=" O SER2d 129 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU2d 131 " --> pdb=" O LEU2d 111 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain '2d' and resid 10 through 13 removed outlier: 5.178A pdb=" N ARG2d 86 " --> pdb=" O ASN2d 107 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN2d 107 " --> pdb=" O ARG2d 86 " (cutoff:3.500A) removed outlier: 16.684A pdb=" N ASN2d 107 " --> pdb=" O GLU2e 35 " (cutoff:3.500A) removed outlier: 12.736A pdb=" N GLU2e 35 " --> pdb=" O ASN2d 107 " (cutoff:3.500A) removed outlier: 13.080A pdb=" N TRP2d 109 " --> pdb=" O ILE2e 33 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N ILE2e 33 " --> pdb=" O TRP2d 109 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU2d 111 " --> pdb=" O THR2e 31 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASP2e 28 " --> pdb=" O PHE2e 55 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE2e 55 " --> pdb=" O ASP2e 28 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLU2e 30 " --> pdb=" O GLN2e 53 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN2e 53 " --> pdb=" O GLU2e 30 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU2e 32 " --> pdb=" O GLY2e 51 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain '2d' and resid 118 through 119 removed outlier: 6.868A pdb=" N SER2e 129 " --> pdb=" O VAL2e 113 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL2e 113 " --> pdb=" O SER2e 129 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU2e 131 " --> pdb=" O LEU2e 111 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain '2e' and resid 10 through 13 removed outlier: 5.177A pdb=" N ARG2e 86 " --> pdb=" O ASN2e 107 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN2e 107 " --> pdb=" O ARG2e 86 " (cutoff:3.500A) removed outlier: 16.682A pdb=" N ASN2e 107 " --> pdb=" O GLU2f 35 " (cutoff:3.500A) removed outlier: 12.735A pdb=" N GLU2f 35 " --> pdb=" O ASN2e 107 " (cutoff:3.500A) removed outlier: 13.083A pdb=" N TRP2e 109 " --> pdb=" O ILE2f 33 " (cutoff:3.500A) removed outlier: 9.762A pdb=" N ILE2f 33 " --> pdb=" O TRP2e 109 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU2e 111 " --> pdb=" O THR2f 31 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASP2f 28 " --> pdb=" O PHE2f 55 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE2f 55 " --> pdb=" O ASP2f 28 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU2f 30 " --> pdb=" O GLN2f 53 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLN2f 53 " --> pdb=" O GLU2f 30 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU2f 32 " --> pdb=" O GLY2f 51 " (cutoff:3.500A) 2838 hydrogen bonds defined for protein. 7758 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: 32.71 Time building geometry restraints manager: 23.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 11959 1.30 - 1.43: 17783 1.43 - 1.57: 38875 1.57 - 1.70: 263 1.70 - 1.83: 354 Bond restraints: 69234 Sorted by residual: bond pdb=" C LEU0F 82 " pdb=" N ASN0F 83 " ideal model delta sigma weight residual 1.331 1.168 0.163 1.34e-02 5.57e+03 1.48e+02 bond pdb=" C LEU0E 82 " pdb=" N ASN0E 83 " ideal model delta sigma weight residual 1.331 1.168 0.162 1.34e-02 5.57e+03 1.46e+02 bond pdb=" C LEU0B 82 " pdb=" N ASN0B 83 " ideal model delta sigma weight residual 1.331 1.168 0.162 1.34e-02 5.57e+03 1.46e+02 bond pdb=" C LEU0A 82 " pdb=" N ASN0A 83 " ideal model delta sigma weight residual 1.331 1.169 0.162 1.34e-02 5.57e+03 1.46e+02 bond pdb=" C LEU0D 82 " pdb=" N ASN0D 83 " ideal model delta sigma weight residual 1.331 1.169 0.162 1.34e-02 5.57e+03 1.46e+02 ... (remaining 69229 not shown) Histogram of bond angle deviations from ideal: 98.38 - 106.51: 2079 106.51 - 114.63: 38296 114.63 - 122.76: 45382 122.76 - 130.89: 7855 130.89 - 139.02: 246 Bond angle restraints: 93858 Sorted by residual: angle pdb=" O LEU0B 82 " pdb=" C LEU0B 82 " pdb=" N ASN0B 83 " ideal model delta sigma weight residual 123.13 100.59 22.54 1.15e+00 7.56e-01 3.84e+02 angle pdb=" O LEU0E 82 " pdb=" C LEU0E 82 " pdb=" N ASN0E 83 " ideal model delta sigma weight residual 123.13 100.61 22.52 1.15e+00 7.56e-01 3.84e+02 angle pdb=" O LEU0F 82 " pdb=" C LEU0F 82 " pdb=" N ASN0F 83 " ideal model delta sigma weight residual 123.13 100.62 22.51 1.15e+00 7.56e-01 3.83e+02 angle pdb=" O LEU0D 82 " pdb=" C LEU0D 82 " pdb=" N ASN0D 83 " ideal model delta sigma weight residual 123.13 100.64 22.49 1.15e+00 7.56e-01 3.82e+02 angle pdb=" O LEU0A 82 " pdb=" C LEU0A 82 " pdb=" N ASN0A 83 " ideal model delta sigma weight residual 123.13 100.64 22.49 1.15e+00 7.56e-01 3.82e+02 ... (remaining 93853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 39662 17.92 - 35.85: 1462 35.85 - 53.77: 258 53.77 - 71.69: 144 71.69 - 89.62: 48 Dihedral angle restraints: 41574 sinusoidal: 16674 harmonic: 24900 Sorted by residual: dihedral pdb=" CA LEU0F 172 " pdb=" C LEU0F 172 " pdb=" N ILE0F 173 " pdb=" CA ILE0F 173 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA LEU0B 172 " pdb=" C LEU0B 172 " pdb=" N ILE0B 173 " pdb=" CA ILE0B 173 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU0A 172 " pdb=" C LEU0A 172 " pdb=" N ILE0A 173 " pdb=" CA ILE0A 173 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 41571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 6836 0.075 - 0.149: 2659 0.149 - 0.224: 768 0.224 - 0.298: 201 0.298 - 0.373: 18 Chirality restraints: 10482 Sorted by residual: chirality pdb=" CA ASN2C 420 " pdb=" N ASN2C 420 " pdb=" C ASN2C 420 " pdb=" CB ASN2C 420 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA ASN2D 420 " pdb=" N ASN2D 420 " pdb=" C ASN2D 420 " pdb=" CB ASN2D 420 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CA ASN2E 420 " pdb=" N ASN2E 420 " pdb=" C ASN2E 420 " pdb=" CB ASN2E 420 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 10479 not shown) Planarity restraints: 12162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR2B 128 " -0.079 2.00e-02 2.50e+03 4.57e-02 4.17e+01 pdb=" CG TYR2B 128 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR2B 128 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR2B 128 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR2B 128 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR2B 128 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR2B 128 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR2B 128 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR2F 128 " -0.079 2.00e-02 2.50e+03 4.55e-02 4.14e+01 pdb=" CG TYR2F 128 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR2F 128 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR2F 128 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR2F 128 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR2F 128 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR2F 128 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR2F 128 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR2E 128 " -0.079 2.00e-02 2.50e+03 4.54e-02 4.13e+01 pdb=" CG TYR2E 128 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR2E 128 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR2E 128 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR2E 128 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR2E 128 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR2E 128 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR2E 128 " -0.077 2.00e-02 2.50e+03 ... (remaining 12159 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 82 2.05 - 2.77: 11089 2.77 - 3.48: 83707 3.48 - 4.19: 158990 4.19 - 4.90: 272900 Nonbonded interactions: 526768 Sorted by model distance: nonbonded pdb=" ND2 ASN0E 193 " pdb=" OE1 GLN1C 2 " model vdw 1.343 2.520 nonbonded pdb=" ND2 ASN0D 193 " pdb=" OE1 GLN1D 2 " model vdw 1.346 2.520 nonbonded pdb=" ND2 ASN0B 193 " pdb=" OE1 GLN1F 2 " model vdw 1.357 2.520 nonbonded pdb=" ND2 ASN0C 193 " pdb=" OE1 GLN1E 2 " model vdw 1.361 2.520 nonbonded pdb=" ND2 ASN0A 193 " pdb=" OE1 GLN1A 2 " model vdw 1.368 2.520 ... (remaining 526763 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 '0A' selection = chain '0B' selection = chain '0C' selection = chain '0D' selection = chain '0E' selection = chain '0F' } ncs_group { reference = chain '1A' selection = chain '1B' selection = chain '1C' selection = chain '1D' selection = chain '1E' selection = chain '1F' } ncs_group { reference = chain '1a' selection = chain '1b' selection = chain '1c' selection = chain '1d' selection = chain '1e' selection = chain '1f' selection = chain '2a' selection = chain '2b' selection = chain '2c' selection = chain '2d' selection = chain '2e' selection = chain '2f' } ncs_group { reference = chain '2A' selection = chain '2B' selection = chain '2C' selection = chain '2D' selection = chain '2E' selection = chain '2F' } 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 186 5.16 5 C 43248 2.51 5 N 11100 2.21 5 O 13260 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: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 17.140 Check model and map are aligned: 0.820 Process input model: 144.820 Find NCS groups from input model: 3.540 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Set scattering table: 0.500 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 182.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 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 : 0.015 0.163 69234 Z= 0.949 Angle : 1.544 22.625 93858 Z= 1.060 Chirality : 0.087 0.373 10482 Planarity : 0.008 0.049 12162 Dihedral : 11.188 89.617 25482 Min Nonbonded Distance : 1.343 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.09), residues: 8436 helix: 0.04 (0.10), residues: 2322 sheet: 1.02 (0.12), residues: 1746 loop : -0.53 (0.09), residues: 4368 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1554 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1548 time to evaluate : 6.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 1554 average time/residue: 1.5965 time to fit residues: 3179.8404 Evaluate side-chains 860 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 854 time to evaluate : 6.552 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 8.6930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 709 optimal weight: 1.9990 chunk 636 optimal weight: 0.9990 chunk 353 optimal weight: 0.0770 chunk 217 optimal weight: 3.9990 chunk 429 optimal weight: 10.0000 chunk 340 optimal weight: 1.9990 chunk 658 optimal weight: 8.9990 chunk 254 optimal weight: 8.9990 chunk 400 optimal weight: 10.0000 chunk 490 optimal weight: 0.6980 chunk 762 optimal weight: 0.1980 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0A 46 GLN 0A 193 ASN 0B 46 GLN 0B 193 ASN 0C 193 ASN 0D 46 GLN 0D 193 ASN 0E 46 GLN 0E 193 ASN 0F 193 ASN 1B 2 GLN 1E 2 GLN 1a 53 GLN 1a 123 ASN 1b 123 ASN 1c 123 ASN 1c 140 GLN 1d 53 GLN 1d 73 GLN 1d 123 ASN 1e 123 ASN 1f 123 ASN 1f 140 GLN 2A 36 GLN 2A 486 ASN 2A 497 ASN 2A 543 HIS 2A 552 HIS 2B 23 GLN 2B 36 GLN 2B 239 GLN 2B 543 HIS 2B 552 HIS 2C 36 GLN 2C 543 HIS 2C 552 HIS 2D 36 GLN 2D 486 ASN 2D 497 ASN 2D 543 HIS 2D 552 HIS 2E 36 GLN 2E 239 GLN 2E 543 HIS 2E 552 HIS 2F 36 GLN 2F 239 GLN 2F 543 HIS 2a 9 HIS 2a 79 ASN 2a 114 GLN 2b 123 ASN 2c 9 HIS 2c 79 ASN 2d 9 HIS 2d 79 ASN 2d 114 GLN 2e 9 HIS 2e 123 ASN 2f 9 HIS Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 69234 Z= 0.176 Angle : 0.594 6.567 93858 Z= 0.336 Chirality : 0.045 0.155 10482 Planarity : 0.004 0.040 12162 Dihedral : 4.834 23.685 9060 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.09), residues: 8436 helix: 1.73 (0.11), residues: 2280 sheet: 1.16 (0.12), residues: 1872 loop : -0.75 (0.09), residues: 4284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 923 time to evaluate : 6.587 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 198 outliers final: 51 residues processed: 1022 average time/residue: 1.5303 time to fit residues: 2031.0891 Evaluate side-chains 805 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 754 time to evaluate : 6.515 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 25 residues processed: 26 average time/residue: 0.7895 time to fit residues: 40.6358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 423 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 chunk 634 optimal weight: 4.9990 chunk 519 optimal weight: 4.9990 chunk 210 optimal weight: 8.9990 chunk 764 optimal weight: 4.9990 chunk 825 optimal weight: 3.9990 chunk 680 optimal weight: 9.9990 chunk 757 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 613 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0A 46 GLN 0A 193 ASN 0B 46 GLN 0B 121 ASN 0B 193 ASN 0D 46 GLN 0D 193 ASN 0E 46 GLN 0E 121 ASN 0E 193 ASN 1A 169 HIS 1B 169 HIS 1C 169 HIS 1D 169 HIS 1E 169 HIS 1F 169 HIS 1a 53 GLN 1b 114 GLN 1d 53 GLN 1f 114 GLN 2A 23 GLN 2A 36 GLN 2A 543 HIS 2B 110 GLN 2B 202 GLN 2B 543 HIS 2C 23 GLN 2C 36 GLN 2C 486 ASN 2C 543 HIS 2C 626 ASN 2D 23 GLN 2D 36 GLN ** 2D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2D 543 HIS 2E 110 GLN 2E 202 GLN 2E 543 HIS 2F 23 GLN 2F 36 GLN 2F 239 GLN 2F 543 HIS 2F 552 HIS 2F 626 ASN 2a 38 HIS 2b 9 HIS 2b 38 HIS 2b 53 GLN ** 2b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2c 38 HIS 2d 38 HIS 2e 38 HIS 2e 53 GLN ** 2e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2f 38 HIS Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 69234 Z= 0.309 Angle : 0.709 9.580 93858 Z= 0.392 Chirality : 0.049 0.173 10482 Planarity : 0.005 0.068 12162 Dihedral : 5.097 25.243 9060 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.09), residues: 8436 helix: 1.74 (0.11), residues: 2268 sheet: 1.04 (0.12), residues: 1860 loop : -1.00 (0.09), residues: 4308 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 800 time to evaluate : 6.581 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 230 outliers final: 96 residues processed: 943 average time/residue: 1.5582 time to fit residues: 1909.1983 Evaluate side-chains 834 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 738 time to evaluate : 6.499 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 63 residues processed: 33 average time/residue: 0.8373 time to fit residues: 51.0306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 755 optimal weight: 6.9990 chunk 574 optimal weight: 4.9990 chunk 396 optimal weight: 30.0000 chunk 84 optimal weight: 6.9990 chunk 364 optimal weight: 0.9990 chunk 513 optimal weight: 0.9980 chunk 766 optimal weight: 0.8980 chunk 811 optimal weight: 4.9990 chunk 400 optimal weight: 10.0000 chunk 726 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0A 46 GLN 0B 46 GLN 0D 46 GLN 0E 46 GLN 1A 169 HIS 1C 169 HIS 1D 169 HIS 1F 169 HIS 1a 53 GLN 1d 53 GLN 2A 202 GLN 2A 543 HIS 2A 644 HIS 2B 202 GLN 2B 239 GLN 2B 543 HIS 2B 644 HIS 2C 239 GLN 2C 378 ASN 2C 543 HIS 2C 644 HIS 2D 23 GLN 2D 202 GLN 2D 543 HIS 2D 644 HIS 2E 202 GLN 2E 239 GLN 2E 543 HIS 2E 644 HIS 2F 378 ASN 2F 543 HIS 2F 644 HIS 2b 123 ASN 2e 123 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 69234 Z= 0.220 Angle : 0.597 8.475 93858 Z= 0.332 Chirality : 0.045 0.165 10482 Planarity : 0.005 0.048 12162 Dihedral : 4.898 23.641 9060 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 3.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.09), residues: 8436 helix: 1.73 (0.11), residues: 2298 sheet: 0.98 (0.12), residues: 1926 loop : -1.05 (0.09), residues: 4212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 785 time to evaluate : 6.627 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 232 outliers final: 113 residues processed: 930 average time/residue: 1.5947 time to fit residues: 1919.7263 Evaluate side-chains 834 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 721 time to evaluate : 6.544 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 75 residues processed: 38 average time/residue: 0.9264 time to fit residues: 60.9961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 676 optimal weight: 0.7980 chunk 460 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 604 optimal weight: 5.9990 chunk 335 optimal weight: 3.9990 chunk 692 optimal weight: 9.9990 chunk 561 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 414 optimal weight: 7.9990 chunk 728 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0A 46 GLN 0B 46 GLN 0D 46 GLN 0E 46 GLN 1A 169 HIS 1C 169 HIS 1D 169 HIS 1F 169 HIS 1a 53 GLN 1d 53 GLN 2B 202 GLN 2B 239 GLN 2B 470 ASN 2D 23 GLN 2E 202 GLN 2E 239 GLN 2E 470 ASN 2F 239 GLN 2F 486 ASN 2b 53 GLN 2e 53 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 69234 Z= 0.210 Angle : 0.585 8.367 93858 Z= 0.324 Chirality : 0.045 0.163 10482 Planarity : 0.005 0.048 12162 Dihedral : 4.810 23.668 9060 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.09), residues: 8436 helix: 1.78 (0.11), residues: 2292 sheet: 0.99 (0.12), residues: 1926 loop : -1.12 (0.09), residues: 4218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 765 time to evaluate : 6.593 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 231 outliers final: 128 residues processed: 921 average time/residue: 1.5534 time to fit residues: 1857.4855 Evaluate side-chains 856 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 728 time to evaluate : 6.628 Switching outliers to nearest non-outliers outliers start: 128 outliers final: 90 residues processed: 38 average time/residue: 0.9233 time to fit residues: 61.1885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 273 optimal weight: 10.0000 chunk 731 optimal weight: 30.0000 chunk 160 optimal weight: 9.9990 chunk 476 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 812 optimal weight: 0.0000 chunk 674 optimal weight: 0.9980 chunk 376 optimal weight: 0.9980 chunk 67 optimal weight: 0.0060 chunk 268 optimal weight: 9.9990 chunk 426 optimal weight: 7.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0A 46 GLN 0B 46 GLN 0C 46 GLN 0D 46 GLN 0E 46 GLN 1A 88 GLN 1A 169 HIS 1C 169 HIS 1D 169 HIS 1F 169 HIS 1a 53 GLN 1d 53 GLN 2B 239 GLN 2C 239 GLN 2C 470 ASN 2C 626 ASN 2D 23 GLN 2E 239 GLN 2F 486 ASN 2F 626 ASN 2d 114 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 69234 Z= 0.136 Angle : 0.494 7.861 93858 Z= 0.275 Chirality : 0.042 0.151 10482 Planarity : 0.004 0.048 12162 Dihedral : 4.462 24.154 9060 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.09), residues: 8436 helix: 1.96 (0.11), residues: 2298 sheet: 1.08 (0.12), residues: 1956 loop : -1.06 (0.09), residues: 4182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 781 time to evaluate : 6.641 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 182 outliers final: 122 residues processed: 911 average time/residue: 1.5491 time to fit residues: 1840.1663 Evaluate side-chains 839 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 717 time to evaluate : 6.523 Switching outliers to nearest non-outliers outliers start: 122 outliers final: 93 residues processed: 29 average time/residue: 0.9572 time to fit residues: 49.7766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 783 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 463 optimal weight: 10.0000 chunk 593 optimal weight: 8.9990 chunk 459 optimal weight: 20.0000 chunk 684 optimal weight: 0.9980 chunk 453 optimal weight: 3.9990 chunk 809 optimal weight: 0.0170 chunk 506 optimal weight: 9.9990 chunk 493 optimal weight: 3.9990 chunk 373 optimal weight: 6.9990 overall best weight: 3.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0A 46 GLN 0B 46 GLN 0C 46 GLN 0D 46 GLN 0E 46 GLN 0F 46 GLN 1A 169 HIS 1C 163 HIS 1C 169 HIS 1D 169 HIS 1E 169 HIS 1F 163 HIS 1F 169 HIS 1a 53 GLN 1d 53 GLN 2A 202 GLN 2B 202 GLN 2C 239 GLN 2C 486 ASN 2D 23 GLN 2D 202 GLN 2E 202 GLN 2F 239 GLN 2F 470 ASN 2F 486 ASN 2F 626 ASN 2a 114 GLN 2b 53 GLN 2c 114 GLN 2d 114 GLN 2e 53 GLN 2f 114 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 69234 Z= 0.245 Angle : 0.612 7.972 93858 Z= 0.336 Chirality : 0.046 0.163 10482 Planarity : 0.005 0.061 12162 Dihedral : 4.763 23.850 9060 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.09), residues: 8436 helix: 1.82 (0.11), residues: 2292 sheet: 1.09 (0.12), residues: 1938 loop : -1.18 (0.09), residues: 4206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 751 time to evaluate : 7.349 Fit side-chains outliers start: 222 outliers final: 136 residues processed: 893 average time/residue: 1.5249 time to fit residues: 1784.1365 Evaluate side-chains 865 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 729 time to evaluate : 6.501 Switching outliers to nearest non-outliers outliers start: 136 outliers final: 97 residues processed: 39 average time/residue: 0.9207 time to fit residues: 62.4034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 500 optimal weight: 8.9990 chunk 323 optimal weight: 6.9990 chunk 483 optimal weight: 5.9990 chunk 243 optimal weight: 7.9990 chunk 159 optimal weight: 0.0270 chunk 156 optimal weight: 0.0770 chunk 514 optimal weight: 0.9980 chunk 551 optimal weight: 6.9990 chunk 400 optimal weight: 0.0980 chunk 75 optimal weight: 3.9990 chunk 636 optimal weight: 0.8980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0A 46 GLN 0B 46 GLN 0C 46 GLN 0D 46 GLN 0E 46 GLN 0F 46 GLN 1A 169 HIS 1C 163 HIS 1C 169 HIS 1D 169 HIS 1F 163 HIS 1F 169 HIS 1a 53 GLN 1d 53 GLN 2A 202 GLN 2A 239 GLN 2A 470 ASN 2C 23 GLN 2C 239 GLN 2D 23 GLN 2D 202 GLN 2D 239 GLN 2D 470 ASN 2F 23 GLN 2F 626 ASN 2a 114 GLN 2b 53 GLN 2c 114 GLN 2e 53 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.079 69234 Z= 0.124 Angle : 0.476 8.705 93858 Z= 0.264 Chirality : 0.042 0.299 10482 Planarity : 0.004 0.050 12162 Dihedral : 4.324 24.172 9060 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.09), residues: 8436 helix: 2.05 (0.11), residues: 2298 sheet: 1.13 (0.12), residues: 1950 loop : -1.04 (0.09), residues: 4188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 768 time to evaluate : 6.682 Fit side-chains outliers start: 154 outliers final: 112 residues processed: 890 average time/residue: 1.5293 time to fit residues: 1785.7124 Evaluate side-chains 835 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 723 time to evaluate : 6.525 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 93 residues processed: 20 average time/residue: 1.2212 time to fit residues: 42.2270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 736 optimal weight: 0.7980 chunk 775 optimal weight: 5.9990 chunk 707 optimal weight: 5.9990 chunk 754 optimal weight: 10.0000 chunk 454 optimal weight: 9.9990 chunk 328 optimal weight: 0.5980 chunk 592 optimal weight: 7.9990 chunk 231 optimal weight: 10.0000 chunk 681 optimal weight: 0.8980 chunk 713 optimal weight: 7.9990 chunk 751 optimal weight: 0.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0A 46 GLN 0B 46 GLN 0C 46 GLN 0D 46 GLN 0F 46 GLN 1A 169 HIS 1B 169 HIS 1C 163 HIS 1C 169 HIS 1D 169 HIS 1E 169 HIS 1F 163 HIS 1F 169 HIS 1a 53 GLN 1d 53 GLN 2A 202 GLN 2A 486 ASN 2B 202 GLN 2C 23 GLN 2C 239 GLN 2C 486 ASN 2D 23 GLN 2D 202 GLN 2D 486 ASN 2E 202 GLN 2E 393 ASN 2F 23 GLN 2F 239 GLN 2b 53 GLN 2c 114 GLN 2d 114 GLN 2e 53 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 69234 Z= 0.178 Angle : 0.542 7.939 93858 Z= 0.297 Chirality : 0.044 0.243 10482 Planarity : 0.004 0.048 12162 Dihedral : 4.457 22.456 9060 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.09), residues: 8436 helix: 2.02 (0.11), residues: 2298 sheet: 1.19 (0.12), residues: 1938 loop : -1.11 (0.09), residues: 4200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 746 time to evaluate : 6.705 Fit side-chains outliers start: 157 outliers final: 110 residues processed: 856 average time/residue: 1.5452 time to fit residues: 1738.8242 Evaluate side-chains 833 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 723 time to evaluate : 6.542 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 90 residues processed: 20 average time/residue: 1.0621 time to fit residues: 39.2805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 495 optimal weight: 5.9990 chunk 797 optimal weight: 9.9990 chunk 486 optimal weight: 0.8980 chunk 378 optimal weight: 5.9990 chunk 554 optimal weight: 7.9990 chunk 836 optimal weight: 5.9990 chunk 770 optimal weight: 2.9990 chunk 666 optimal weight: 0.0770 chunk 69 optimal weight: 9.9990 chunk 514 optimal weight: 8.9990 chunk 408 optimal weight: 8.9990 overall best weight: 3.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0A 46 GLN 0B 46 GLN 0C 46 GLN 0D 46 GLN 0F 46 GLN 1A 169 HIS 1C 163 HIS 1C 169 HIS 1D 169 HIS 1E 169 HIS 1F 163 HIS 1F 169 HIS 1a 53 GLN 1d 53 GLN 2A 239 GLN 2A 486 ASN 2C 23 GLN 2C 239 GLN 2C 486 ASN 2D 23 GLN 2D 239 GLN 2D 486 ASN 2E 202 GLN 2E 393 ASN 2F 23 GLN 2F 239 GLN 2F 626 ASN 2b 53 GLN 2c 53 GLN 2e 53 GLN 2f 53 GLN 2f 114 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 69234 Z= 0.255 Angle : 0.630 8.358 93858 Z= 0.345 Chirality : 0.046 0.238 10482 Planarity : 0.005 0.066 12162 Dihedral : 4.777 24.552 9060 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.09), residues: 8436 helix: 1.81 (0.11), residues: 2292 sheet: 1.13 (0.12), residues: 1926 loop : -1.25 (0.09), residues: 4218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 737 time to evaluate : 6.570 Fit side-chains outliers start: 140 outliers final: 103 residues processed: 842 average time/residue: 1.5354 time to fit residues: 1692.2060 Evaluate side-chains 817 residues out of total 7596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 714 time to evaluate : 6.574 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 84 residues processed: 19 average time/residue: 0.8434 time to fit residues: 33.5255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 529 optimal weight: 4.9990 chunk 709 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 chunk 614 optimal weight: 9.9990 chunk 98 optimal weight: 0.1980 chunk 185 optimal weight: 0.7980 chunk 667 optimal weight: 9.9990 chunk 279 optimal weight: 4.9990 chunk 685 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0A 46 GLN 0B 46 GLN 0C 46 GLN 0D 46 GLN 0E 46 GLN 0F 46 GLN 1A 169 HIS 1C 163 HIS 1C 169 HIS 1D 169 HIS 1F 163 HIS 1F 169 HIS 1a 53 GLN 1d 53 GLN 2A 239 GLN 2C 23 GLN 2D 23 GLN 2D 486 ASN 2F 23 GLN 2F 486 ASN 2F 626 ASN 2a 114 GLN 2b 53 GLN 2e 53 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.143726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113713 restraints weight = 74896.581| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.46 r_work: 0.2962 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 69234 Z= 0.163 Angle : 0.528 10.355 93858 Z= 0.292 Chirality : 0.043 0.224 10482 Planarity : 0.004 0.049 12162 Dihedral : 4.533 23.146 9060 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.09), residues: 8436 helix: 1.94 (0.11), residues: 2298 sheet: 1.11 (0.12), residues: 1908 loop : -1.15 (0.09), residues: 4230 =============================================================================== Job complete usr+sys time: 26940.72 seconds wall clock time: 466 minutes 20.73 seconds (27980.73 seconds total)