Starting phenix.real_space_refine (version: dev) on Thu Apr 21 15:10:48 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p5n_20258/04_2022/6p5n_20258.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p5n_20258/04_2022/6p5n_20258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p5n_20258/04_2022/6p5n_20258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p5n_20258/04_2022/6p5n_20258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p5n_20258/04_2022/6p5n_20258.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p5n_20258/04_2022/6p5n_20258.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "AA ARG 6": "NH1" <-> "NH2" Residue "AA TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA GLU 74": "OE1" <-> "OE2" Residue "AA GLU 80": "OE1" <-> "OE2" Residue "AA TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA ARG 242": "NH1" <-> "NH2" Residue "AB ARG 10": "NH1" <-> "NH2" Residue "AB ARG 242": "NH1" <-> "NH2" Residue "AB ARG 268": "NH1" <-> "NH2" Residue "AC ARG 5": "NH1" <-> "NH2" Residue "AC ARG 49": "NH1" <-> "NH2" Residue "AC ARG 306": "NH1" <-> "NH2" Residue "AC ARG 323": "NH1" <-> "NH2" Residue "AC ARG 337": "NH1" <-> "NH2" Residue "AC ASP 363": "OD1" <-> "OD2" Residue "AD ARG 15": "NH1" <-> "NH2" Residue "AD ARG 23": "NH1" <-> "NH2" Residue "AD ARG 24": "NH1" <-> "NH2" Residue "AD ARG 33": "NH1" <-> "NH2" Residue "AD TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AD ARG 50": "NH1" <-> "NH2" Residue "AD ARG 108": "NH1" <-> "NH2" Residue "AD ARG 179": "NH1" <-> "NH2" Residue "AD GLU 238": "OE1" <-> "OE2" Residue "AD GLU 249": "OE1" <-> "OE2" Residue "AD ARG 259": "NH1" <-> "NH2" Residue "AE ARG 61": "NH1" <-> "NH2" Residue "AE TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE ARG 126": "NH1" <-> "NH2" Residue "AE ARG 164": "NH1" <-> "NH2" Residue "AE ARG 191": "NH1" <-> "NH2" Residue "AF ARG 45": "NH1" <-> "NH2" Residue "AF GLU 59": "OE1" <-> "OE2" Residue "AF GLU 67": "OE1" <-> "OE2" Residue "AF ARG 93": "NH1" <-> "NH2" Residue "AF ARG 156": "NH1" <-> "NH2" Residue "AF ARG 235": "NH1" <-> "NH2" Residue "AF ARG 244": "NH1" <-> "NH2" Residue "AG ARG 142": "NH1" <-> "NH2" Residue "AG GLU 158": "OE1" <-> "OE2" Residue "AG ARG 166": "NH1" <-> "NH2" Residue "AG GLU 172": "OE1" <-> "OE2" Residue "AG ARG 242": "NH1" <-> "NH2" Residue "AG TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG ARG 287": "NH1" <-> "NH2" Residue "AH ARG 23": "NH1" <-> "NH2" Residue "AH ARG 89": "NH1" <-> "NH2" Residue "AH GLU 107": "OE1" <-> "OE2" Residue "AH ARG 127": "NH1" <-> "NH2" Residue "AH GLU 183": "OE1" <-> "OE2" Residue "AI ARG 4": "NH1" <-> "NH2" Residue "AI PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI ARG 69": "NH1" <-> "NH2" Residue "AI ARG 98": "NH1" <-> "NH2" Residue "AI ARG 116": "NH1" <-> "NH2" Residue "AI ARG 153": "NH1" <-> "NH2" Residue "AI ARG 154": "NH1" <-> "NH2" Residue "AI ARG 162": "NH1" <-> "NH2" Residue "AI ARG 203": "NH1" <-> "NH2" Residue "AI ARG 210": "NH1" <-> "NH2" Residue "AJ ARG 35": "NH1" <-> "NH2" Residue "AJ ARG 64": "NH1" <-> "NH2" Residue "AJ ARG 146": "NH1" <-> "NH2" Residue "AJ ARG 164": "NH1" <-> "NH2" Residue "AL ARG 31": "NH1" <-> "NH2" Residue "AL ARG 49": "NH1" <-> "NH2" Residue "AL ARG 65": "NH1" <-> "NH2" Residue "AL ARG 102": "NH1" <-> "NH2" Residue "AL ARG 116": "NH1" <-> "NH2" Residue "AL ARG 158": "NH1" <-> "NH2" Residue "AM ARG 11": "NH1" <-> "NH2" Residue "AM PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM ASP 39": "OD1" <-> "OD2" Residue "AM GLU 96": "OE1" <-> "OE2" Residue "AM ARG 98": "NH1" <-> "NH2" Residue "AM ARG 109": "NH1" <-> "NH2" Residue "AM ARG 119": "NH1" <-> "NH2" Residue "AM ARG 121": "NH1" <-> "NH2" Residue "AN TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AN ARG 24": "NH1" <-> "NH2" Residue "AN ARG 50": "NH1" <-> "NH2" Residue "AN TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AN ARG 65": "NH1" <-> "NH2" Residue "AN ARG 96": "NH1" <-> "NH2" Residue "AN TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AN ARG 169": "NH1" <-> "NH2" Residue "AN ARG 189": "NH1" <-> "NH2" Residue "AN ARG 194": "NH1" <-> "NH2" Residue "AO ARG 78": "NH1" <-> "NH2" Residue "AO ARG 128": "NH1" <-> "NH2" Residue "AO ARG 140": "NH1" <-> "NH2" Residue "AP ARG 3": "NH1" <-> "NH2" Residue "AP ARG 62": "NH1" <-> "NH2" Residue "AP GLU 103": "OE1" <-> "OE2" Residue "AP GLU 152": "OE1" <-> "OE2" Residue "AQ ARG 33": "NH1" <-> "NH2" Residue "AQ ARG 37": "NH1" <-> "NH2" Residue "AQ ARG 55": "NH1" <-> "NH2" Residue "AQ ASP 74": "OD1" <-> "OD2" Residue "AQ ARG 91": "NH1" <-> "NH2" Residue "AQ ARG 134": "NH1" <-> "NH2" Residue "AQ ARG 180": "NH1" <-> "NH2" Residue "AR ARG 42": "NH1" <-> "NH2" Residue "AR ARG 74": "NH1" <-> "NH2" Residue "AR ARG 117": "NH1" <-> "NH2" Residue "AR ARG 162": "NH1" <-> "NH2" Residue "AR ARG 173": "NH1" <-> "NH2" Residue "AR ARG 176": "NH1" <-> "NH2" Residue "AS ARG 31": "NH1" <-> "NH2" Residue "AS ARG 43": "NH1" <-> "NH2" Residue "AS GLU 50": "OE1" <-> "OE2" Residue "AS ARG 83": "NH1" <-> "NH2" Residue "AS ARG 111": "NH1" <-> "NH2" Residue "AS ARG 118": "NH1" <-> "NH2" Residue "AS GLU 130": "OE1" <-> "OE2" Residue "AS ARG 139": "NH1" <-> "NH2" Residue "AS PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS ARG 161": "NH1" <-> "NH2" Residue "AS ARG 166": "NH1" <-> "NH2" Residue "AS PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AT GLU 111": "OE1" <-> "OE2" Residue "AT ARG 130": "NH1" <-> "NH2" Residue "AT GLU 137": "OE1" <-> "OE2" Residue "AU GLU 64": "OE1" <-> "OE2" Residue "AU ARG 65": "NH1" <-> "NH2" Residue "AU GLU 111": "OE1" <-> "OE2" Residue "AV ARG 48": "NH1" <-> "NH2" Residue "AV ARG 51": "NH1" <-> "NH2" Residue "AV ARG 85": "NH1" <-> "NH2" Residue "AV ARG 89": "NH1" <-> "NH2" Residue "AV ARG 131": "NH1" <-> "NH2" Residue "AW ARG 19": "NH1" <-> "NH2" Residue "AW TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AX PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AX ARG 53": "NH1" <-> "NH2" Residue "AX GLU 84": "OE1" <-> "OE2" Residue "AX ARG 129": "NH1" <-> "NH2" Residue "AX ARG 139": "NH1" <-> "NH2" Residue "AY ARG 27": "NH1" <-> "NH2" Residue "AY ARG 87": "NH1" <-> "NH2" Residue "AZ PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AZ ARG 65": "NH1" <-> "NH2" Residue "AZ TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa ARG 4": "NH1" <-> "NH2" Residue "Aa ARG 9": "NH1" <-> "NH2" Residue "Aa ARG 21": "NH1" <-> "NH2" Residue "Aa ARG 65": "NH1" <-> "NH2" Residue "Aa ARG 105": "NH1" <-> "NH2" Residue "Ab ARG 14": "NH1" <-> "NH2" Residue "Ab ARG 18": "NH1" <-> "NH2" Residue "Ab ARG 25": "NH1" <-> "NH2" Residue "Ab ARG 28": "NH1" <-> "NH2" Residue "Ab ARG 95": "NH1" <-> "NH2" Residue "Ab ARG 109": "NH1" <-> "NH2" Residue "Ab ARG 111": "NH1" <-> "NH2" Residue "Ac ARG 39": "NH1" <-> "NH2" Residue "Ac GLU 59": "OE1" <-> "OE2" Residue "Ac TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ad ARG 90": "NH1" <-> "NH2" Residue "Ae ARG 36": "NH1" <-> "NH2" Residue "Ae ARG 39": "NH1" <-> "NH2" Residue "Ae ARG 108": "NH1" <-> "NH2" Residue "Ae ARG 128": "NH1" <-> "NH2" Residue "Af ARG 89": "NH1" <-> "NH2" Residue "Ag ARG 29": "NH1" <-> "NH2" Residue "Ag ARG 60": "NH1" <-> "NH2" Residue "Ag GLU 98": "OE1" <-> "OE2" Residue "Ah ARG 48": "NH1" <-> "NH2" Residue "Ah TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ah ARG 94": "NH1" <-> "NH2" Residue "Ah TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ai ARG 4": "NH1" <-> "NH2" Residue "Ai GLU 59": "OE1" <-> "OE2" Residue "Ai ARG 68": "NH1" <-> "NH2" Residue "Ai ARG 76": "NH1" <-> "NH2" Residue "Aj ARG 11": "NH1" <-> "NH2" Residue "Aj ARG 20": "NH1" <-> "NH2" Residue "Aj ARG 45": "NH1" <-> "NH2" Residue "Aj ARG 55": "NH1" <-> "NH2" Residue "Aj ARG 56": "NH1" <-> "NH2" Residue "Aj ARG 72": "NH1" <-> "NH2" Residue "Aj ARG 79": "NH1" <-> "NH2" Residue "Ak ASP 49": "OD1" <-> "OD2" Residue "Al ARG 8": "NH1" <-> "NH2" Residue "Al ARG 21": "NH1" <-> "NH2" Residue "Al ARG 36": "NH1" <-> "NH2" Residue "Am GLU 53": "OE1" <-> "OE2" Residue "Am ARG 71": "NH1" <-> "NH2" Residue "Am ARG 85": "NH1" <-> "NH2" Residue "An ARG 2": "NH1" <-> "NH2" Residue "An ARG 9": "NH1" <-> "NH2" Residue "An ARG 15": "NH1" <-> "NH2" Residue "An ARG 23": "NH1" <-> "NH2" Residue "Ao PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao ARG 40": "NH1" <-> "NH2" Residue "Ao ARG 43": "NH1" <-> "NH2" Residue "Ao ARG 69": "NH1" <-> "NH2" Residue "Ao ARG 78": "NH1" <-> "NH2" Residue "Ap ARG 17": "NH1" <-> "NH2" Residue "Ap ARG 49": "NH1" <-> "NH2" Residue "Ap ARG 84": "NH1" <-> "NH2" Residue "Ar ARG 35": "NH1" <-> "NH2" Residue "Ar ARG 39": "NH1" <-> "NH2" Residue "Ar ARG 71": "NH1" <-> "NH2" Residue "Ar TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ar ARG 107": "NH1" <-> "NH2" Residue "Ar ARG 112": "NH1" <-> "NH2" Residue "Ar ARG 113": "NH1" <-> "NH2" Residue "AK TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK GLU 142": "OE1" <-> "OE2" Residue "AK PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B ASP 206": "OD1" <-> "OD2" Residue "C TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ASP 126": "OD1" <-> "OD2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C ASP 191": "OD1" <-> "OD2" Residue "C TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "E ASP 14": "OD1" <-> "OD2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E GLU 38": "OE1" <-> "OE2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 169": "OD1" <-> "OD2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 11": "NH1" <-> "NH2" Residue "F PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 68": "NH1" <-> "NH2" Residue "F ARG 77": "NH1" <-> "NH2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 171": "OD1" <-> "OD2" Residue "F PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 191": "NH1" <-> "NH2" Residue "F ARG 198": "NH1" <-> "NH2" Residue "F PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "F PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 251": "OE1" <-> "OE2" Residue "F ARG 252": "NH1" <-> "NH2" Residue "G ASP 27": "OD1" <-> "OD2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "G ARG 127": "NH1" <-> "NH2" Residue "G ASP 175": "OD1" <-> "OD2" Residue "G ARG 198": "NH1" <-> "NH2" Residue "H PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 131": "NH1" <-> "NH2" Residue "H ARG 132": "NH1" <-> "NH2" Residue "H ARG 178": "NH1" <-> "NH2" Residue "H ARG 191": "NH1" <-> "NH2" Residue "H ARG 198": "NH1" <-> "NH2" Residue "H TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 216": "NH1" <-> "NH2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H ARG 233": "NH1" <-> "NH2" Residue "I ASP 17": "OD1" <-> "OD2" Residue "I GLU 18": "OE1" <-> "OE2" Residue "I ARG 41": "NH1" <-> "NH2" Residue "I GLU 42": "OE1" <-> "OE2" Residue "I PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 81": "NH1" <-> "NH2" Residue "I GLU 84": "OE1" <-> "OE2" Residue "I ARG 143": "NH1" <-> "NH2" Residue "I PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 12": "NH1" <-> "NH2" Residue "J ARG 25": "NH1" <-> "NH2" Residue "J ARG 41": "NH1" <-> "NH2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "J GLU 135": "OE1" <-> "OE2" Residue "J ARG 141": "NH1" <-> "NH2" Residue "J TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 150": "OD1" <-> "OD2" Residue "J ARG 205": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K GLU 65": "OE1" <-> "OE2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K ARG 83": "NH1" <-> "NH2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 138": "NH1" <-> "NH2" Residue "K PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 65": "NH1" <-> "NH2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "L ARG 95": "NH1" <-> "NH2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "M TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 91": "OD1" <-> "OD2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "M PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 20": "OE1" <-> "OE2" Residue "N GLU 37": "OE1" <-> "OE2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N GLU 58": "OE1" <-> "OE2" Residue "N GLU 66": "OE1" <-> "OE2" Residue "N ASP 80": "OD1" <-> "OD2" Residue "N ASP 95": "OD1" <-> "OD2" Residue "N ASP 122": "OD1" <-> "OD2" Residue "N TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 20": "NH1" <-> "NH2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 121": "NH1" <-> "NH2" Residue "P PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 66": "NH1" <-> "NH2" Residue "P ARG 104": "NH1" <-> "NH2" Residue "P ARG 117": "NH1" <-> "NH2" Residue "P ARG 128": "NH1" <-> "NH2" Residue "P ARG 141": "NH1" <-> "NH2" Residue "P ARG 150": "NH1" <-> "NH2" Residue "Q ASP 21": "OD1" <-> "OD2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 44": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 51": "NH1" <-> "NH2" Residue "Q ARG 59": "NH1" <-> "NH2" Residue "Q ARG 61": "NH1" <-> "NH2" Residue "Q GLU 71": "OE1" <-> "OE2" Residue "Q PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 130": "NH1" <-> "NH2" Residue "R PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 53": "OE1" <-> "OE2" Residue "R PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 110": "OD1" <-> "OD2" Residue "R ASP 123": "OD1" <-> "OD2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R ARG 146": "NH1" <-> "NH2" Residue "S ARG 5": "NH1" <-> "NH2" Residue "S GLU 18": "OE1" <-> "OE2" Residue "S TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 37": "OE1" <-> "OE2" Residue "S ARG 63": "NH1" <-> "NH2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "S ARG 80": "NH1" <-> "NH2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "S GLU 87": "OE1" <-> "OE2" Residue "T ARG 14": "NH1" <-> "NH2" Residue "T ARG 39": "NH1" <-> "NH2" Residue "T ARG 55": "NH1" <-> "NH2" Residue "T ASP 81": "OD1" <-> "OD2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 89": "OD1" <-> "OD2" Residue "T ARG 121": "NH1" <-> "NH2" Residue "T ARG 142": "NH1" <-> "NH2" Residue "U ARG 16": "NH1" <-> "NH2" Residue "U ARG 62": "NH1" <-> "NH2" Residue "U ARG 84": "NH1" <-> "NH2" Residue "U ARG 102": "NH1" <-> "NH2" Residue "U ASP 118": "OD1" <-> "OD2" Residue "U ARG 121": "NH1" <-> "NH2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ASP 38": "OD1" <-> "OD2" Residue "V ARG 87": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 8": "NH1" <-> "NH2" Residue "Y ARG 17": "NH1" <-> "NH2" Residue "Y ARG 18": "NH1" <-> "NH2" Residue "Y ARG 67": "NH1" <-> "NH2" Residue "Y PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 107": "NH1" <-> "NH2" Residue "Z PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 20": "NH1" <-> "NH2" Residue "Z PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 61": "NH1" <-> "NH2" Residue "Z PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 80": "OD1" <-> "OD2" Residue "Z GLU 98": "OE1" <-> "OE2" Residue "Z ARG 110": "NH1" <-> "NH2" Residue "a ASP 56": "OD1" <-> "OD2" Residue "a ARG 80": "NH1" <-> "NH2" Residue "a ARG 85": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 85": "NH1" <-> "NH2" Residue "b ARG 87": "NH1" <-> "NH2" Residue "b ARG 89": "NH1" <-> "NH2" Residue "c TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 72": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 36": "OD1" <-> "OD2" Residue "d ASP 37": "OD1" <-> "OD2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d GLU 60": "OE1" <-> "OE2" Residue "d ARG 66": "NH1" <-> "NH2" Residue "d ARG 67": "NH1" <-> "NH2" Residue "e PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 81": "NH1" <-> "NH2" Residue "f GLU 96": "OE1" <-> "OE2" Residue "f ARG 101": "NH1" <-> "NH2" Residue "f ARG 104": "NH1" <-> "NH2" Residue "f PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 138": "NH1" <-> "NH2" Residue "h ARG 47": "NH1" <-> "NH2" Residue "h ARG 60": "NH1" <-> "NH2" Residue "h ARG 100": "NH1" <-> "NH2" Residue "h PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 203": "OD1" <-> "OD2" Residue "h ASP 231": "OD1" <-> "OD2" Residue "h ASP 234": "OD1" <-> "OD2" Residue "Aq ASP 43": "OD1" <-> "OD2" Residue "Aq ARG 47": "NH1" <-> "NH2" Residue "Aq ARG 65": "NH1" <-> "NH2" Residue "Aq ARG 68": "NH1" <-> "NH2" Residue "Aq GLU 107": "OE1" <-> "OE2" Residue "Aq PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aq TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aq PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aq ARG 166": "NH1" <-> "NH2" Residue "Aq ARG 182": "NH1" <-> "NH2" Residue "Aq ARG 192": "NH1" <-> "NH2" Residue "Aq ARG 194": "NH1" <-> "NH2" Residue "Aq ASP 240": "OD1" <-> "OD2" Residue "Aq ASP 243": "OD1" <-> "OD2" Residue "Aq ARG 245": "NH1" <-> "NH2" Residue "Aq ASP 255": "OD1" <-> "OD2" Residue "Aq TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aq ASP 307": "OD1" <-> "OD2" Residue "Aq ASP 327": "OD1" <-> "OD2" Residue "Aq ARG 330": "NH1" <-> "NH2" Residue "Aq TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aq GLU 361": "OE1" <-> "OE2" Residue "Aq GLU 376": "OE1" <-> "OE2" Residue "Aq ASP 394": "OD1" <-> "OD2" Residue "Aq GLU 398": "OE1" <-> "OE2" Residue "Aq ASP 418": "OD1" <-> "OD2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 219295 Number of models: 1 Model: "" Number of chains: 82 Chain: "5" Number of atoms: 77074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3594, 77074 Classifications: {'RNA': 3594} Modifications used: {'rna3p_pyr': 1401, 'rna2p_pur': 366, 'rna3p_pur': 1613, 'rna2p_pyr': 214} Link IDs: {'rna3p': 3013, 'rna2p': 580} Chain breaks: 26 Chain: "7" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2538 Classifications: {'RNA': 119} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna3p_pur': 55, 'rna2p_pyr': 6, 'rna3p_pyr': 52} Link IDs: {'rna3p': 106, 'rna2p': 12} Chain: "8" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3208 Classifications: {'RNA': 151} Modifications used: {'rna3p_pyr': 63, 'rna2p_pur': 14, 'rna3p_pur': 59, 'rna2p_pyr': 15, '5*END': 1} Link IDs: {'rna3p': 122, 'rna2p': 28} Chain breaks: 1 Chain: "AA" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1895 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 233} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "AB" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3172 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} Chain: "AC" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2883 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "AD" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2391 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain: "AE" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1729 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain breaks: 3 Chain: "AF" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1875 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "AG" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1819 Classifications: {'peptide': 225} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "AH" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1516 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "AI" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1664 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain breaks: 1 Chain: "AJ" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1362 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "AL" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1627 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 14, 'TRANS': 186} Chain: "AM" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1137 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "AN" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "AO" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1631 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "AP" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "AQ" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1526 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "AR" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1503 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 3, 'TRANS': 176} Chain: "AS" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1457 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 163} Chain: "AT" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1298 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "AU" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 818 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "AV" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 969 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "AW" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 528 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "AX" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 967 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "AY" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "AZ" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "Aa" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "Ab" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 1 Chain: "Ac" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 761 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "Ad" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "Ae" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "Af" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "Ag" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 906 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Ah" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1013 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Ai" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 830 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Aj" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "Ak" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "Al" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 447 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Am" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "An" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "Ao" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 851 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "Ap" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "Ar" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "AK" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1705 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 203} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "2" Number of atoms: 36229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36229 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 149, 'rna3p_pur': 749, 'rna2p_pyr': 113, 'rna3p_pyr': 686} Link IDs: {'rna3p': 1434, 'rna2p': 262} Chain breaks: 11 Chain: "B" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1706 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1712 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "F" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2073 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1471 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain breaks: 1 Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "M" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1175 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain breaks: 1 Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 990 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135, 'PCIS': 1} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "T" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "U" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 630 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "X" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 125, 'PCIS': 1} Chain: "Y" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "b" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 778 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "c" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "d" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 488 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "e" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "f" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 447 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "Aq" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3278 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 9, 'TRANS': 406} Chain: "1" Number of atoms: 4407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 4407 Classifications: {'RNA': 207} Modifications used: {'rna3p_pyr': 81, 'rna2p_pur': 17, 'rna3p_pur': 90, 'rna2p_pyr': 19} Link IDs: {'rna3p': 171, 'rna2p': 35} Time building chain proxies: 84.68, per 1000 atoms: 0.39 Number of scatterers: 219295 At special positions: 0 Unit cell: (303.303, 294.819, 266.185, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 438 16.00 P 5765 15.00 O 56588 8.00 N 40852 7.00 C 115652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYSAj 22 " - pdb=" SG CYSAj 37 " distance=2.99 Simple disulfide: pdb=" SG CYS e 24 " - pdb=" SG CYS e 42 " distance=2.96 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: 59.54 Conformation dependent library (CDL) restraints added in 11.4 seconds 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22160 Finding SS restraints... Secondary structure from input PDB file: 381 helices and 134 sheets defined 33.4% alpha, 15.5% beta 1501 base pairs and 3034 stacking pairs defined. Time for finding SS restraints: 52.85 Creating SS restraints... Processing helix chain 'AA' and resid 5 through 11 removed outlier: 4.014A pdb=" N GLYAA 11 " --> pdb=" O GLYAA 7 " (cutoff:3.500A) Processing helix chain 'AA' and resid 33 through 38 Processing helix chain 'AA' and resid 181 through 190 removed outlier: 3.582A pdb=" N ALAAA 185 " --> pdb=" O LYSAA 181 " (cutoff:3.500A) Processing helix chain 'AA' and resid 200 through 204 Processing helix chain 'AB' and resid 111 through 116 Processing helix chain 'AB' and resid 117 through 119 No H-bonds generated for 'chain 'AB' and resid 117 through 119' Processing helix chain 'AB' and resid 133 through 138 removed outlier: 3.636A pdb=" N TRPAB 137 " --> pdb=" O CYSAB 134 " (cutoff:3.500A) Processing helix chain 'AB' and resid 142 through 147 Processing helix chain 'AB' and resid 147 through 152 Processing helix chain 'AB' and resid 189 through 200 removed outlier: 3.570A pdb=" N GLUAB 199 " --> pdb=" O ASPAB 195 " (cutoff:3.500A) Processing helix chain 'AB' and resid 206 through 211 removed outlier: 4.117A pdb=" N VALAB 210 " --> pdb=" O PROAB 206 " (cutoff:3.500A) Processing helix chain 'AB' and resid 230 through 235 Processing helix chain 'AB' and resid 381 through 390 Processing helix chain 'AC' and resid 25 through 30 Processing helix chain 'AC' and resid 33 through 45 Processing helix chain 'AC' and resid 46 through 48 No H-bonds generated for 'chain 'AC' and resid 46 through 48' Processing helix chain 'AC' and resid 116 through 133 removed outlier: 4.162A pdb=" N SERAC 126 " --> pdb=" O TYRAC 122 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ALAAC 129 " --> pdb=" O CYSAC 125 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SERAC 131 " --> pdb=" O ALAAC 127 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALAAC 132 " --> pdb=" O LEUAC 128 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEUAC 133 " --> pdb=" O ALAAC 129 " (cutoff:3.500A) Processing helix chain 'AC' and resid 133 through 139 removed outlier: 3.758A pdb=" N VALAC 137 " --> pdb=" O LEUAC 133 " (cutoff:3.500A) Processing helix chain 'AC' and resid 163 through 174 Processing helix chain 'AC' and resid 176 through 187 removed outlier: 3.888A pdb=" N ILEAC 180 " --> pdb=" O ALAAC 176 " (cutoff:3.500A) Processing helix chain 'AC' and resid 192 through 196 Processing helix chain 'AC' and resid 216 through 222 Processing helix chain 'AC' and resid 233 through 235 No H-bonds generated for 'chain 'AC' and resid 233 through 235' Processing helix chain 'AC' and resid 253 through 259 removed outlier: 3.623A pdb=" N LYSAC 259 " --> pdb=" O SERAC 255 " (cutoff:3.500A) Processing helix chain 'AC' and resid 259 through 264 Processing helix chain 'AC' and resid 288 through 295 removed outlier: 4.004A pdb=" N LYSAC 294 " --> pdb=" O SERAC 290 " (cutoff:3.500A) Processing helix chain 'AC' and resid 295 through 301 removed outlier: 3.917A pdb=" N ALAAC 301 " --> pdb=" O GLUAC 297 " (cutoff:3.500A) Processing helix chain 'AC' and resid 321 through 329 Processing helix chain 'AC' and resid 330 through 363 removed outlier: 4.537A pdb=" N THRAC 334 " --> pdb=" O PROAC 330 " (cutoff:3.500A) Processing helix chain 'AD' and resid 9 through 16 Processing helix chain 'AD' and resid 20 through 26 Processing helix chain 'AD' and resid 29 through 38 removed outlier: 4.190A pdb=" N ARGAD 35 " --> pdb=" O TYRAD 31 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILEAD 38 " --> pdb=" O LYSAD 34 " (cutoff:3.500A) Processing helix chain 'AD' and resid 79 through 86 removed outlier: 3.799A pdb=" N GLUAD 82 " --> pdb=" O TYRAD 79 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEUAD 83 " --> pdb=" O ALAAD 80 " (cutoff:3.500A) Proline residue: AD 84 - end of helix No H-bonds generated for 'chain 'AD' and resid 79 through 86' Processing helix chain 'AD' and resid 94 through 113 Processing helix chain 'AD' and resid 157 through 170 removed outlier: 3.859A pdb=" N GLYAD 161 " --> pdb=" O ASNAD 157 " (cutoff:3.500A) Processing helix chain 'AD' and resid 191 through 200 removed outlier: 3.637A pdb=" N HISAD 195 " --> pdb=" O ASNAD 191 " (cutoff:3.500A) Processing helix chain 'AD' and resid 201 through 215 removed outlier: 3.714A pdb=" N ALAAD 205 " --> pdb=" O GLYAD 201 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYRAD 207 " --> pdb=" O ASNAD 203 " (cutoff:3.500A) Processing helix chain 'AD' and resid 215 through 223 Processing helix chain 'AD' and resid 225 through 230 removed outlier: 3.601A pdb=" N ASNAD 229 " --> pdb=" O GLNAD 225 " (cutoff:3.500A) Processing helix chain 'AD' and resid 235 through 250 removed outlier: 3.531A pdb=" N TYRAD 240 " --> pdb=" O METAD 236 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALAAD 243 " --> pdb=" O METAD 239 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALAAD 245 " --> pdb=" O LYSAD 241 " (cutoff:3.500A) Processing helix chain 'AD' and resid 272 through 295 removed outlier: 3.608A pdb=" N LEUAD 288 " --> pdb=" O LYSAD 284 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLUAD 292 " --> pdb=" O LEUAD 288 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARGAD 293 " --> pdb=" O ARGAD 289 " (cutoff:3.500A) Processing helix chain 'AE' and resid 62 through 69 removed outlier: 3.556A pdb=" N SERAE 66 " --> pdb=" O SERAE 62 " (cutoff:3.500A) Processing helix chain 'AE' and resid 70 through 73 Processing helix chain 'AE' and resid 135 through 139 Processing helix chain 'AE' and resid 193 through 197 Processing helix chain 'AE' and resid 246 through 265 removed outlier: 4.280A pdb=" N GLNAE 259 " --> pdb=" O ALAAE 255 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILEAE 260 " --> pdb=" O VALAE 256 " (cutoff:3.500A) Proline residue: AE 262 - end of helix Processing helix chain 'AE' and resid 269 through 276 Processing helix chain 'AF' and resid 24 through 78 removed outlier: 4.095A pdb=" N GLUAF 67 " --> pdb=" O METAF 63 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILEAF 68 " --> pdb=" O TYRAF 64 " (cutoff:3.500A) Processing helix chain 'AF' and resid 101 through 111 Processing helix chain 'AF' and resid 128 through 133 Processing helix chain 'AF' and resid 134 through 137 Proline residue: AF 137 - end of helix No H-bonds generated for 'chain 'AF' and resid 134 through 137' Processing helix chain 'AF' and resid 145 through 156 Processing helix chain 'AF' and resid 173 through 178 Processing helix chain 'AF' and resid 185 through 195 Processing helix chain 'AF' and resid 199 through 205 Processing helix chain 'AF' and resid 238 through 247 removed outlier: 3.930A pdb=" N LEUAF 242 " --> pdb=" O GLNAF 238 " (cutoff:3.500A) Processing helix chain 'AG' and resid 111 through 122 Processing helix chain 'AG' and resid 122 through 127 Processing helix chain 'AG' and resid 130 through 135 Processing helix chain 'AG' and resid 136 through 138 No H-bonds generated for 'chain 'AG' and resid 136 through 138' Processing helix chain 'AG' and resid 141 through 153 removed outlier: 3.589A pdb=" N GLNAG 147 " --> pdb=" O GLNAG 143 " (cutoff:3.500A) Processing helix chain 'AG' and resid 163 through 169 removed outlier: 3.532A pdb=" N ALAAG 169 " --> pdb=" O GLNAG 165 " (cutoff:3.500A) Processing helix chain 'AG' and resid 193 through 198 Processing helix chain 'AG' and resid 216 through 220 removed outlier: 3.636A pdb=" N LEUAG 219 " --> pdb=" O PROAG 216 " (cutoff:3.500A) Processing helix chain 'AG' and resid 222 through 230 Processing helix chain 'AG' and resid 239 through 244 Processing helix chain 'AG' and resid 261 through 263 No H-bonds generated for 'chain 'AG' and resid 261 through 263' Processing helix chain 'AG' and resid 264 through 277 removed outlier: 3.993A pdb=" N LEUAG 268 " --> pdb=" O ASPAG 264 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALAAG 274 " --> pdb=" O LYSAG 270 " (cutoff:3.500A) Processing helix chain 'AG' and resid 282 through 287 Processing helix chain 'AG' and resid 296 through 308 Processing helix chain 'AG' and resid 309 through 311 No H-bonds generated for 'chain 'AG' and resid 309 through 311' Processing helix chain 'AH' and resid 65 through 69 removed outlier: 3.505A pdb=" N ALAAH 68 " --> pdb=" O LYSAH 65 " (cutoff:3.500A) Processing helix chain 'AH' and resid 70 through 86 Processing helix chain 'AH' and resid 150 through 165 removed outlier: 3.742A pdb=" N ASNAH 156 " --> pdb=" O GLUAH 152 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILEAH 161 " --> pdb=" O SERAH 157 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THRAH 165 " --> pdb=" O ILEAH 161 " (cutoff:3.500A) Processing helix chain 'AI' and resid 5 through 10 removed outlier: 3.652A pdb=" N CYSAI 8 " --> pdb=" O PROAI 5 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARGAI 10 " --> pdb=" O ARGAI 7 " (cutoff:3.500A) Processing helix chain 'AI' and resid 62 through 80 Processing helix chain 'AI' and resid 144 through 156 removed outlier: 3.774A pdb=" N VALAI 148 " --> pdb=" O ASNAI 144 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VALAI 149 " --> pdb=" O LYSAI 145 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLUAI 150 " --> pdb=" O GLUAI 146 " (cutoff:3.500A) Processing helix chain 'AI' and resid 157 through 159 No H-bonds generated for 'chain 'AI' and resid 157 through 159' Processing helix chain 'AI' and resid 180 through 187 Processing helix chain 'AI' and resid 206 through 213 Processing helix chain 'AJ' and resid 30 through 35 Processing helix chain 'AJ' and resid 35 through 45 removed outlier: 4.121A pdb=" N VALAJ 39 " --> pdb=" O ARGAJ 35 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEUAJ 40 " --> pdb=" O ALAAJ 36 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 76 through 90 removed outlier: 4.109A pdb=" N GLUAJ 80 " --> pdb=" O GLYAJ 76 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLUAJ 81 " --> pdb=" O ALAAJ 77 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYSAJ 85 " --> pdb=" O GLUAJ 81 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 95 through 99 Processing helix chain 'AJ' and resid 111 through 116 removed outlier: 3.697A pdb=" N ASPAJ 114 " --> pdb=" O GLUAJ 111 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 139 through 143 removed outlier: 4.010A pdb=" N ALAAJ 142 " --> pdb=" O PHEAJ 139 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 158 through 170 removed outlier: 3.869A pdb=" N ARGAJ 164 " --> pdb=" O GLUAJ 160 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLNAJ 168 " --> pdb=" O ARGAJ 164 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYRAJ 170 " --> pdb=" O PHEAJ 166 " (cutoff:3.500A) Processing helix chain 'AL' and resid 17 through 20 Processing helix chain 'AL' and resid 27 through 46 Processing helix chain 'AL' and resid 77 through 85 removed outlier: 3.878A pdb=" N VALAL 83 " --> pdb=" O GLUAL 79 " (cutoff:3.500A) Processing helix chain 'AL' and resid 90 through 95 removed outlier: 3.709A pdb=" N GLYAL 95 " --> pdb=" O ARGAL 92 " (cutoff:3.500A) Processing helix chain 'AL' and resid 107 through 123 removed outlier: 3.770A pdb=" N ASNAL 113 " --> pdb=" O SERAL 109 " (cutoff:3.500A) Processing helix chain 'AL' and resid 140 through 146 Processing helix chain 'AL' and resid 177 through 202 removed outlier: 3.520A pdb=" N PHEAL 192 " --> pdb=" O ASNAL 188 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLYAL 193 " --> pdb=" O ALAAL 189 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILEAL 194 " --> pdb=" O ARGAL 190 " (cutoff:3.500A) Processing helix chain 'AM' and resid 69 through 81 removed outlier: 3.737A pdb=" N VALAM 73 " --> pdb=" O ARGAM 69 " (cutoff:3.500A) Processing helix chain 'AM' and resid 81 through 89 removed outlier: 3.871A pdb=" N ALAAM 87 " --> pdb=" O ASNAM 83 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALAAM 88 " --> pdb=" O THRAM 84 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THRAM 89 " --> pdb=" O LYSAM 85 " (cutoff:3.500A) Processing helix chain 'AM' and resid 89 through 104 Processing helix chain 'AM' and resid 105 through 136 removed outlier: 3.598A pdb=" N METAM 118 " --> pdb=" O LYSAM 114 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYSAM 128 " --> pdb=" O LYSAM 124 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARGAM 132 " --> pdb=" O LYSAM 128 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALAAM 133 " --> pdb=" O LYSAM 129 " (cutoff:3.500A) Processing helix chain 'AN' and resid 3 through 11 Processing helix chain 'AN' and resid 16 through 32 removed outlier: 3.688A pdb=" N ARGAN 24 " --> pdb=" O ARGAN 20 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARGAN 31 " --> pdb=" O CYSAN 27 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLNAN 32 " --> pdb=" O TRPAN 28 " (cutoff:3.500A) Processing helix chain 'AN' and resid 44 through 52 Processing helix chain 'AN' and resid 75 through 79 removed outlier: 3.556A pdb=" N ALAAN 79 " --> pdb=" O PROAN 76 " (cutoff:3.500A) Processing helix chain 'AN' and resid 83 through 87 removed outlier: 3.597A pdb=" N HISAN 87 " --> pdb=" O PROAN 84 " (cutoff:3.500A) Processing helix chain 'AN' and resid 97 through 110 Processing helix chain 'AN' and resid 139 through 144 Processing helix chain 'AN' and resid 153 through 157 Processing helix chain 'AN' and resid 158 through 163 Processing helix chain 'AN' and resid 165 through 170 Processing helix chain 'AN' and resid 187 through 197 Processing helix chain 'AO' and resid 15 through 29 removed outlier: 3.746A pdb=" N ILEAO 22 " --> pdb=" O ARGAO 18 " (cutoff:3.500A) Processing helix chain 'AO' and resid 38 through 40 No H-bonds generated for 'chain 'AO' and resid 38 through 40' Processing helix chain 'AO' and resid 46 through 60 removed outlier: 3.758A pdb=" N LYSAO 60 " --> pdb=" O ALAAO 56 " (cutoff:3.500A) Processing helix chain 'AO' and resid 75 through 86 Processing helix chain 'AO' and resid 92 through 100 Processing helix chain 'AO' and resid 109 through 114 removed outlier: 4.041A pdb=" N LYSAO 114 " --> pdb=" O PROAO 110 " (cutoff:3.500A) Processing helix chain 'AO' and resid 120 through 123 Processing helix chain 'AO' and resid 124 through 129 Processing helix chain 'AO' and resid 138 through 145 Processing helix chain 'AO' and resid 150 through 184 removed outlier: 3.729A pdb=" N THRAO 155 " --> pdb=" O ALAAO 151 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYSAO 183 " --> pdb=" O LYSAO 179 " (cutoff:3.500A) Processing helix chain 'AO' and resid 189 through 198 removed outlier: 3.861A pdb=" N GLUAO 194 " --> pdb=" O SERAO 190 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VALAO 195 " --> pdb=" O LYSAO 191 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEUAO 196 " --> pdb=" O PHEAO 192 " (cutoff:3.500A) Processing helix chain 'AP' and resid 25 through 36 removed outlier: 4.568A pdb=" N GLUAP 31 " --> pdb=" O LYSAP 27 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILEAP 36 " --> pdb=" O THRAP 32 " (cutoff:3.500A) Processing helix chain 'AP' and resid 40 through 53 Processing helix chain 'AP' and resid 84 through 105 removed outlier: 3.690A pdb=" N METAP 94 " --> pdb=" O PHEAP 90 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEUAP 95 " --> pdb=" O LEUAP 91 " (cutoff:3.500A) Processing helix chain 'AP' and resid 108 through 110 No H-bonds generated for 'chain 'AP' and resid 108 through 110' Processing helix chain 'AQ' and resid 22 through 39 removed outlier: 3.666A pdb=" N PHEAQ 34 " --> pdb=" O LYSAQ 30 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEUAQ 35 " --> pdb=" O LEUAQ 31 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 42 through 53 removed outlier: 3.641A pdb=" N PHEAQ 52 " --> pdb=" O LEUAQ 48 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N METAQ 53 " --> pdb=" O LYSAQ 49 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 63 through 69 Processing helix chain 'AQ' and resid 106 through 114 Processing helix chain 'AQ' and resid 122 through 130 removed outlier: 3.559A pdb=" N LEUAQ 128 " --> pdb=" O HISAQ 124 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 146 through 152 removed outlier: 3.545A pdb=" N TYRAQ 149 " --> pdb=" O ARGAQ 146 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 177 through 181 removed outlier: 4.056A pdb=" N ARGAQ 180 " --> pdb=" O ALAAQ 177 " (cutoff:3.500A) Processing helix chain 'AR' and resid 4 through 16 Processing helix chain 'AR' and resid 38 through 47 removed outlier: 3.827A pdb=" N LEUAR 44 " --> pdb=" O GLNAR 40 " (cutoff:3.500A) Processing helix chain 'AR' and resid 60 through 73 removed outlier: 3.738A pdb=" N ALAAR 69 " --> pdb=" O LYSAR 65 " (cutoff:3.500A) Processing helix chain 'AR' and resid 77 through 81 removed outlier: 3.902A pdb=" N LYSAR 80 " --> pdb=" O GLYAR 77 " (cutoff:3.500A) Processing helix chain 'AR' and resid 84 through 89 Processing helix chain 'AR' and resid 90 through 112 Processing helix chain 'AR' and resid 116 through 129 Processing helix chain 'AR' and resid 134 through 180 removed outlier: 3.613A pdb=" N LEUAR 138 " --> pdb=" O ASNAR 134 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYSAR 144 " --> pdb=" O GLUAR 140 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYSAR 153 " --> pdb=" O LYSAR 149 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEUAR 154 " --> pdb=" O ALAAR 150 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEUAR 155 " --> pdb=" O ARGAR 151 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALAAR 156 " --> pdb=" O LYSAR 152 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARGAR 162 " --> pdb=" O GLNAR 158 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARGAR 163 " --> pdb=" O ALAAR 159 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYSAR 171 " --> pdb=" O LYSAR 167 " (cutoff:3.500A) Processing helix chain 'AS' and resid 36 through 52 removed outlier: 3.917A pdb=" N SERAS 42 " --> pdb=" O VALAS 38 " (cutoff:3.500A) Processing helix chain 'AS' and resid 101 through 118 Processing helix chain 'AS' and resid 139 through 144 Processing helix chain 'AT' and resid 27 through 32 Processing helix chain 'AT' and resid 104 through 118 removed outlier: 3.526A pdb=" N ARGAT 108 " --> pdb=" O SERAT 104 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYSAT 116 " --> pdb=" O ASNAT 112 " (cutoff:3.500A) Processing helix chain 'AU' and resid 26 through 32 removed outlier: 3.952A pdb=" N GLUAU 30 " --> pdb=" O THRAU 26 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASPAU 31 " --> pdb=" O HISAU 27 " (cutoff:3.500A) Processing helix chain 'AU' and resid 35 through 47 Processing helix chain 'AU' and resid 79 through 94 removed outlier: 3.720A pdb=" N LEUAU 83 " --> pdb=" O SERAU 79 " (cutoff:3.500A) Processing helix chain 'AV' and resid 122 through 129 Processing helix chain 'AW' and resid 33 through 42 Processing helix chain 'AW' and resid 45 through 49 removed outlier: 3.626A pdb=" N GLNAW 48 " --> pdb=" O ASNAW 45 " (cutoff:3.500A) Processing helix chain 'AW' and resid 52 through 59 Processing helix chain 'AX' and resid 72 through 76 Processing helix chain 'AX' and resid 83 through 94 removed outlier: 3.540A pdb=" N ASNAX 94 " --> pdb=" O ILEAX 90 " (cutoff:3.500A) Processing helix chain 'AX' and resid 105 through 118 removed outlier: 3.711A pdb=" N LYSAX 114 " --> pdb=" O LYSAX 110 " (cutoff:3.500A) Processing helix chain 'AX' and resid 145 through 154 removed outlier: 3.656A pdb=" N ASNAX 151 " --> pdb=" O LEUAX 147 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYSAX 152 " --> pdb=" O ASPAX 148 " (cutoff:3.500A) Processing helix chain 'AY' and resid 10 through 20 Processing helix chain 'AY' and resid 22 through 30 removed outlier: 4.112A pdb=" N LYSAY 28 " --> pdb=" O HISAY 24 " (cutoff:3.500A) Processing helix chain 'AY' and resid 35 through 43 Processing helix chain 'AY' and resid 114 through 134 removed outlier: 3.726A pdb=" N GLNAY 127 " --> pdb=" O ALAAY 123 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 58 through 66 Processing helix chain 'AZ' and resid 103 through 123 removed outlier: 4.154A pdb=" N LYSAZ 123 " --> pdb=" O GLUAZ 119 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 127 through 132 removed outlier: 3.820A pdb=" N PHEAZ 131 " --> pdb=" O ASNAZ 127 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLNAZ 132 " --> pdb=" O LYSAZ 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'AZ' and resid 127 through 132' Processing helix chain 'Aa' and resid 7 through 11 Processing helix chain 'Aa' and resid 41 through 49 Processing helix chain 'Aa' and resid 74 through 81 removed outlier: 3.510A pdb=" N LEUAa 78 " --> pdb=" O LEUAa 75 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TRPAa 79 " --> pdb=" O ASPAa 76 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 83 through 93 removed outlier: 3.968A pdb=" N ARGAa 87 " --> pdb=" O SERAa 83 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 130 through 140 removed outlier: 3.639A pdb=" N ILEAa 137 " --> pdb=" O ALAAa 133 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 11 through 19 removed outlier: 3.506A pdb=" N ARGAb 18 " --> pdb=" O ARGAb 14 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASNAb 19 " --> pdb=" O LYSAb 15 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 36 through 49 Processing helix chain 'Ab' and resid 50 through 53 removed outlier: 3.533A pdb=" N GLYAb 53 " --> pdb=" O ASNAb 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ab' and resid 50 through 53' Processing helix chain 'Ab' and resid 54 through 65 Processing helix chain 'Ab' and resid 65 through 76 removed outlier: 3.728A pdb=" N ALAAb 69 " --> pdb=" O METAb 65 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALAAb 71 " --> pdb=" O ALAAb 67 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYSAb 73 " --> pdb=" O ALAAb 69 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALAAb 74 " --> pdb=" O GLUAb 70 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VALAb 76 " --> pdb=" O ILEAb 72 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 90 through 100 Processing helix chain 'Ab' and resid 107 through 115 Processing helix chain 'Ac' and resid 11 through 25 removed outlier: 3.772A pdb=" N ASNAc 15 " --> pdb=" O LEUAc 11 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SERAc 16 " --> pdb=" O GLUAc 12 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLNAc 19 " --> pdb=" O ASNAc 15 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 31 through 40 removed outlier: 3.546A pdb=" N ARGAc 39 " --> pdb=" O LEUAc 35 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 53 through 68 removed outlier: 3.504A pdb=" N TYRAc 62 " --> pdb=" O SERAc 58 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 77 through 85 Processing helix chain 'Ad' and resid 29 through 34 Processing helix chain 'Ad' and resid 37 through 40 Processing helix chain 'Ad' and resid 41 through 57 removed outlier: 3.590A pdb=" N ARGAd 50 " --> pdb=" O LEUAd 46 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHEAd 52 " --> pdb=" O GLUAd 48 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N METAd 57 " --> pdb=" O ALAAd 53 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 65 through 73 Processing helix chain 'Ae' and resid 81 through 85 Processing helix chain 'Ae' and resid 87 through 91 removed outlier: 4.298A pdb=" N METAe 90 " --> pdb=" O VALAe 87 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 104 through 119 removed outlier: 4.002A pdb=" N ALAAe 110 " --> pdb=" O LYSAe 106 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLUAe 113 " --> pdb=" O LYSAe 109 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLNAe 117 " --> pdb=" O GLUAe 113 " (cutoff:3.500A) Processing helix chain 'Af' and resid 93 through 97 Processing helix chain 'Ag' and resid 62 through 66 removed outlier: 3.780A pdb=" N METAg 65 " --> pdb=" O LYSAg 62 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 68 through 72 Processing helix chain 'Ag' and resid 83 through 107 removed outlier: 3.794A pdb=" N LYSAg 92 " --> pdb=" O ARGAg 88 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLUAg 98 " --> pdb=" O ALAAg 94 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILEAg 102 " --> pdb=" O GLUAg 98 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 8 through 12 removed outlier: 3.637A pdb=" N LYSAh 12 " --> pdb=" O LEUAh 9 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 13 through 38 removed outlier: 4.098A pdb=" N LEUAh 18 " --> pdb=" O LYSAh 14 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VALAh 33 " --> pdb=" O SERAh 29 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALAAh 34 " --> pdb=" O GLNAh 30 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VALAh 36 " --> pdb=" O ARGAh 32 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 40 through 44 removed outlier: 3.501A pdb=" N LEUAh 44 " --> pdb=" O ALAAh 41 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 45 through 73 removed outlier: 4.289A pdb=" N VALAh 49 " --> pdb=" O SERAh 45 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 88 through 94 Processing helix chain 'Ah' and resid 96 through 102 removed outlier: 3.864A pdb=" N SERAh 101 " --> pdb=" O LYSAh 97 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 104 through 114 removed outlier: 3.630A pdb=" N ARGAh 112 " --> pdb=" O GLNAh 108 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 34 through 49 removed outlier: 3.621A pdb=" N VALAi 40 " --> pdb=" O HISAi 36 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLUAi 46 " --> pdb=" O ASPAi 42 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 51 through 62 removed outlier: 3.622A pdb=" N ARGAi 56 " --> pdb=" O PROAi 52 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 65 through 78 Processing helix chain 'Ai' and resid 79 through 103 removed outlier: 3.501A pdb=" N ALAAi 83 " --> pdb=" O THRAi 79 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SERAi 92 " --> pdb=" O GLUAi 88 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALAAi 102 " --> pdb=" O ARGAi 98 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 50 through 57 removed outlier: 3.586A pdb=" N ASNAj 57 " --> pdb=" O ALAAj 53 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 66 through 75 removed outlier: 3.661A pdb=" N TYRAj 71 " --> pdb=" O LEUAj 67 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARGAj 75 " --> pdb=" O TYRAj 71 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 7 through 16 removed outlier: 3.727A pdb=" N LEUAk 13 " --> pdb=" O LYSAk 9 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THRAk 14 " --> pdb=" O ASPAk 10 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 50 through 59 removed outlier: 3.542A pdb=" N LYSAk 55 " --> pdb=" O GLUAk 51 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLNAk 58 " --> pdb=" O GLUAk 54 " (cutoff:3.500A) Processing helix chain 'Al' and resid 6 through 20 Processing helix chain 'Am' and resid 53 through 65 removed outlier: 4.045A pdb=" N LEUAm 59 " --> pdb=" O SERAm 55 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYRAm 63 " --> pdb=" O LEUAm 59 " (cutoff:3.500A) Processing helix chain 'An' and resid 2 through 22 Processing helix chain 'Ao' and resid 35 through 46 Processing helix chain 'Ap' and resid 9 through 15 Processing helix chain 'Ap' and resid 19 through 33 removed outlier: 3.680A pdb=" N LYSAp 27 " --> pdb=" O ARGAp 23 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYSAp 28 " --> pdb=" O LYSAp 24 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILEAp 29 " --> pdb=" O METAp 25 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SERAp 32 " --> pdb=" O LYSAp 28 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 73 through 92 removed outlier: 3.552A pdb=" N VALAp 79 " --> pdb=" O SERAp 75 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 85 through 98 Processing helix chain 'Ar' and resid 103 through 105 No H-bonds generated for 'chain 'Ar' and resid 103 through 105' Processing helix chain 'Ar' and resid 106 through 121 Processing helix chain 'AK' and resid 72 through 77 Processing helix chain 'AK' and resid 86 through 90 removed outlier: 3.666A pdb=" N LEUAK 90 " --> pdb=" O ILEAK 87 " (cutoff:3.500A) Processing helix chain 'AK' and resid 91 through 96 Processing helix chain 'AK' and resid 125 through 129 Processing helix chain 'AK' and resid 147 through 151 removed outlier: 3.678A pdb=" N GLUAK 150 " --> pdb=" O LYSAK 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.702A pdb=" N VAL B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 38 removed outlier: 3.805A pdb=" N GLU B 35 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLN B 36 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 38 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 67 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 83 through 95 removed outlier: 3.658A pdb=" N VAL B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 137 removed outlier: 3.544A pdb=" N MET B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 186 removed outlier: 4.081A pdb=" N GLY B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 178 " --> pdb=" O MET B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.675A pdb=" N TYR B 202 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.787A pdb=" N VAL C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 178 removed outlier: 3.582A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 186 Processing helix chain 'C' and resid 191 through 201 removed outlier: 3.581A pdb=" N LYS C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP C 196 " --> pdb=" O SER C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.808A pdb=" N GLU C 230 " --> pdb=" O GLY C 226 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 72 removed outlier: 3.520A pdb=" N LEU D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 72 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 removed outlier: 3.787A pdb=" N TYR D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 99 Processing helix chain 'D' and resid 146 through 160 removed outlier: 3.854A pdb=" N ILE D 156 " --> pdb=" O ARG D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 218 removed outlier: 3.625A pdb=" N GLY D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 246 removed outlier: 3.832A pdb=" N THR D 240 " --> pdb=" O PHE D 236 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS D 246 " --> pdb=" O ASP D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 250 removed outlier: 3.781A pdb=" N TYR D 250 " --> pdb=" O THR D 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 247 through 250' Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 264 through 269 Processing helix chain 'D' and resid 269 through 274 Processing helix chain 'E' and resid 6 through 29 removed outlier: 3.723A pdb=" N PHE E 11 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU E 28 " --> pdb=" O PHE E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 76 removed outlier: 3.744A pdb=" N LYS E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 112 removed outlier: 3.596A pdb=" N GLN E 101 " --> pdb=" O CYS E 97 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU E 103 " --> pdb=" O ILE E 99 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 130 removed outlier: 3.611A pdb=" N TYR E 120 " --> pdb=" O ARG E 116 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY E 121 " --> pdb=" O ARG E 117 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 43 through 50 removed outlier: 3.603A pdb=" N PHE F 47 " --> pdb=" O PRO F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 66 Processing helix chain 'F' and resid 115 through 120 removed outlier: 3.560A pdb=" N LYS F 120 " --> pdb=" O PRO F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 262 removed outlier: 3.796A pdb=" N ALA F 257 " --> pdb=" O ASP F 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 76 Processing helix chain 'G' and resid 85 through 104 removed outlier: 3.780A pdb=" N ARG G 91 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE G 100 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS G 101 " --> pdb=" O PHE G 97 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU G 102 " --> pdb=" O GLU G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 118 Processing helix chain 'G' and resid 142 through 162 Processing helix chain 'G' and resid 168 through 183 Processing helix chain 'G' and resid 187 through 202 Processing helix chain 'H' and resid 20 through 25 removed outlier: 3.508A pdb=" N LEU H 24 " --> pdb=" O ASP H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 28 No H-bonds generated for 'chain 'H' and resid 26 through 28' Processing helix chain 'H' and resid 137 through 141 Processing helix chain 'H' and resid 181 through 201 removed outlier: 3.751A pdb=" N HIS H 187 " --> pdb=" O ARG H 183 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS H 188 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG H 189 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS H 201 " --> pdb=" O GLN H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 237 removed outlier: 3.528A pdb=" N ALA H 210 " --> pdb=" O ALA H 206 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN H 225 " --> pdb=" O LYS H 221 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG H 232 " --> pdb=" O ILE H 228 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU H 237 " --> pdb=" O ARG H 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 34 removed outlier: 3.785A pdb=" N MET I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 41 removed outlier: 3.603A pdb=" N LEU I 40 " --> pdb=" O LYS I 37 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG I 41 " --> pdb=" O ALA I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 75 Processing helix chain 'I' and resid 78 through 80 No H-bonds generated for 'chain 'I' and resid 78 through 80' Processing helix chain 'I' and resid 81 through 87 removed outlier: 3.650A pdb=" N LYS I 85 " --> pdb=" O ARG I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 134 removed outlier: 3.764A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 182 Processing helix chain 'J' and resid 88 through 93 removed outlier: 3.627A pdb=" N ARG J 92 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 118 removed outlier: 3.695A pdb=" N TRP J 112 " --> pdb=" O PRO J 108 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR J 117 " --> pdb=" O TYR J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 138 removed outlier: 3.759A pdb=" N ILE J 136 " --> pdb=" O GLU J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 153 removed outlier: 3.707A pdb=" N TYR J 149 " --> pdb=" O ILE J 145 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU J 151 " --> pdb=" O LYS J 147 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG J 152 " --> pdb=" O LYS J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 168 removed outlier: 4.204A pdb=" N GLU J 164 " --> pdb=" O SER J 160 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLN J 165 " --> pdb=" O LEU J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 183 Processing helix chain 'J' and resid 192 through 206 removed outlier: 3.889A pdb=" N GLU J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG J 205 " --> pdb=" O LYS J 201 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS J 206 " --> pdb=" O ILE J 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 36 removed outlier: 3.528A pdb=" N LYS K 30 " --> pdb=" O ASP K 26 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU K 31 " --> pdb=" O GLN K 27 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU K 34 " --> pdb=" O LYS K 30 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR K 35 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 62 removed outlier: 3.734A pdb=" N VAL K 46 " --> pdb=" O GLU K 42 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU K 60 " --> pdb=" O ALA K 56 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR K 62 " --> pdb=" O ARG K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 85 removed outlier: 3.842A pdb=" N GLU K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 107 removed outlier: 3.655A pdb=" N LEU K 106 " --> pdb=" O ILE K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 117 removed outlier: 4.263A pdb=" N PHE K 115 " --> pdb=" O GLN K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 132 removed outlier: 3.703A pdb=" N VAL K 128 " --> pdb=" O HIS K 124 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ILE K 130 " --> pdb=" O ALA K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 177 removed outlier: 3.711A pdb=" N ARG K 175 " --> pdb=" O GLY K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 186 Processing helix chain 'L' and resid 7 through 10 Processing helix chain 'L' and resid 11 through 18 Processing helix chain 'L' and resid 41 through 56 removed outlier: 3.702A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER L 51 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU L 52 " --> pdb=" O ALA L 48 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS L 53 " --> pdb=" O MET L 49 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG L 55 " --> pdb=" O SER L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 77 removed outlier: 3.989A pdb=" N ILE L 76 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLN L 77 " --> pdb=" O ASN L 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 72 through 77' Processing helix chain 'L' and resid 77 through 82 Processing helix chain 'M' and resid 47 through 51 Processing helix chain 'N' and resid 18 through 22 removed outlier: 3.904A pdb=" N VAL N 21 " --> pdb=" O LEU N 18 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU N 22 " --> pdb=" O GLN N 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 18 through 22' Processing helix chain 'N' and resid 36 through 41 removed outlier: 3.577A pdb=" N ALA N 39 " --> pdb=" O ARG N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 90 removed outlier: 4.338A pdb=" N TRP N 88 " --> pdb=" O LYS N 84 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY N 90 " --> pdb=" O GLY N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 125 removed outlier: 3.736A pdb=" N ILE N 124 " --> pdb=" O ALA N 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 42 removed outlier: 4.213A pdb=" N GLU O 35 " --> pdb=" O ASP O 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 58 removed outlier: 3.676A pdb=" N ARG O 55 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 67 Processing helix chain 'O' and resid 70 through 77 Processing helix chain 'O' and resid 85 through 105 removed outlier: 3.954A pdb=" N LEU O 91 " --> pdb=" O ASP O 87 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG O 104 " --> pdb=" O LYS O 100 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 132 removed outlier: 3.659A pdb=" N THR O 131 " --> pdb=" O ARG O 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 61 removed outlier: 3.559A pdb=" N MET P 60 " --> pdb=" O THR P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 69 removed outlier: 3.617A pdb=" N GLU P 68 " --> pdb=" O ASP P 65 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER P 69 " --> pdb=" O ARG P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 89 removed outlier: 3.781A pdb=" N MET P 75 " --> pdb=" O PRO P 71 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU P 87 " --> pdb=" O GLN P 83 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU P 88 " --> pdb=" O ARG P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 121 removed outlier: 3.888A pdb=" N LEU P 119 " --> pdb=" O ALA P 115 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA P 120 " --> pdb=" O LEU P 116 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG P 121 " --> pdb=" O ARG P 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 27 removed outlier: 4.173A pdb=" N ASP Q 27 " --> pdb=" O ASP Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 46 Processing helix chain 'Q' and resid 58 through 64 removed outlier: 3.646A pdb=" N LYS Q 62 " --> pdb=" O LYS Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 120 removed outlier: 3.503A pdb=" N PHE Q 119 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 42 No H-bonds generated for 'chain 'R' and resid 40 through 42' Processing helix chain 'R' and resid 48 through 59 Proline residue: R 54 - end of helix removed outlier: 3.937A pdb=" N LEU R 58 " --> pdb=" O PRO R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 99 removed outlier: 3.532A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.700A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP R 116 " --> pdb=" O LEU R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 120 Processing helix chain 'S' and resid 6 through 20 removed outlier: 3.568A pdb=" N ALA S 12 " --> pdb=" O THR S 8 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL S 15 " --> pdb=" O LYS S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 33 removed outlier: 4.026A pdb=" N ASN S 31 " --> pdb=" O ASP S 27 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG S 33 " --> pdb=" O HIS S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 39 removed outlier: 4.431A pdb=" N GLU S 37 " --> pdb=" O ARG S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 62 removed outlier: 3.815A pdb=" N GLN S 62 " --> pdb=" O MET S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 83 removed outlier: 3.736A pdb=" N GLU S 77 " --> pdb=" O LEU S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 107 Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.861A pdb=" N ILE T 30 " --> pdb=" O ILE T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 33 No H-bonds generated for 'chain 'T' and resid 31 through 33' Processing helix chain 'T' and resid 37 through 48 removed outlier: 4.114A pdb=" N ALA T 41 " --> pdb=" O GLY T 37 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA T 48 " --> pdb=" O VAL T 44 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 73 removed outlier: 3.597A pdb=" N ILE T 68 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR T 69 " --> pdb=" O GLU T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 78 removed outlier: 3.584A pdb=" N LYS T 78 " --> pdb=" O ARG T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 84 removed outlier: 3.512A pdb=" N PHE T 83 " --> pdb=" O PRO T 80 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU T 84 " --> pdb=" O ASP T 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 80 through 84' Processing helix chain 'T' and resid 99 through 117 removed outlier: 3.763A pdb=" N ASP T 104 " --> pdb=" O ALA T 100 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG T 108 " --> pdb=" O ASP T 104 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE T 117 " --> pdb=" O ARG T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 119 through 127 removed outlier: 3.651A pdb=" N ARG T 124 " --> pdb=" O HIS T 120 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS T 125 " --> pdb=" O ARG T 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 9 removed outlier: 3.617A pdb=" N VAL U 9 " --> pdb=" O VAL U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 26 removed outlier: 3.520A pdb=" N PHE U 14 " --> pdb=" O ASN U 10 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL U 15 " --> pdb=" O GLN U 11 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 52 through 67 removed outlier: 3.794A pdb=" N ARG U 56 " --> pdb=" O TRP U 52 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA U 58 " --> pdb=" O TYR U 54 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA U 61 " --> pdb=" O ALA U 57 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG U 62 " --> pdb=" O ALA U 58 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG U 67 " --> pdb=" O HIS U 63 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 79 Processing helix chain 'U' and resid 96 through 105 removed outlier: 4.258A pdb=" N ALA U 100 " --> pdb=" O SER U 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL U 103 " --> pdb=" O VAL U 99 " (cutoff:3.500A) Processing helix chain 'U' and resid 105 through 110 removed outlier: 3.960A pdb=" N LEU U 110 " --> pdb=" O ALA U 106 " (cutoff:3.500A) Processing helix chain 'U' and resid 126 through 140 removed outlier: 4.512A pdb=" N ILE U 134 " --> pdb=" O ASP U 130 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA U 135 " --> pdb=" O LEU U 131 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLN U 137 " --> pdb=" O ARG U 133 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA U 140 " --> pdb=" O GLY U 136 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 39 Processing helix chain 'V' and resid 95 through 103 removed outlier: 4.700A pdb=" N ILE V 101 " --> pdb=" O ILE V 97 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 62 removed outlier: 3.667A pdb=" N ARG W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 75 Processing helix chain 'X' and resid 5 through 20 removed outlier: 3.716A pdb=" N ASP X 9 " --> pdb=" O ASN X 5 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA X 17 " --> pdb=" O SER X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 43 removed outlier: 3.886A pdb=" N VAL X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL X 40 " --> pdb=" O ARG X 36 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 91 removed outlier: 3.501A pdb=" N GLN X 90 " --> pdb=" O GLU X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 119 Processing helix chain 'Y' and resid 9 through 21 removed outlier: 3.575A pdb=" N LEU Y 13 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 30 Processing helix chain 'Y' and resid 34 through 39 Processing helix chain 'Y' and resid 130 through 135 Processing helix chain 'Z' and resid 36 through 48 removed outlier: 3.865A pdb=" N GLU Z 42 " --> pdb=" O THR Z 38 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA Z 45 " --> pdb=" O ARG Z 41 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 93 Processing helix chain 'Z' and resid 103 through 114 removed outlier: 3.897A pdb=" N ASN Z 112 " --> pdb=" O LYS Z 108 " (cutoff:3.500A) Processing helix chain 'Z' and resid 119 through 123 removed outlier: 4.185A pdb=" N ALA Z 123 " --> pdb=" O THR Z 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 61 removed outlier: 3.511A pdb=" N LYS a 60 " --> pdb=" O ASP a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 77 Processing helix chain 'a' and resid 80 through 95 removed outlier: 4.704A pdb=" N GLN a 89 " --> pdb=" O ARG a 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 55 Processing helix chain 'b' and resid 74 through 81 removed outlier: 3.924A pdb=" N HIS b 80 " --> pdb=" O SER b 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 90 through 94 removed outlier: 3.510A pdb=" N LYS b 93 " --> pdb=" O GLU b 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 11 through 16 removed outlier: 3.697A pdb=" N LYS c 16 " --> pdb=" O PRO c 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 36 removed outlier: 3.582A pdb=" N LEU e 36 " --> pdb=" O LYS e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 46 Processing helix chain 'e' and resid 46 through 51 Processing helix chain 'f' and resid 103 through 115 removed outlier: 3.655A pdb=" N ARG f 107 " --> pdb=" O GLY f 103 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG f 114 " --> pdb=" O GLN f 110 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 105 removed outlier: 4.084A pdb=" N LYS g 104 " --> pdb=" O LEU g 100 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 10 through 16 removed outlier: 3.836A pdb=" N TRPAq 15 " --> pdb=" O ASNAq 11 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYSAq 16 " --> pdb=" O VALAq 12 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 17 through 26 removed outlier: 3.584A pdb=" N GLUAq 25 " --> pdb=" O ILEAq 21 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ALAAq 26 " --> pdb=" O LYSAq 22 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 45 through 59 removed outlier: 4.358A pdb=" N METAq 51 " --> pdb=" O ARGAq 47 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASPAq 54 " --> pdb=" O LYSAq 50 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLUAq 55 " --> pdb=" O METAq 51 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHEAq 56 " --> pdb=" O LEUAq 52 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLYAq 57 " --> pdb=" O ALAAq 53 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 60 through 62 No H-bonds generated for 'chain 'Aq' and resid 60 through 62' Processing helix chain 'Aq' and resid 64 through 81 removed outlier: 4.449A pdb=" N THRAq 76 " --> pdb=" O LEUAq 72 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VALAq 78 " --> pdb=" O ALAAq 74 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLNAq 80 " --> pdb=" O THRAq 76 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 183 through 210 removed outlier: 5.361A pdb=" N ARGAq 192 " --> pdb=" O LEUAq 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEUAq 193 " --> pdb=" O ARGAq 189 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYSAq 197 " --> pdb=" O LEUAq 193 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARGAq 198 " --> pdb=" O ARGAq 194 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYRAq 201 " --> pdb=" O LYSAq 197 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 233 through 238 Processing helix chain 'Aq' and resid 261 through 270 removed outlier: 3.584A pdb=" N ASNAq 265 " --> pdb=" O GLUAq 261 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLNAq 266 " --> pdb=" O ASNAq 262 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALAAq 267 " --> pdb=" O GLYAq 263 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLUAq 269 " --> pdb=" O ASNAq 265 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 271 through 276 removed outlier: 3.630A pdb=" N LEUAq 275 " --> pdb=" O SERAq 271 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SERAq 276 " --> pdb=" O THRAq 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aq' and resid 271 through 276' Processing helix chain 'Aq' and resid 277 through 291 removed outlier: 4.041A pdb=" N LEUAq 286 " --> pdb=" O GLNAq 282 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHEAq 291 " --> pdb=" O ILEAq 287 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 291 through 296 Processing helix chain 'Aq' and resid 309 through 313 removed outlier: 3.544A pdb=" N GLUAq 313 " --> pdb=" O LYSAq 310 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 347 through 353 removed outlier: 4.103A pdb=" N LYSAq 352 " --> pdb=" O PROAq 348 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASPAq 353 " --> pdb=" O GLUAq 349 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 373 through 378 Processing helix chain 'Aq' and resid 401 through 406 Processing sheet with id=AA1, first strand: chain 'AA' and resid 72 through 77 Processing sheet with id=AA2, first strand: chain 'AA' and resid 101 through 103 removed outlier: 3.576A pdb=" N LEUAA 102 " --> pdb=" O ALAAA 164 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALAAA 164 " --> pdb=" O LEUAA 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AA' and resid 136 through 138 removed outlier: 6.958A pdb=" N ARGAA 147 " --> pdb=" O ILEAA 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AA' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'AB' and resid 42 through 43 removed outlier: 5.222A pdb=" N ILEAB 160 " --> pdb=" O VALAB 185 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLYAB 88 " --> pdb=" O LEUAB 163 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HISAB 165 " --> pdb=" O VALAB 86 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VALAB 86 " --> pdb=" O HISAB 165 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYSAB 103 " --> pdb=" O GLYAB 91 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VALAB 93 " --> pdb=" O THRAB 101 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N THRAB 101 " --> pdb=" O VALAB 93 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THRAB 95 " --> pdb=" O LEUAB 99 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEUAB 99 " --> pdb=" O THRAB 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'AB' and resid 42 through 43 removed outlier: 5.222A pdb=" N ILEAB 160 " --> pdb=" O VALAB 185 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLYAB 88 " --> pdb=" O LEUAB 163 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HISAB 165 " --> pdb=" O VALAB 86 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VALAB 86 " --> pdb=" O HISAB 165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'AB' and resid 276 through 283 removed outlier: 5.174A pdb=" N THRAB 278 " --> pdb=" O GLYAB 221 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLYAB 221 " --> pdb=" O THRAB 278 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILEAB 280 " --> pdb=" O VALAB 219 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VALAB 219 " --> pdb=" O ILEAB 280 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VALAB 222 " --> pdb=" O VALAB 344 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VALAB 344 " --> pdb=" O VALAB 222 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LYSAB 50 " --> pdb=" O GLUAB 80 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLUAB 80 " --> pdb=" O LYSAB 50 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLYAB 52 " --> pdb=" O ILEAB 78 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARGAB 58 " --> pdb=" O VALAB 72 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THRAB 77 " --> pdb=" O LEUAB 333 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYSAB 286 " --> pdb=" O METAB 332 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'AB' and resid 276 through 283 removed outlier: 5.174A pdb=" N THRAB 278 " --> pdb=" O GLYAB 221 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLYAB 221 " --> pdb=" O THRAB 278 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILEAB 280 " --> pdb=" O VALAB 219 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VALAB 219 " --> pdb=" O ILEAB 280 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VALAB 222 " --> pdb=" O VALAB 344 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VALAB 344 " --> pdb=" O VALAB 222 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N HISAB 55 " --> pdb=" O ILEAB 368 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILEAB 368 " --> pdb=" O HISAB 55 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VALAB 57 " --> pdb=" O LYSAB 366 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'AB' and resid 228 through 229 Processing sheet with id=AB1, first strand: chain 'AB' and resid 292 through 294 removed outlier: 3.606A pdb=" N LEUAB 292 " --> pdb=" O ILEAB 299 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYSAB 294 " --> pdb=" O LYSAB 297 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'AC' and resid 7 through 11 removed outlier: 5.106A pdb=" N LYSAC 20 " --> pdb=" O VALAC 10 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'AC' and resid 65 through 66 Processing sheet with id=AB4, first strand: chain 'AC' and resid 188 through 189 Processing sheet with id=AB5, first strand: chain 'AC' and resid 228 through 231 Processing sheet with id=AB6, first strand: chain 'AD' and resid 73 through 78 removed outlier: 5.496A pdb=" N ILEAD 74 " --> pdb=" O TYRAD 66 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYRAD 66 " --> pdb=" O ILEAD 74 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYSAD 76 " --> pdb=" O ILEAD 64 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYRAD 49 " --> pdb=" O TYRAD 145 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ASPAD 147 " --> pdb=" O TYRAD 49 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N METAD 51 " --> pdb=" O ASPAD 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'AD' and resid 183 through 184 removed outlier: 3.835A pdb=" N GLUAD 189 " --> pdb=" O ASPAD 184 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'AE' and resid 51 through 53 removed outlier: 3.865A pdb=" N VALAE 53 " --> pdb=" O ILEAE 56 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'AE' and resid 96 through 98 Processing sheet with id=AC1, first strand: chain 'AE' and resid 152 through 154 removed outlier: 3.634A pdb=" N VALAE 166 " --> pdb=" O THRAE 179 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEUAE 177 " --> pdb=" O LEUAE 168 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'AF' and resid 80 through 82 Processing sheet with id=AC3, first strand: chain 'AF' and resid 210 through 211 removed outlier: 4.103A pdb=" N ASNAF 118 " --> pdb=" O ARGAF 93 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILEAF 139 " --> pdb=" O GLYAF 233 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'AF' and resid 158 through 161 Processing sheet with id=AC5, first strand: chain 'AG' and resid 128 through 129 Processing sheet with id=AC6, first strand: chain 'AG' and resid 189 through 191 removed outlier: 3.534A pdb=" N LEUAG 207 " --> pdb=" O PHEAG 257 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VALAG 208 " --> pdb=" O CYSAG 235 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEUAG 237 " --> pdb=" O VALAG 208 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILEAG 210 " --> pdb=" O LEUAG 237 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'AH' and resid 3 through 11 removed outlier: 7.124A pdb=" N ILEAH 4 " --> pdb=" O TRPAH 61 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARGAH 54 " --> pdb=" O LEUAH 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'AH' and resid 17 through 21 removed outlier: 4.029A pdb=" N GLYAH 32 " --> pdb=" O GLYAH 29 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'AH' and resid 132 through 136 removed outlier: 7.066A pdb=" N ARGAH 89 " --> pdb=" O LYSAH 184 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LYSAH 184 " --> pdb=" O ARGAH 89 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYSAH 91 " --> pdb=" O SERAH 182 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'AH' and resid 102 through 106 Processing sheet with id=AD2, first strand: chain 'AI' and resid 35 through 37 removed outlier: 7.002A pdb=" N METAI 52 " --> pdb=" O ILEAI 135 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SERAI 137 " --> pdb=" O GLYAI 50 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLYAI 50 " --> pdb=" O SERAI 137 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARGAI 139 " --> pdb=" O LEUAI 48 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEUAI 48 " --> pdb=" O ARGAI 139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'AI' and resid 59 through 61 removed outlier: 5.776A pdb=" N ILEAI 99 " --> pdb=" O PROAI 122 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLYAI 124 " --> pdb=" O ILEAI 97 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'AI' and resid 190 through 193 Processing sheet with id=AD5, first strand: chain 'AJ' and resid 49 through 52 removed outlier: 3.604A pdb=" N ALAAJ 69 " --> pdb=" O SERAJ 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYSAJ 19 " --> pdb=" O VALAJ 133 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEUAJ 128 " --> pdb=" O ILEAJ 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'AL' and resid 22 through 24 Processing sheet with id=AD7, first strand: chain 'AL' and resid 58 through 60 removed outlier: 3.828A pdb=" N VALAL 59 " --> pdb=" O ARGAL 71 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'AL' and resid 124 through 126 Processing sheet with id=AD9, first strand: chain 'AM' and resid 45 through 51 removed outlier: 4.804A pdb=" N ARGAM 46 " --> pdb=" O GLYAM 40 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N GLYAM 40 " --> pdb=" O ARGAM 46 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLNAM 48 " --> pdb=" O VALAM 38 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ARGAM 35 " --> pdb=" O ILEAM 31 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASPAM 39 " --> pdb=" O ILEAM 27 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILEAM 27 " --> pdb=" O ASPAM 39 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARGAM 11 " --> pdb=" O ILEAM 27 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VALAM 12 " --> pdb=" O THRAM 58 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'AN' and resid 36 through 39 removed outlier: 3.689A pdb=" N HISAN 37 " --> pdb=" O ARGAN 63 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILEAN 61 " --> pdb=" O ALAAN 39 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYRAN 127 " --> pdb=" O GLUAN 123 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLUAN 123 " --> pdb=" O TYRAN 127 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHEAN 129 " --> pdb=" O VALAN 121 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASNAN 117 " --> pdb=" O ILEAN 133 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILEAN 135 " --> pdb=" O VALAN 115 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VALAN 115 " --> pdb=" O ILEAN 135 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'AO' and resid 6 through 10 removed outlier: 6.749A pdb=" N LEUAO 7 " --> pdb=" O VALAO 34 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VALAO 36 " --> pdb=" O LEUAO 7 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEUAO 9 " --> pdb=" O VALAO 36 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'AO' and resid 42 through 44 Processing sheet with id=AE4, first strand: chain 'AP' and resid 16 through 22 removed outlier: 3.956A pdb=" N ASNAP 21 " --> pdb=" O CYSAP 144 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYSAP 144 " --> pdb=" O ASNAP 21 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THRAP 151 " --> pdb=" O ILEAP 114 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILEAP 114 " --> pdb=" O THRAP 151 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'AP' and resid 58 through 59 Processing sheet with id=AE6, first strand: chain 'AP' and resid 128 through 131 removed outlier: 3.560A pdb=" N ARGAP 135 " --> pdb=" O ARGAP 131 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'AQ' and resid 60 through 62 Processing sheet with id=AE8, first strand: chain 'AQ' and resid 119 through 121 removed outlier: 6.905A pdb=" N VALAQ 100 " --> pdb=" O LEUAQ 121 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THRAQ 79 " --> pdb=" O VALAQ 137 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'AR' and resid 22 through 24 Processing sheet with id=AF1, first strand: chain 'AS' and resid 31 through 34 removed outlier: 6.999A pdb=" N ARGAS 15 " --> pdb=" O ILEAS 61 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ILEAS 61 " --> pdb=" O ARGAS 15 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'AS' and resid 28 through 29 Processing sheet with id=AF3, first strand: chain 'AS' and resid 90 through 91 Processing sheet with id=AF4, first strand: chain 'AS' and resid 90 through 91 removed outlier: 4.100A pdb=" N ASNAS 77 " --> pdb=" O METAS 132 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYSAS 128 " --> pdb=" O TRPAS 81 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARGAS 83 " --> pdb=" O VALAS 126 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VALAS 126 " --> pdb=" O ARGAS 83 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'AT' and resid 84 through 92 removed outlier: 3.936A pdb=" N ASNAT 66 " --> pdb=" O GLYAT 73 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VALAT 75 " --> pdb=" O VALAT 64 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VALAT 64 " --> pdb=" O VALAT 75 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ASNAT 77 " --> pdb=" O GLYAT 62 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N GLYAT 62 " --> pdb=" O ASNAT 77 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'AU' and resid 62 through 65 removed outlier: 3.751A pdb=" N THRAU 62 " --> pdb=" O THRAU 73 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THRAU 73 " --> pdb=" O THRAU 62 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'AV' and resid 20 through 21 Processing sheet with id=AF8, first strand: chain 'AV' and resid 25 through 28 removed outlier: 6.950A pdb=" N METAV 62 " --> pdb=" O ILEAV 40 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VALAV 42 " --> pdb=" O METAV 60 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N METAV 60 " --> pdb=" O VALAV 42 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALAAV 102 " --> pdb=" O ILEAV 82 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N GLYAV 103 " --> pdb=" O VALAV 25 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASNAV 27 " --> pdb=" O GLYAV 103 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ILEAV 105 " --> pdb=" O ASNAV 27 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'AV' and resid 88 through 89 removed outlier: 6.328A pdb=" N PHEAV 95 " --> pdb=" O ARGAW 20 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ALAAW 22 " --> pdb=" O PHEAV 95 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYRAV 97 " --> pdb=" O ALAAW 22 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARGAW 23 " --> pdb=" O LYSAW 27 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LYSAW 27 " --> pdb=" O ARGAW 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'AW' and resid 4 through 5 removed outlier: 3.619A pdb=" N ILEAW 13 " --> pdb=" O GLUAW 4 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'AX' and resid 77 through 80 removed outlier: 3.747A pdb=" N PHEAX 79 " --> pdb=" O ILEAX 99 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYSAX 134 " --> pdb=" O VALAX 100 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'AY' and resid 31 through 33 Processing sheet with id=AG4, first strand: chain 'AY' and resid 79 through 82 removed outlier: 6.811A pdb=" N VALAY 79 " --> pdb=" O VALAY 73 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VALAY 73 " --> pdb=" O VALAY 79 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYRAY 81 " --> pdb=" O VALAY 71 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLUAY 54 " --> pdb=" O THRAY 107 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'AY' and resid 86 through 88 Processing sheet with id=AG6, first strand: chain 'AZ' and resid 69 through 76 removed outlier: 6.677A pdb=" N LYSAZ 69 " --> pdb=" O ASPAZ 47 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N HISAZ 40 " --> pdb=" O ASNAZ 28 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASNAZ 28 " --> pdb=" O HISAZ 40 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEUAZ 42 " --> pdb=" O VALAZ 26 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LYSAZ 22 " --> pdb=" O ILEAZ 46 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYSAZ 9 " --> pdb=" O ILEAZ 25 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VALAZ 10 " --> pdb=" O THRAZ 83 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Aa' and resid 72 through 73 removed outlier: 3.533A pdb=" N VALAa 111 " --> pdb=" O PHEAa 128 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Aa' and resid 100 through 102 removed outlier: 6.951A pdb=" N ALAAa 143 " --> pdb=" O VALAa 124 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ALAAa 126 " --> pdb=" O ALAAa 143 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VALAa 145 " --> pdb=" O ALAAa 126 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Ac' and resid 26 through 29 removed outlier: 6.853A pdb=" N VALAc 28 " --> pdb=" O ILEAc 96 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILEAc 96 " --> pdb=" O VALAc 28 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEUAc 45 " --> pdb=" O ILEAc 96 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VALAc 46 " --> pdb=" O HISAc 72 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Ad' and resid 62 through 64 removed outlier: 4.810A pdb=" N THRAd 22 " --> pdb=" O VALAd 122 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Ae' and resid 75 through 79 removed outlier: 5.939A pdb=" N ARGAe 75 " --> pdb=" O CYSAe 96 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLUAe 98 " --> pdb=" O ARGAe 75 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHEAe 77 " --> pdb=" O GLUAe 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'Af' and resid 65 through 71 removed outlier: 5.440A pdb=" N LYSAf 66 " --> pdb=" O ALAAf 53 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N VALAf 50 " --> pdb=" O ARGAf 100 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ARGAf 100 " --> pdb=" O VALAf 50 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N CYSAf 7 " --> pdb=" O ILEAf 30 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ILEAf 30 " --> pdb=" O CYSAf 7 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ALAAf 9 " --> pdb=" O LEUAf 28 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEUAf 28 " --> pdb=" O ALAAf 9 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N PHEAf 11 " --> pdb=" O ALAAf 26 " (cutoff:3.500A) removed outlier: 10.104A pdb=" N ALAAf 26 " --> pdb=" O PHEAf 11 " (cutoff:3.500A) removed outlier: 11.742A pdb=" N GLYAf 13 " --> pdb=" O HISAf 24 " (cutoff:3.500A) removed outlier: 9.198A pdb=" N HISAf 24 " --> pdb=" O GLYAf 13 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYSAf 15 " --> pdb=" O ARGAf 22 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N METAf 83 " --> pdb=" O HISAf 78 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYSAf 87 " --> pdb=" O VALAf 74 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VALAf 74 " --> pdb=" O LYSAf 87 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Ag' and resid 20 through 24 Processing sheet with id=AH5, first strand: chain 'Aj' and resid 16 through 17 Processing sheet with id=AH6, first strand: chain 'Ak' and resid 3 through 5 removed outlier: 3.606A pdb=" N GLNAk 3 " --> pdb=" O LEUAk 42 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VALAk 46 " --> pdb=" O ILEAk 5 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SERAk 22 " --> pdb=" O ARGAk 37 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VALAk 23 " --> pdb=" O LYSAk 67 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEUAk 69 " --> pdb=" O VALAk 23 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILEAk 25 " --> pdb=" O LEUAk 69 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Am' and resid 76 through 77 Processing sheet with id=AH8, first strand: chain 'Ao' and resid 3 through 4 Processing sheet with id=AH9, first strand: chain 'Ao' and resid 7 through 12 removed outlier: 6.987A pdb=" N LYSAo 64 " --> pdb=" O ARGAo 87 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ARGAo 87 " --> pdb=" O LYSAo 64 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILEAo 66 " --> pdb=" O ILEAo 85 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Ap' and resid 47 through 51 removed outlier: 7.130A pdb=" N ILEAp 54 " --> pdb=" O ARGAp 50 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Ar' and resid 17 through 20 removed outlier: 3.529A pdb=" N TYRAr 25 " --> pdb=" O ILEAr 18 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Ar' and resid 49 through 53 Processing sheet with id=AI4, first strand: chain 'AK' and resid 31 through 36 removed outlier: 7.314A pdb=" N VALAK 32 " --> pdb=" O VALAK 169 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEUAK 165 " --> pdb=" O ILEAK 36 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'AK' and resid 52 through 53 Processing sheet with id=AI6, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.806A pdb=" N VAL B 76 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU B 122 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N LEU B 147 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL B 124 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR B 144 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE B 161 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA B 146 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'C' and resid 43 through 49 removed outlier: 3.773A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N CYS C 96 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR C 98 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS C 34 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N PHE C 100 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN C 95 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL C 91 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU C 97 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS C 85 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N MET C 103 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LYS C 83 " --> pdb=" O MET C 103 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'C' and resid 43 through 49 removed outlier: 3.773A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N CYS C 96 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR C 98 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS C 34 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N PHE C 100 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ARG C 213 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL C 212 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL C 140 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'D' and resid 104 through 113 removed outlier: 5.196A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'D' and resid 184 through 188 Processing sheet with id=AJ2, first strand: chain 'E' and resid 34 through 41 removed outlier: 3.593A pdb=" N TYR E 87 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'E' and resid 148 through 155 removed outlier: 4.053A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'F' and resid 70 through 72 removed outlier: 4.233A pdb=" N ASN F 98 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N HIS F 112 " --> pdb=" O ARG F 100 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'F' and resid 146 through 148 removed outlier: 6.403A pdb=" N ASP F 163 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE F 169 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 216 through 221 removed outlier: 3.635A pdb=" N ASN F 216 " --> pdb=" O ASP F 212 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN F 197 " --> pdb=" O HIS F 209 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS F 211 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE F 195 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'F' and resid 229 through 230 Processing sheet with id=AJ8, first strand: chain 'G' and resid 123 through 126 removed outlier: 8.323A pdb=" N ALA G 138 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LYS d 47 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU d 33 " --> pdb=" O VAL d 14 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL d 14 " --> pdb=" O GLU d 33 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'H' and resid 13 through 17 removed outlier: 4.268A pdb=" N TYR H 48 " --> pdb=" O ALA H 38 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA H 38 " --> pdb=" O TYR H 48 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'H' and resid 72 through 77 Processing sheet with id=AK2, first strand: chain 'H' and resid 160 through 162 Processing sheet with id=AK3, first strand: chain 'I' and resid 47 through 53 removed outlier: 3.933A pdb=" N ARG I 57 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N HIS I 91 " --> pdb=" O LYS I 58 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'I' and resid 184 through 188 removed outlier: 4.788A pdb=" N ASP I 184 " --> pdb=" O ARG I 152 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS I 142 " --> pdb=" O ASP X 54 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE X 50 " --> pdb=" O VAL I 146 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'J' and resid 42 through 47 removed outlier: 6.536A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'J' and resid 72 through 74 removed outlier: 6.758A pdb=" N ASN J 64 " --> pdb=" O GLY J 187 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL J 189 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER J 66 " --> pdb=" O VAL J 189 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE J 101 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP J 80 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP J 105 " --> pdb=" O ILE J 78 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE J 78 " --> pdb=" O ASP J 105 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'K' and resid 140 through 141 Processing sheet with id=AK8, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AK9, first strand: chain 'M' and resid 72 through 79 removed outlier: 6.682A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N SER M 110 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE M 140 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL M 142 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY M 129 " --> pdb=" O VAL M 142 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'M' and resid 91 through 96 removed outlier: 3.701A pdb=" N ARG M 101 " --> pdb=" O ILE M 96 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'P' and resid 52 through 54 removed outlier: 3.508A pdb=" N CYS P 54 " --> pdb=" O VAL P 44 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLY P 29 " --> pdb=" O HIS P 94 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N LYS P 96 " --> pdb=" O GLY P 29 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS P 31 " --> pdb=" O LYS P 96 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ARG P 98 " --> pdb=" O CYS P 31 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE P 33 " --> pdb=" O ARG P 98 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'P' and resid 52 through 54 removed outlier: 3.508A pdb=" N CYS P 54 " --> pdb=" O VAL P 44 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLY P 29 " --> pdb=" O HIS P 94 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N LYS P 96 " --> pdb=" O GLY P 29 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS P 31 " --> pdb=" O LYS P 96 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ARG P 98 " --> pdb=" O CYS P 31 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE P 33 " --> pdb=" O ARG P 98 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'Q' and resid 76 through 77 removed outlier: 3.713A pdb=" N SER Q 92 " --> pdb=" O ILE Q 107 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'R' and resid 10 through 15 Processing sheet with id=AL6, first strand: chain 'R' and resid 33 through 34 Processing sheet with id=AL7, first strand: chain 'S' and resid 96 through 98 removed outlier: 6.217A pdb=" N ILE S 96 " --> pdb=" O GLN S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL7 Processing sheet with id=AL8, first strand: chain 'T' and resid 12 through 14 Processing sheet with id=AL9, first strand: chain 'U' and resid 81 through 83 Processing sheet with id=AM1, first strand: chain 'U' and resid 114 through 115 Processing sheet with id=AM2, first strand: chain 'V' and resid 50 through 55 removed outlier: 4.192A pdb=" N ASP V 90 " --> pdb=" O LYS V 51 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU V 88 " --> pdb=" O PRO V 53 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ARG V 55 " --> pdb=" O LYS V 86 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LYS V 86 " --> pdb=" O ARG V 55 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'V' and resid 50 through 55 removed outlier: 4.192A pdb=" N ASP V 90 " --> pdb=" O LYS V 51 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU V 88 " --> pdb=" O PRO V 53 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ARG V 55 " --> pdb=" O LYS V 86 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LYS V 86 " --> pdb=" O ARG V 55 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU V 91 " --> pdb=" O ILE V 20 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE V 20 " --> pdb=" O LEU V 91 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'V' and resid 63 through 66 Processing sheet with id=AM5, first strand: chain 'W' and resid 32 through 37 Processing sheet with id=AM6, first strand: chain 'X' and resid 71 through 74 removed outlier: 7.006A pdb=" N VAL X 103 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE X 128 " --> pdb=" O PHE X 101 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE X 101 " --> pdb=" O PHE X 128 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'Y' and resid 128 through 129 removed outlier: 6.566A pdb=" N LEU Y 101 " --> pdb=" O VAL Y 123 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL Y 125 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU Y 99 " --> pdb=" O VAL Y 125 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL Y 51 " --> pdb=" O GLN Y 73 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN Y 73 " --> pdb=" O VAL Y 51 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU Y 53 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N PHE Y 120 " --> pdb=" O LYS Y 80 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N THR Y 82 " --> pdb=" O PHE Y 120 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL Y 122 " --> pdb=" O THR Y 82 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE Y 84 " --> pdb=" O VAL Y 122 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LYS Y 124 " --> pdb=" O PHE Y 84 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'Z' and resid 6 through 15 removed outlier: 5.321A pdb=" N ILE Z 7 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU Z 28 " --> pdb=" O ILE Z 7 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR Z 9 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP Z 26 " --> pdb=" O THR Z 9 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS Z 11 " --> pdb=" O VAL Z 24 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL Z 24 " --> pdb=" O LYS Z 11 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'a' and resid 98 through 102 removed outlier: 7.295A pdb=" N ILE a 108 " --> pdb=" O VAL a 100 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'b' and resid 20 through 21 Processing sheet with id=AN2, first strand: chain 'b' and resid 36 through 43 Processing sheet with id=AN3, first strand: chain 'c' and resid 44 through 47 Processing sheet with id=AN4, first strand: chain 'c' and resid 64 through 65 Processing sheet with id=AN5, first strand: chain 'e' and resid 30 through 31 Processing sheet with id=AN6, first strand: chain 'h' and resid 9 through 12 removed outlier: 4.435A pdb=" N GLY h 9 " --> pdb=" O VAL h 309 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL h 309 " --> pdb=" O GLY h 9 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP h 310 " --> pdb=" O LEU h 298 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU h 298 " --> pdb=" O TRP h 310 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'h' and resid 20 through 23 removed outlier: 3.636A pdb=" N GLN h 20 " --> pdb=" O ALA h 34 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE h 40 " --> pdb=" O ALA h 58 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA h 58 " --> pdb=" O ILE h 40 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N MET h 42 " --> pdb=" O GLN h 56 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'h' and resid 66 through 71 removed outlier: 6.235A pdb=" N LEU h 87 " --> pdb=" O ARG h 100 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG h 100 " --> pdb=" O LEU h 87 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU h 89 " --> pdb=" O THR h 98 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR h 96 " --> pdb=" O ASP h 91 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'h' and resid 108 through 112 removed outlier: 3.701A pdb=" N VAL h 121 " --> pdb=" O ALA h 112 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR h 140 " --> pdb=" O LEU h 131 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'h' and resid 151 through 156 removed outlier: 3.992A pdb=" N THR h 186 " --> pdb=" O VAL h 176 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASN h 178 " --> pdb=" O LEU h 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LEU h 184 " --> pdb=" O ASN h 178 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'h' and resid 195 through 200 removed outlier: 3.910A pdb=" N THR h 197 " --> pdb=" O GLY h 210 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLY h 211 " --> pdb=" O GLN h 215 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLN h 215 " --> pdb=" O GLY h 211 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR h 228 " --> pdb=" O LEU h 218 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASP h 220 " --> pdb=" O HIS h 226 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N HIS h 226 " --> pdb=" O ASP h 220 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'h' and resid 236 through 241 removed outlier: 7.179A pdb=" N ALA h 251 " --> pdb=" O ASN h 237 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU h 239 " --> pdb=" O CYS h 249 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N CYS h 249 " --> pdb=" O LEU h 239 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE h 241 " --> pdb=" O TRP h 247 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N TRP h 247 " --> pdb=" O PHE h 241 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU h 248 " --> pdb=" O TRP h 259 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TRP h 259 " --> pdb=" O LEU h 248 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASP h 260 " --> pdb=" O ILE h 266 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE h 266 " --> pdb=" O ASP h 260 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'h' and resid 286 through 288 removed outlier: 3.534A pdb=" N SER h 288 " --> pdb=" O GLY h 301 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'Aq' and resid 108 through 114 removed outlier: 3.868A pdb=" N VALAq 110 " --> pdb=" O GLYAq 98 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYSAq 97 " --> pdb=" O ILEAq 35 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N METAq 34 " --> pdb=" O ASPAq 128 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASPAq 128 " --> pdb=" O METAq 34 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'Aq' and resid 166 through 173 removed outlier: 6.991A pdb=" N PHEAq 158 " --> pdb=" O LEUAq 169 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYSAq 171 " --> pdb=" O ALAAq 156 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALAAq 156 " --> pdb=" O LYSAq 171 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLYAq 147 " --> pdb=" O VALAq 225 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALAAq 227 " --> pdb=" O GLYAq 147 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILEAq 149 " --> pdb=" O ALAAq 227 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEUAq 224 " --> pdb=" O VALAq 250 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYSAq 252 " --> pdb=" O LEUAq 224 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'Aq' and resid 321 through 322 Processing sheet with id=AO8, first strand: chain 'Aq' and resid 342 through 345 3130 hydrogen bonds defined for protein. 8757 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3866 hydrogen bonds 6534 hydrogen bond angles 0 basepair planarities 1501 basepair parallelities 3034 stacking parallelities Total time for adding SS restraints: 417.81 Time building geometry restraints manager: 66.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 27752 1.32 - 1.45: 93245 1.45 - 1.57: 102441 1.57 - 1.70: 11487 1.70 - 1.82: 687 Bond restraints: 235612 Sorted by residual: bond pdb=" N ILEAO 108 " pdb=" CA ILEAO 108 " ideal model delta sigma weight residual 1.454 1.496 -0.041 7.70e-03 1.69e+04 2.84e+01 bond pdb=" N ILE S 41 " pdb=" CA ILE S 41 " ideal model delta sigma weight residual 1.454 1.495 -0.041 7.70e-03 1.69e+04 2.79e+01 bond pdb=" N ILE Y 115 " pdb=" CA ILE Y 115 " ideal model delta sigma weight residual 1.460 1.496 -0.035 7.30e-03 1.88e+04 2.33e+01 bond pdb=" N GLYAf 3 " pdb=" CA GLYAf 3 " ideal model delta sigma weight residual 1.442 1.479 -0.037 7.70e-03 1.69e+04 2.28e+01 bond pdb=" N VALAT 25 " pdb=" CA VALAT 25 " ideal model delta sigma weight residual 1.460 1.494 -0.035 7.50e-03 1.78e+04 2.17e+01 ... (remaining 235607 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.33: 27451 105.33 - 112.74: 127228 112.74 - 120.15: 107402 120.15 - 127.56: 73345 127.56 - 134.97: 10460 Bond angle restraints: 345886 Sorted by residual: angle pdb=" C4' C 2 884 " pdb=" C3' C 2 884 " pdb=" O3' C 2 884 " ideal model delta sigma weight residual 113.00 97.91 15.09 1.50e+00 4.44e-01 1.01e+02 angle pdb=" O3' G 21858 " pdb=" C3' G 21858 " pdb=" C2' G 21858 " ideal model delta sigma weight residual 113.70 128.52 -14.82 1.50e+00 4.44e-01 9.76e+01 angle pdb=" C4' A 21664 " pdb=" C3' A 21664 " pdb=" O3' A 21664 " ideal model delta sigma weight residual 109.40 123.62 -14.22 1.50e+00 4.44e-01 8.98e+01 angle pdb=" O3' G 5 48 " pdb=" C3' G 5 48 " pdb=" C2' G 5 48 " ideal model delta sigma weight residual 109.50 123.07 -13.57 1.50e+00 4.44e-01 8.18e+01 angle pdb=" O3' U 16506 " pdb=" C3' U 16506 " pdb=" C2' U 16506 " ideal model delta sigma weight residual 109.50 123.05 -13.55 1.50e+00 4.44e-01 8.17e+01 ... (remaining 345881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 123426 35.96 - 71.92: 5724 71.92 - 107.88: 404 107.88 - 143.84: 62 143.84 - 179.80: 115 Dihedral angle restraints: 129731 sinusoidal: 95371 harmonic: 34360 Sorted by residual: dihedral pdb=" CA HISAB 258 " pdb=" C HISAB 258 " pdb=" N PROAB 259 " pdb=" CA PROAB 259 " ideal model delta harmonic sigma weight residual 180.00 114.02 65.98 0 5.00e+00 4.00e-02 1.74e+02 dihedral pdb=" CA GLUAK 150 " pdb=" C GLUAK 150 " pdb=" N VALAK 151 " pdb=" CA VALAK 151 " ideal model delta harmonic sigma weight residual 180.00 128.11 51.89 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA GLN Y 61 " pdb=" C GLN Y 61 " pdb=" N PRO Y 62 " pdb=" CA PRO Y 62 " ideal model delta harmonic sigma weight residual -180.00 -128.29 -51.71 0 5.00e+00 4.00e-02 1.07e+02 ... (remaining 129728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.171: 38620 0.171 - 0.343: 4383 0.343 - 0.514: 27 0.514 - 0.686: 16 0.686 - 0.857: 2 Chirality restraints: 43048 Sorted by residual: chirality pdb=" C3' G 5 48 " pdb=" C4' G 5 48 " pdb=" O3' G 5 48 " pdb=" C2' G 5 48 " both_signs ideal model delta sigma weight residual False -2.74 -1.89 -0.86 2.00e-01 2.50e+01 1.84e+01 chirality pdb=" C3' A 54170 " pdb=" C4' A 54170 " pdb=" O3' A 54170 " pdb=" C2' A 54170 " both_signs ideal model delta sigma weight residual False -2.74 -2.02 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C3' U 52661 " pdb=" C4' U 52661 " pdb=" O3' U 52661 " pdb=" C2' U 52661 " both_signs ideal model delta sigma weight residual False -2.74 -2.07 -0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 43045 not shown) Planarity restraints: 22335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASNAK 96 " -0.023 2.00e-02 2.50e+03 4.81e-02 2.31e+01 pdb=" C ASNAK 96 " 0.083 2.00e-02 2.50e+03 pdb=" O ASNAK 96 " -0.031 2.00e-02 2.50e+03 pdb=" N LYSAK 97 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 21260 " 0.040 2.00e-02 2.50e+03 1.93e-02 1.02e+01 pdb=" N9 A 21260 " -0.048 2.00e-02 2.50e+03 pdb=" C8 A 21260 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A 21260 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A 21260 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A 21260 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A 21260 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A 21260 " 0.006 2.00e-02 2.50e+03 pdb=" C2 A 21260 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A 21260 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A 21260 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 5 925 " 0.042 2.00e-02 2.50e+03 1.77e-02 9.41e+00 pdb=" N9 G 5 925 " -0.039 2.00e-02 2.50e+03 pdb=" C8 G 5 925 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G 5 925 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 5 925 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G 5 925 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G 5 925 " 0.017 2.00e-02 2.50e+03 pdb=" N1 G 5 925 " 0.000 2.00e-02 2.50e+03 pdb=" C2 G 5 925 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G 5 925 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G 5 925 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G 5 925 " -0.014 2.00e-02 2.50e+03 ... (remaining 22332 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 18690 2.72 - 3.27: 181137 3.27 - 3.81: 403902 3.81 - 4.36: 541674 4.36 - 4.90: 751352 Nonbonded interactions: 1896755 Sorted by model distance: nonbonded pdb=" O2' G 52259 " pdb=" OP1 C 52260 " model vdw 2.180 2.440 nonbonded pdb=" O2' U 21360 " pdb=" OP2 A 21379 " model vdw 2.208 2.440 nonbonded pdb=" O2' G 21550 " pdb=" O2 C 21558 " model vdw 2.227 2.440 nonbonded pdb=" OP2 G 5 151 " pdb=" OH TYRAN 4 " model vdw 2.245 2.440 nonbonded pdb=" O2' U 2 220 " pdb=" O5' A 2 221 " model vdw 2.246 2.440 ... (remaining 1896750 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5 Type Number sf(0) Gaussians P 5765 5.49 5 S 438 5.16 5 C 115652 2.51 5 N 40852 2.21 5 O 56588 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: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 29.600 Check model and map are aligned: 2.510 Convert atoms to be neutral: 1.340 Process input model: 750.770 Find NCS groups from input model: 5.450 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:1.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 795.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.054 235612 Z= 0.631 Angle : 1.366 15.086 345886 Z= 0.964 Chirality : 0.098 0.857 43048 Planarity : 0.003 0.061 22335 Dihedral : 17.733 179.797 107565 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.98 % Favored : 91.45 % Rotamer Outliers : 2.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.06), residues: 11735 helix: -2.97 (0.06), residues: 3593 sheet: -2.19 (0.12), residues: 1605 loop : -2.65 (0.06), residues: 6537 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2752 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 2518 time to evaluate : 10.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 234 outliers final: 89 residues processed: 2684 average time/residue: 1.7982 time to fit residues: 8175.1247 Evaluate side-chains 1794 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1705 time to evaluate : 11.036 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 0 residues processed: 89 average time/residue: 1.3857 time to fit residues: 246.1411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1459 optimal weight: 2.9990 chunk 1309 optimal weight: 4.9990 chunk 726 optimal weight: 0.3980 chunk 447 optimal weight: 7.9990 chunk 883 optimal weight: 5.9990 chunk 699 optimal weight: 9.9990 chunk 1354 optimal weight: 6.9990 chunk 524 optimal weight: 4.9990 chunk 823 optimal weight: 4.9990 chunk 1008 optimal weight: 0.9990 chunk 1569 optimal weight: 1.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 22 HIS ** AB 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 203 GLN AB 258 HIS AB 271 GLN AC 38 ASN AC 50 GLN AC 119 GLN AC 245 HIS AC 286 ASN AC 343 GLN AC 346 ASN AD 45 ASN AD 138 GLN AD 244 HIS AD 282 GLN ** AE 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 287 HIS AF 98 ASN AF 130 ASN AG 96 GLN AG 99 GLN AI 59 GLN AI 95 HIS AI 143 GLN AI 163 GLN AI 166 HIS AJ 104 ASN AL 159 ASN AL 188 ASN AM 56 GLN AN 99 GLN AN 139 HIS AN 178 HIS AO 42 ASN AP 28 ASN AP 75 GLN AP 80 GLN AP 97 ASN AP 120 ASN AQ 8 ASN AQ 93 GLN AR 36 ASN AR 75 HIS AR 121 HIS AS 163 HIS AT 98 HIS AT 127 GLN AT 144 ASN AX 69 ASN AX 93 ASN AY 14 ASN AY 65 GLN AZ 40 HIS AZ 79 HIS Aa 40 HIS Aa 62 HIS Aa 67 GLN Ab 49 HIS ** Ab 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 23 HIS Ae 52 GLN Af 24 HIS Af 56 ASN Af 65 ASN Af 80 ASN Ag 73 HIS Ag 100 GLN Ai 36 HIS Aj 76 HIS ** Am 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 36 GLN Ar 30 ASN AK 184 HIS AK 197 ASN B 84 GLN B 113 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN C 40 ASN D 178 HIS E 101 GLN ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN F 216 ASN G 83 ASN G 101 HIS G 118 ASN H 110 ASN H 163 ASN H 177 GLN H 202 ASN ** I 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 GLN I 114 GLN I 186 ASN I 193 GLN J 155 ASN J 168 GLN K 27 GLN K 111 GLN K 134 HIS M 19 ASN ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 119 GLN O 36 GLN O 49 GLN R 8 GLN R 86 GLN S 26 ASN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 GLN T 19 ASN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 HIS X 16 ASN X 24 GLN X 90 GLN X 113 HIS Y 46 HIS c 26 GLN c 49 HIS e 5 GLN g 91 ASN h 104 HIS ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 143 GLN h 178 ASN h 311 GLN Aq 247 GLN Aq 401 GLN Total number of N/Q/H flips: 120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.096 235612 Z= 0.194 Angle : 0.654 14.020 345886 Z= 0.340 Chirality : 0.040 0.328 43048 Planarity : 0.005 0.097 22335 Dihedral : 16.886 179.927 82479 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.58 % Favored : 95.38 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.07), residues: 11735 helix: -1.14 (0.08), residues: 3669 sheet: -1.61 (0.11), residues: 1799 loop : -2.11 (0.07), residues: 6267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2163 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1877 time to evaluate : 10.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 286 outliers final: 162 residues processed: 2052 average time/residue: 1.7596 time to fit residues: 6301.0051 Evaluate side-chains 1778 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1616 time to evaluate : 10.098 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 162 outliers final: 1 residues processed: 162 average time/residue: 1.4063 time to fit residues: 448.7006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 872 optimal weight: 0.6980 chunk 487 optimal weight: 0.2980 chunk 1306 optimal weight: 10.0000 chunk 1068 optimal weight: 10.0000 chunk 432 optimal weight: 10.0000 chunk 1572 optimal weight: 7.9990 chunk 1698 optimal weight: 0.9980 chunk 1400 optimal weight: 4.9990 chunk 1558 optimal weight: 4.9990 chunk 535 optimal weight: 7.9990 chunk 1261 optimal weight: 9.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 45 ASN ** AE 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 238 GLN AG 117 GLN AL 159 ASN AP 25 HIS AQ 93 GLN AR 36 ASN AT 95 HIS AU 27 HIS ** AV 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 85 GLN ** Ad 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 80 ASN Ah 20 GLN Ah 107 GLN Aj 66 HIS Ar 30 ASN AK 184 HIS ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN E 74 GLN E 174 HIS F 161 GLN F 197 ASN F 201 HIS G 83 ASN G 95 HIS G 165 ASN K 27 GLN K 156 HIS L 73 ASN ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 GLN Q 24 GLN Q 53 GLN Q 103 ASN R 8 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 GLN X 5 ASN X 91 ASN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 92 ASN c 51 GLN d 45 ASN e 37 ASN f 117 ASN h 14 HIS ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 334 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.146 235612 Z= 0.190 Angle : 0.591 13.790 345886 Z= 0.307 Chirality : 0.037 0.305 43048 Planarity : 0.005 0.090 22335 Dihedral : 16.596 179.971 82479 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.69 % Favored : 94.27 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.07), residues: 11735 helix: -0.49 (0.08), residues: 3686 sheet: -1.30 (0.12), residues: 1812 loop : -1.87 (0.07), residues: 6237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2064 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1779 time to evaluate : 10.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 285 outliers final: 145 residues processed: 1960 average time/residue: 1.6777 time to fit residues: 5777.2423 Evaluate side-chains 1748 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1603 time to evaluate : 11.259 Switching outliers to nearest non-outliers outliers start: 145 outliers final: 0 residues processed: 145 average time/residue: 1.3944 time to fit residues: 398.8279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1553 optimal weight: 0.9990 chunk 1181 optimal weight: 10.0000 chunk 815 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 750 optimal weight: 4.9990 chunk 1055 optimal weight: 10.0000 chunk 1577 optimal weight: 0.0070 chunk 1670 optimal weight: 1.9990 chunk 824 optimal weight: 2.9990 chunk 1495 optimal weight: 5.9990 chunk 450 optimal weight: 7.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 8 GLN AA 140 ASN AA 217 GLN ** AB 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 202 GLN ** AE 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 96 GLN AL 159 ASN AQ 93 GLN AU 97 HIS AV 135 ASN AY 66 GLN ** Ad 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 80 ASN Ag 100 GLN Ah 98 HIS Ah 107 GLN Ao 45 GLN Ao 51 GLN Ar 30 ASN AK 129 ASN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN F 161 GLN I 162 GLN ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 127 ASN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 GLN W 76 HIS X 5 ASN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 63 HIS d 45 ASN ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 111 ASN Aq 162 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.137 235612 Z= 0.176 Angle : 0.573 13.942 345886 Z= 0.294 Chirality : 0.036 0.291 43048 Planarity : 0.005 0.129 22335 Dihedral : 16.437 179.925 82479 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.58 % Favored : 95.38 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.07), residues: 11735 helix: -0.19 (0.09), residues: 3714 sheet: -1.02 (0.12), residues: 1807 loop : -1.74 (0.07), residues: 6214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1969 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1719 time to evaluate : 10.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 250 outliers final: 127 residues processed: 1867 average time/residue: 1.7163 time to fit residues: 5625.5817 Evaluate side-chains 1703 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1576 time to evaluate : 10.127 Switching outliers to nearest non-outliers outliers start: 127 outliers final: 0 residues processed: 127 average time/residue: 1.3901 time to fit residues: 348.7577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1391 optimal weight: 7.9990 chunk 948 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 1243 optimal weight: 10.0000 chunk 689 optimal weight: 1.9990 chunk 1425 optimal weight: 7.9990 chunk 1154 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 852 optimal weight: 10.0000 chunk 1499 optimal weight: 4.9990 chunk 421 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 38 HIS AB 42 HIS AE 193 HIS ** AE 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 253 GLN ** AG 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 117 GLN AJ 112 HIS AL 159 ASN AQ 188 ASN AR 36 ASN AS 37 HIS AT 127 GLN AV 84 GLN AZ 127 ASN Ag 100 GLN Ah 107 GLN Aj 30 GLN Am 64 ASN Ao 36 GLN Ao 45 GLN AK 84 HIS ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN F 142 HIS ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN I 126 HIS ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 105 ASN V 18 HIS X 5 ASN X 90 GLN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 89 HIS d 45 ASN e 5 GLN h 119 GLN h 133 ASN Aq 79 GLN ** Aq 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 199 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.184 235612 Z= 0.378 Angle : 0.743 16.701 345886 Z= 0.376 Chirality : 0.044 0.393 43048 Planarity : 0.006 0.104 22335 Dihedral : 16.743 179.750 82479 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.73 % Favored : 93.23 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.07), residues: 11735 helix: -0.50 (0.08), residues: 3712 sheet: -1.16 (0.12), residues: 1821 loop : -1.90 (0.07), residues: 6202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1977 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 1637 time to evaluate : 11.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 340 outliers final: 199 residues processed: 1869 average time/residue: 1.7091 time to fit residues: 5637.7762 Evaluate side-chains 1736 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1537 time to evaluate : 10.112 Switching outliers to nearest non-outliers outliers start: 199 outliers final: 0 residues processed: 199 average time/residue: 1.3562 time to fit residues: 530.1471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 561 optimal weight: 0.3980 chunk 1504 optimal weight: 5.9990 chunk 330 optimal weight: 10.0000 chunk 980 optimal weight: 4.9990 chunk 412 optimal weight: 3.9990 chunk 1671 optimal weight: 10.0000 chunk 1387 optimal weight: 9.9990 chunk 774 optimal weight: 0.6980 chunk 139 optimal weight: 10.0000 chunk 553 optimal weight: 0.0030 chunk 877 optimal weight: 5.9990 overall best weight: 2.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 138 GLN AG 96 GLN AG 117 GLN AJ 46 GLN AJ 65 ASN AL 159 ASN AM 33 GLN AO 72 HIS AR 36 ASN AT 49 GLN AV 135 ASN AY 96 HIS ** Ad 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 80 ASN Ag 100 GLN Ah 20 GLN Ah 107 GLN Ao 36 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN E 174 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 GLN F 197 ASN J 168 GLN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 GLN X 90 GLN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 GLN b 17 HIS h 191 HIS ** Aq 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.188 235612 Z= 0.169 Angle : 0.581 21.395 345886 Z= 0.300 Chirality : 0.036 0.334 43048 Planarity : 0.005 0.123 22335 Dihedral : 16.473 179.975 82479 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.52 % Favored : 95.45 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.07), residues: 11735 helix: -0.12 (0.09), residues: 3718 sheet: -0.98 (0.12), residues: 1809 loop : -1.72 (0.07), residues: 6208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1833 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1680 time to evaluate : 10.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 153 outliers final: 79 residues processed: 1762 average time/residue: 1.7045 time to fit residues: 5246.4990 Evaluate side-chains 1658 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1579 time to evaluate : 10.170 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 0 residues processed: 79 average time/residue: 1.3917 time to fit residues: 221.0980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1611 optimal weight: 10.0000 chunk 188 optimal weight: 20.0000 chunk 952 optimal weight: 8.9990 chunk 1220 optimal weight: 4.9990 chunk 945 optimal weight: 7.9990 chunk 1407 optimal weight: 2.9990 chunk 933 optimal weight: 10.0000 chunk 1665 optimal weight: 8.9990 chunk 1042 optimal weight: 20.0000 chunk 1015 optimal weight: 0.0770 chunk 768 optimal weight: 9.9990 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 138 GLN AF 199 HIS AG 117 GLN ** AG 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 149 GLN AL 159 ASN AR 36 ASN AV 135 ASN ** Ad 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 96 ASN Ah 107 GLN Ao 36 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 174 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN Q 104 GLN R 8 GLN R 114 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 GLN d 45 ASN ** Aq 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.111 235612 Z= 0.368 Angle : 0.657 106.074 345886 Z= 0.325 Chirality : 0.039 0.364 43048 Planarity : 0.005 0.116 22335 Dihedral : 16.463 179.948 82479 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.01 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.07), residues: 11735 helix: -0.15 (0.09), residues: 3709 sheet: -0.97 (0.12), residues: 1820 loop : -1.73 (0.07), residues: 6206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1701 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1584 time to evaluate : 11.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 82 residues processed: 1643 average time/residue: 1.7459 time to fit residues: 5056.5986 Evaluate side-chains 1634 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1552 time to evaluate : 10.254 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 0 residues processed: 82 average time/residue: 1.4708 time to fit residues: 241.4673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1030 optimal weight: 10.0000 chunk 665 optimal weight: 0.9990 chunk 994 optimal weight: 2.9990 chunk 501 optimal weight: 0.7980 chunk 327 optimal weight: 10.0000 chunk 322 optimal weight: 10.0000 chunk 1058 optimal weight: 10.0000 chunk 1134 optimal weight: 10.0000 chunk 823 optimal weight: 0.9990 chunk 155 optimal weight: 20.0000 chunk 1309 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 138 GLN AG 117 GLN ** AG 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 149 GLN AL 159 ASN AU 97 HIS AV 36 ASN AV 135 ASN AZ 127 ASN ** Ad 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 80 ASN Ah 98 HIS Ah 107 GLN Ao 36 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 GLN d 45 ASN h 14 HIS h 272 GLN ** Aq 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 1.045 235612 Z= 0.265 Angle : 0.626 84.705 345886 Z= 0.314 Chirality : 0.036 0.336 43048 Planarity : 0.005 0.112 22335 Dihedral : 16.466 179.976 82479 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.03 % Favored : 94.95 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.07), residues: 11735 helix: -0.09 (0.09), residues: 3708 sheet: -0.93 (0.12), residues: 1810 loop : -1.71 (0.07), residues: 6217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1678 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1597 time to evaluate : 11.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 53 residues processed: 1631 average time/residue: 1.8326 time to fit residues: 5267.4918 Evaluate side-chains 1621 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1568 time to evaluate : 10.135 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 1.5018 time to fit residues: 163.2905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1515 optimal weight: 9.9990 chunk 1595 optimal weight: 10.0000 chunk 1455 optimal weight: 0.1980 chunk 1552 optimal weight: 6.9990 chunk 934 optimal weight: 2.9990 chunk 676 optimal weight: 7.9990 chunk 1218 optimal weight: 8.9990 chunk 476 optimal weight: 9.9990 chunk 1402 optimal weight: 10.0000 chunk 1467 optimal weight: 0.4980 chunk 1546 optimal weight: 0.8980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 138 GLN AG 117 GLN ** AG 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 162 GLN AL 149 GLN AL 159 ASN AN 15 GLN AT 139 HIS AV 135 ASN ** Ad 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 98 HIS Ah 107 GLN Ao 36 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 174 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 GLN d 45 ASN ** Aq 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.587 235612 Z= 0.221 Angle : 0.608 73.858 345886 Z= 0.308 Chirality : 0.036 0.416 43048 Planarity : 0.005 0.117 22335 Dihedral : 16.459 179.989 82479 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.10 % Favored : 94.88 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.07), residues: 11735 helix: -0.08 (0.09), residues: 3693 sheet: -0.92 (0.12), residues: 1801 loop : -1.70 (0.07), residues: 6241 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1627 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1570 time to evaluate : 10.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 39 residues processed: 1599 average time/residue: 1.6981 time to fit residues: 4772.6399 Evaluate side-chains 1597 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1558 time to evaluate : 10.221 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 1.4310 time to fit residues: 116.4300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1019 optimal weight: 3.9990 chunk 1641 optimal weight: 0.3980 chunk 1001 optimal weight: 0.0070 chunk 778 optimal weight: 9.9990 chunk 1140 optimal weight: 20.0000 chunk 1721 optimal weight: 20.0000 chunk 1584 optimal weight: 2.9990 chunk 1370 optimal weight: 0.0980 chunk 142 optimal weight: 10.0000 chunk 1058 optimal weight: 10.0000 chunk 840 optimal weight: 3.9990 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 138 GLN AG 117 GLN ** AG 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 149 GLN AL 159 ASN AU 97 HIS AV 135 ASN ** Ad 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 80 ASN Ah 98 HIS Ah 107 GLN Ao 36 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN R 97 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 GLN d 45 ASN ** Aq 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.818 235612 Z= 0.249 Angle : 0.629 106.100 345886 Z= 0.313 Chirality : 0.036 0.334 43048 Planarity : 0.005 0.118 22335 Dihedral : 16.458 179.985 82479 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.07), residues: 11735 helix: -0.07 (0.09), residues: 3694 sheet: -0.91 (0.12), residues: 1799 loop : -1.70 (0.07), residues: 6242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23470 Ramachandran restraints generated. 11735 Oldfield, 0 Emsley, 11735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1607 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1574 time to evaluate : 10.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 26 residues processed: 1585 average time/residue: 1.7940 time to fit residues: 5024.9613 Evaluate side-chains 1588 residues out of total 10257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1562 time to evaluate : 10.154 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 1.4934 time to fit residues: 85.9118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1088 optimal weight: 10.0000 chunk 1460 optimal weight: 3.9990 chunk 419 optimal weight: 5.9990 chunk 1264 optimal weight: 4.9990 chunk 202 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 chunk 1373 optimal weight: 4.9990 chunk 574 optimal weight: 6.9990 chunk 1409 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 138 GLN AG 117 GLN ** AG 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 149 GLN AL 159 ASN AV 135 ASN ** Ad 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 98 HIS Ah 107 GLN Ao 36 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 GLN d 45 ASN ** Aq 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.153667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.129581 restraints weight = 358099.427| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.42 r_work: 0.3512 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work: 0.3444 rms_B_bonded: 2.52 restraints_weight: 0.1250 r_work: 0.3392 rms_B_bonded: 3.61 restraints_weight: 0.0625 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.818 235612 Z= 0.250 Angle : 0.630 106.100 345886 Z= 0.313 Chirality : 0.036 0.334 43048 Planarity : 0.005 0.146 22335 Dihedral : 16.458 179.985 82479 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.07), residues: 11735 helix: -0.07 (0.09), residues: 3694 sheet: -0.91 (0.12), residues: 1799 loop : -1.70 (0.07), residues: 6242 =============================================================================== Job complete usr+sys time: 71086.61 seconds wall clock time: 1229 minutes 3.09 seconds (73743.09 seconds total)