Starting phenix.real_space_refine (version: dev) on Sat Apr 16 12:52:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9z_6315/04_2022/3j9z_6315_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9z_6315/04_2022/3j9z_6315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9z_6315/04_2022/3j9z_6315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9z_6315/04_2022/3j9z_6315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9z_6315/04_2022/3j9z_6315_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9z_6315/04_2022/3j9z_6315_updated.pdb" } resolution = 3.6 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= 0.002 sd= 0.017 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 "SJ ASP 19": "OD1" <-> "OD2" Residue "SJ GLU 47": "OE1" <-> "OE2" Residue "SJ GLU 66": "OE1" <-> "OE2" Residue "SJ ASP 75": "OD1" <-> "OD2" Residue "SJ ASP 97": "OD1" <-> "OD2" Residue "SK PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK ASP 35": "OD1" <-> "OD2" Residue "SK PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK GLU 67": "OE1" <-> "OE2" Residue "SK TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL GLU 24": "OE1" <-> "OE2" Residue "SL PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL GLU 75": "OE1" <-> "OE2" Residue "SL ASP 102": "OD1" <-> "OD2" Residue "SL ASP 108": "OD1" <-> "OD2" Residue "SL TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM ASP 10": "OD1" <-> "OD2" Residue "SM TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM GLU 49": "OE1" <-> "OE2" Residue "SM ASP 53": "OD1" <-> "OD2" Residue "SM PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM GLU 65": "OE1" <-> "OE2" Residue "SM ASP 67": "OD1" <-> "OD2" Residue "SM ASP 81": "OD1" <-> "OD2" Residue "SN GLU 9": "OE1" <-> "OE2" Residue "SN PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SN GLU 25": "OE1" <-> "OE2" Residue "SN ASP 37": "OD1" <-> "OD2" Residue "SN ARG 62": "NH1" <-> "NH2" Residue "SN PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SN PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SN GLU 85": "OE1" <-> "OE2" Residue "SO GLU 13": "OE1" <-> "OE2" Residue "SO GLU 25": "OE1" <-> "OE2" Residue "SO ASP 67": "OD1" <-> "OD2" Residue "SO ASP 73": "OD1" <-> "OD2" Residue "SP PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SP TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SP PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SP GLU 48": "OE1" <-> "OE2" Residue "SP ASP 55": "OD1" <-> "OD2" Residue "SP GLU 77": "OE1" <-> "OE2" Residue "SQ GLU 25": "OE1" <-> "OE2" Residue "SQ PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ ASP 47": "OD1" <-> "OD2" Residue "SQ GLU 51": "OE1" <-> "OE2" Residue "SQ GLU 59": "OE1" <-> "OE2" Residue "SQ GLU 62": "OE1" <-> "OE2" Residue "SR PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR ARG 11": "NH1" <-> "NH2" Residue "SR GLU 15": "OE1" <-> "OE2" Residue "SR ASP 21": "OD1" <-> "OD2" Residue "SR TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR GLU 34": "OE1" <-> "OE2" Residue "SR TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR ASP 71": "OD1" <-> "OD2" Residue "SS GLU 23": "OE1" <-> "OE2" Residue "SS PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS ASP 63": "OD1" <-> "OD2" Residue "SS GLU 72": "OE1" <-> "OE2" Residue "SS ASP 85": "OD1" <-> "OD2" Residue "SB PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB GLU 43": "OE1" <-> "OE2" Residue "SB PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB GLU 51": "OE1" <-> "OE2" Residue "SB GLU 55": "OE1" <-> "OE2" Residue "SB PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB GLU 117": "OE1" <-> "OE2" Residue "SB ASP 122": "OD1" <-> "OD2" Residue "SB PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB ASP 126": "OD1" <-> "OD2" Residue "SB GLU 132": "OE1" <-> "OE2" Residue "SB GLU 139": "OE1" <-> "OE2" Residue "SB GLU 141": "OE1" <-> "OE2" Residue "SB ASP 164": "OD1" <-> "OD2" Residue "SB GLU 168": "OE1" <-> "OE2" Residue "SB ASP 187": "OD1" <-> "OD2" Residue "SB PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB GLU 222": "OE1" <-> "OE2" Residue "SB ASP 227": "OD1" <-> "OD2" Residue "SB GLU 233": "OE1" <-> "OE2" Residue "SB GLU 234": "OE1" <-> "OE2" Residue "SB PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ST GLU 14": "OE1" <-> "OE2" Residue "ST TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ST GLU 39": "OE1" <-> "OE2" Residue "ST ASP 42": "OD1" <-> "OD2" Residue "ST PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ST GLU 52": "OE1" <-> "OE2" Residue "SU GLU 9": "OE1" <-> "OE2" Residue "SU PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SU GLU 35": "OE1" <-> "OE2" Residue "SU TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SU GLU 38": "OE1" <-> "OE2" Residue "SU GLU 62": "OE1" <-> "OE2" Residue "SC GLU 27": "OE1" <-> "OE2" Residue "SC PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC ASP 30": "OD1" <-> "OD2" Residue "SC ASP 33": "OD1" <-> "OD2" Residue "SC ASP 35": "OD1" <-> "OD2" Residue "SC PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC GLU 45": "OE1" <-> "OE2" Residue "SC GLU 81": "OE1" <-> "OE2" Residue "SC ASP 82": "OD1" <-> "OD2" Residue "SC GLU 84": "OE1" <-> "OE2" Residue "SC ASP 111": "OD1" <-> "OD2" Residue "SC GLU 124": "OE1" <-> "OE2" Residue "SC GLU 160": "OE1" <-> "OE2" Residue "SC GLU 165": "OE1" <-> "OE2" Residue "SC GLU 169": "OE1" <-> "OE2" Residue "SC ASP 180": "OD1" <-> "OD2" Residue "SC ASP 182": "OD1" <-> "OD2" Residue "SC GLU 187": "OE1" <-> "OE2" Residue "SC TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC GLU 205": "OE1" <-> "OE2" Residue "SC GLU 214": "OE1" <-> "OE2" Residue "SC ARG 231": "NH1" <-> "NH2" Residue "SD TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD GLU 14": "OE1" <-> "OE2" Residue "SD ASP 17": "OD1" <-> "OD2" Residue "SD PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD ASP 28": "OD1" <-> "OD2" Residue "SD GLU 34": "OE1" <-> "OE2" Residue "SD ASP 49": "OD1" <-> "OD2" Residue "SD GLU 68": "OE1" <-> "OE2" Residue "SD PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD GLU 77": "OE1" <-> "OE2" Residue "SD GLU 87": "OE1" <-> "OE2" Residue "SD TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD ASP 140": "OD1" <-> "OD2" Residue "SD GLU 146": "OE1" <-> "OE2" Residue "SD GLU 162": "OE1" <-> "OE2" Residue "SD GLU 165": "OE1" <-> "OE2" Residue "SD GLU 171": "OE1" <-> "OE2" Residue "SD ASP 173": "OD1" <-> "OD2" Residue "SD GLU 178": "OE1" <-> "OE2" Residue "SD ASP 189": "OD1" <-> "OD2" Residue "SD ASP 193": "OD1" <-> "OD2" Residue "SD GLU 196": "OE1" <-> "OE2" Residue "SD TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE GLU 9": "OE1" <-> "OE2" Residue "SE GLU 12": "OE1" <-> "OE2" Residue "SE PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE ASP 40": "OD1" <-> "OD2" Residue "SE PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE GLU 54": "OE1" <-> "OE2" Residue "SE GLU 64": "OE1" <-> "OE2" Residue "SE GLU 115": "OE1" <-> "OE2" Residue "SE ASP 141": "OD1" <-> "OD2" Residue "SE GLU 161": "OE1" <-> "OE2" Residue "SE GLU 162": "OE1" <-> "OE2" Residue "SF ASP 13": "OD1" <-> "OD2" Residue "SF GLU 23": "OE1" <-> "OE2" Residue "SF ASP 41": "OD1" <-> "OD2" Residue "SF GLU 69": "OE1" <-> "OE2" Residue "SF ASP 72": "OD1" <-> "OD2" Residue "SF GLU 75": "OE1" <-> "OE2" Residue "SF PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SF GLU 111": "OE1" <-> "OE2" Residue "SF ASP 115": "OD1" <-> "OD2" Residue "SF GLU 119": "OE1" <-> "OE2" Residue "SF ASP 128": "OD1" <-> "OD2" Residue "SF GLU 132": "OE1" <-> "OE2" Residue "SF GLU 134": "OE1" <-> "OE2" Residue "SG ASP 14": "OD1" <-> "OD2" Residue "SG GLU 20": "OE1" <-> "OE2" Residue "SG ASP 32": "OD1" <-> "OD2" Residue "SG PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SG GLU 62": "OE1" <-> "OE2" Residue "SG GLU 89": "OE1" <-> "OE2" Residue "SG GLU 105": "OE1" <-> "OE2" Residue "SG ASP 112": "OD1" <-> "OD2" Residue "SG GLU 122": "OE1" <-> "OE2" Residue "SG ASP 125": "OD1" <-> "OD2" Residue "SG GLU 128": "OE1" <-> "OE2" Residue "SG GLU 138": "OE1" <-> "OE2" Residue "SG PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH GLU 41": "OE1" <-> "OE2" Residue "SH GLU 46": "OE1" <-> "OE2" Residue "SH ASP 47": "OD1" <-> "OD2" Residue "SH GLU 59": "OE1" <-> "OE2" Residue "SH TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH ASP 112": "OD1" <-> "OD2" Residue "SH GLU 123": "OE1" <-> "OE2" Residue "SI TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI GLU 41": "OE1" <-> "OE2" Residue "SI ASP 55": "OD1" <-> "OD2" Residue "SI ASP 61": "OD1" <-> "OD2" Residue "SI TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI ASP 90": "OD1" <-> "OD2" Residue "SI ASP 106": "OD1" <-> "OD2" Residue "SI PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 GLU 41": "OE1" <-> "OE2" Residue "S1 GLU 53": "OE1" <-> "OE2" Residue "S1 GLU 55": "OE1" <-> "OE2" Residue "S1 GLU 57": "OE1" <-> "OE2" Residue "S1 PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 GLU 79": "OE1" <-> "OE2" Residue "S1 ASP 93": "OD1" <-> "OD2" Residue "S1 GLU 99": "OE1" <-> "OE2" Residue "S1 ASP 106": "OD1" <-> "OD2" Residue "S1 TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 GLU 123": "OE1" <-> "OE2" Residue "S1 TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 GLU 175": "OE1" <-> "OE2" Residue "S1 GLU 176": "OE1" <-> "OE2" Residue "S1 ASP 183": "OD1" <-> "OD2" Residue "S1 ASP 194": "OD1" <-> "OD2" Residue "S1 PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 ASP 205": "OD1" <-> "OD2" Residue "S1 ASP 209": "OD1" <-> "OD2" Residue "S1 GLU 216": "OE1" <-> "OE2" Residue "S1 GLU 223": "OE1" <-> "OE2" Residue "S1 GLU 227": "OE1" <-> "OE2" Residue "S1 GLU 231": "OE1" <-> "OE2" Residue "S1 GLU 246": "OE1" <-> "OE2" Residue "S1 ASP 279": "OD1" <-> "OD2" Residue "S1 ASP 283": "OD1" <-> "OD2" Residue "S1 TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 ASP 290": "OD1" <-> "OD2" Residue "S1 ASP 303": "OD1" <-> "OD2" Residue "S1 ASP 312": "OD1" <-> "OD2" Residue "S1 ASP 313": "OD1" <-> "OD2" Residue "S1 PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 ASP 326": "OD1" <-> "OD2" Residue "S1 PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 ASP 346": "OD1" <-> "OD2" Residue "S1 GLU 375": "OE1" <-> "OE2" Residue "S1 ASP 380": "OD1" <-> "OD2" Residue "S1 ASP 394": "OD1" <-> "OD2" Residue "S1 ASP 398": "OD1" <-> "OD2" Residue "S1 ASP 400": "OD1" <-> "OD2" Residue "S1 GLU 406": "OE1" <-> "OE2" Residue "S1 GLU 409": "OE1" <-> "OE2" Residue "S1 GLU 412": "OE1" <-> "OE2" Residue "S1 GLU 428": "OE1" <-> "OE2" Residue "S1 GLU 440": "OE1" <-> "OE2" Residue "S1 ASP 441": "OD1" <-> "OD2" Residue "S1 ASP 449": "OD1" <-> "OD2" Residue "S1 ASP 466": "OD1" <-> "OD2" Residue "S1 ASP 470": "OD1" <-> "OD2" Residue "S1 GLU 475": "OE1" <-> "OE2" Residue "S1 PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 GLU 491": "OE1" <-> "OE2" Residue "S1 ASP 499": "OD1" <-> "OD2" Residue "S1 TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 ASP 520": "OD1" <-> "OD2" Residue "S1 GLU 534": "OE1" <-> "OE2" Residue "S1 GLU 558": "OE1" <-> "OE2" Residue "S1 TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 ASP 572": "OD1" <-> "OD2" Residue "S1 PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 ASP 586": "OD1" <-> "OD2" Residue "S1 PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 GLU 602": "OE1" <-> "OE2" Residue "S1 GLU 613": "OE1" <-> "OE2" Residue "S1 GLU 619": "OE1" <-> "OE2" Residue "S1 ASP 633": "OD1" <-> "OD2" Residue "S1 GLU 656": "OE1" <-> "OE2" Residue "S1 GLU 661": "OE1" <-> "OE2" Residue "S1 PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 GLU 699": "OE1" <-> "OE2" Residue "LC ASP 51": "OD1" <-> "OD2" Residue "LC ASP 56": "OD1" <-> "OD2" Residue "LC GLU 93": "OE1" <-> "OE2" Residue "LC GLU 98": "OE1" <-> "OE2" Residue "LC ASP 102": "OD1" <-> "OD2" Residue "LC PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC ASP 112": "OD1" <-> "OD2" Residue "LC TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC ASP 183": "OD1" <-> "OD2" Residue "LC GLU 187": "OE1" <-> "OE2" Residue "LC GLU 190": "OE1" <-> "OE2" Residue "LM GLU 8": "OE1" <-> "OE2" Residue "LM ASP 15": "OD1" <-> "OD2" Residue "LM ARG 20": "NH1" <-> "NH2" Residue "LM GLU 26": "OE1" <-> "OE2" Residue "LM ARG 38": "NH1" <-> "NH2" Residue "LM GLU 43": "OE1" <-> "OE2" Residue "LM ARG 50": "NH1" <-> "NH2" Residue "LM ARG 61": "NH1" <-> "NH2" Residue "LM GLU 67": "OE1" <-> "OE2" Residue "LM ASP 81": "OD1" <-> "OD2" Residue "LM ARG 88": "NH1" <-> "NH2" Residue "LM TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LM ARG 100": "NH1" <-> "NH2" Residue "LM ARG 108": "NH1" <-> "NH2" Residue "LN GLU 78": "OE1" <-> "OE2" Residue "LN TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN ASP 97": "OD1" <-> "OD2" Residue "LN GLU 99": "OE1" <-> "OE2" Residue "LN GLU 144": "OE1" <-> "OE2" Residue "LN TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN GLU 184": "OE1" <-> "OE2" Residue "LN ASP 186": "OD1" <-> "OD2" Residue "LN GLU 193": "OE1" <-> "OE2" Residue "LN ASP 228": "OD1" <-> "OD2" Residue "LN GLU 235": "OE1" <-> "OE2" Residue "LN ASP 263": "OD1" <-> "OD2" Residue "LO ARG 2": "NH1" <-> "NH2" Residue "LO ARG 5": "NH1" <-> "NH2" Residue "LO ARG 12": "NH1" <-> "NH2" Residue "LO TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO ARG 32": "NH1" <-> "NH2" Residue "LO TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO ARG 47": "NH1" <-> "NH2" Residue "LO PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO ARG 69": "NH1" <-> "NH2" Residue "LO PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO ASP 90": "OD1" <-> "OD2" Residue "LO ASP 96": "OD1" <-> "OD2" Residue "LO ASP 101": "OD1" <-> "OD2" Residue "LO PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO GLU 110": "OE1" <-> "OE2" Residue "LP TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LP ARG 21": "NH1" <-> "NH2" Residue "LP GLU 23": "OE1" <-> "OE2" Residue "LP GLU 34": "OE1" <-> "OE2" Residue "LP GLU 45": "OE1" <-> "OE2" Residue "LP GLU 62": "OE1" <-> "OE2" Residue "LP ARG 68": "NH1" <-> "NH2" Residue "LP GLU 70": "OE1" <-> "OE2" Residue "LP PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LP ARG 78": "NH1" <-> "NH2" Residue "LP ARG 79": "NH1" <-> "NH2" Residue "LP TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LP ARG 84": "NH1" <-> "NH2" Residue "LP ASP 95": "OD1" <-> "OD2" Residue "LQ ASP 34": "OD1" <-> "OD2" Residue "LQ TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ GLU 52": "OE1" <-> "OE2" Residue "LQ GLU 59": "OE1" <-> "OE2" Residue "LQ ASP 67": "OD1" <-> "OD2" Residue "LQ PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ ARG 84": "NH1" <-> "NH2" Residue "LQ ARG 88": "NH1" <-> "NH2" Residue "LQ ARG 95": "NH1" <-> "NH2" Residue "LQ ARG 110": "NH1" <-> "NH2" Residue "LR GLU 18": "OE1" <-> "OE2" Residue "LR GLU 25": "OE1" <-> "OE2" Residue "LR GLU 42": "OE1" <-> "OE2" Residue "LR PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LR GLU 52": "OE1" <-> "OE2" Residue "LR GLU 56": "OE1" <-> "OE2" Residue "LR GLU 89": "OE1" <-> "OE2" Residue "LR ASP 94": "OD1" <-> "OD2" Residue "LR PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS ASP 8": "OD1" <-> "OD2" Residue "LS ASP 17": "OD1" <-> "OD2" Residue "LS GLU 36": "OE1" <-> "OE2" Residue "LS GLU 61": "OE1" <-> "OE2" Residue "LS ASP 80": "OD1" <-> "OD2" Residue "LS PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT GLU 11": "OE1" <-> "OE2" Residue "LT PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT GLU 35": "OE1" <-> "OE2" Residue "LT ASP 43": "OD1" <-> "OD2" Residue "LT ASP 45": "OD1" <-> "OD2" Residue "LT GLU 55": "OE1" <-> "OE2" Residue "LT TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT GLU 59": "OE1" <-> "OE2" Residue "LT ASP 66": "OD1" <-> "OD2" Residue "LT ASP 76": "OD1" <-> "OD2" Residue "LT ASP 90": "OD1" <-> "OD2" Residue "LT PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU ASP 55": "OD1" <-> "OD2" Residue "LU ASP 63": "OD1" <-> "OD2" Residue "LU GLU 84": "OE1" <-> "OE2" Residue "LV ARG 2": "NH1" <-> "NH2" Residue "LV ARG 10": "NH1" <-> "NH2" Residue "LV ARG 17": "NH1" <-> "NH2" Residue "LV PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LV ARG 36": "NH1" <-> "NH2" Residue "LV GLU 40": "OE1" <-> "OE2" Residue "LV GLU 42": "OE1" <-> "OE2" Residue "LV ARG 49": "NH1" <-> "NH2" Residue "LV ARG 56": "NH1" <-> "NH2" Residue "LV ASP 64": "OD1" <-> "OD2" Residue "LV ARG 73": "NH1" <-> "NH2" Residue "LV GLU 75": "OE1" <-> "OE2" Residue "LV TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD ASP 6": "OD1" <-> "OD2" Residue "LD GLU 13": "OE1" <-> "OE2" Residue "LD ASP 28": "OD1" <-> "OD2" Residue "LD GLU 39": "OE1" <-> "OE2" Residue "LD TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD GLU 64": "OE1" <-> "OE2" Residue "LD GLU 69": "OE1" <-> "OE2" Residue "LD PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD GLU 86": "OE1" <-> "OE2" Residue "LD GLU 113": "OE1" <-> "OE2" Residue "LD ASP 123": "OD1" <-> "OD2" Residue "LD TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD GLU 132": "OE1" <-> "OE2" Residue "LD ASP 159": "OD1" <-> "OD2" Residue "LD GLU 162": "OE1" <-> "OE2" Residue "LW GLU 13": "OE1" <-> "OE2" Residue "LW GLU 24": "OE1" <-> "OE2" Residue "LW PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LW ARG 29": "NH1" <-> "NH2" Residue "LW ARG 47": "NH1" <-> "NH2" Residue "LW ARG 52": "NH1" <-> "NH2" Residue "LX ARG 13": "NH1" <-> "NH2" Residue "LX PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX GLU 17": "OE1" <-> "OE2" Residue "LX ARG 33": "NH1" <-> "NH2" Residue "LX ARG 59": "NH1" <-> "NH2" Residue "LX PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX GLU 74": "OE1" <-> "OE2" Residue "LX ARG 77": "NH1" <-> "NH2" Residue "LX GLU 81": "OE1" <-> "OE2" Residue "LX PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX ARG 83": "NH1" <-> "NH2" Residue "LX GLU 86": "OE1" <-> "OE2" Residue "LX PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX GLU 99": "OE1" <-> "OE2" Residue "LX PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX ASP 103": "OD1" <-> "OD2" Residue "LX ASP 108": "OD1" <-> "OD2" Residue "LX PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX ASP 131": "OD1" <-> "OD2" Residue "LX PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX GLU 168": "OE1" <-> "OE2" Residue "LX ARG 169": "NH1" <-> "NH2" Residue "LX ARG 184": "NH1" <-> "NH2" Residue "LY ARG 10": "NH1" <-> "NH2" Residue "LY ARG 29": "NH1" <-> "NH2" Residue "LY ARG 44": "NH1" <-> "NH2" Residue "LY GLU 57": "OE1" <-> "OE2" Residue "LY GLU 58": "OE1" <-> "OE2" Residue "L1 ARG 9": "NH1" <-> "NH2" Residue "L1 ARG 15": "NH1" <-> "NH2" Residue "L1 ASP 19": "OD1" <-> "OD2" Residue "L1 ASP 30": "OD1" <-> "OD2" Residue "L1 ARG 51": "NH1" <-> "NH2" Residue "L2 GLU 6": "OE1" <-> "OE2" Residue "L2 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L2 ASP 39": "OD1" <-> "OD2" Residue "L3 ARG 3": "NH1" <-> "NH2" Residue "L3 ARG 12": "NH1" <-> "NH2" Residue "L3 ARG 14": "NH1" <-> "NH2" Residue "L3 ARG 19": "NH1" <-> "NH2" Residue "L3 ARG 21": "NH1" <-> "NH2" Residue "L3 ARG 33": "NH1" <-> "NH2" Residue "L3 ARG 41": "NH1" <-> "NH2" Residue "L4 ARG 12": "NH1" <-> "NH2" Residue "L4 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L4 ARG 29": "NH1" <-> "NH2" Residue "L4 ARG 39": "NH1" <-> "NH2" Residue "L4 ARG 41": "NH1" <-> "NH2" Residue "L4 ASP 53": "OD1" <-> "OD2" Residue "L4 TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L5 ARG 24": "NH1" <-> "NH2" Residue "L6 GLU 16": "OE1" <-> "OE2" Residue "L6 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L6 ARG 21": "NH1" <-> "NH2" Residue "L6 ASP 22": "OD1" <-> "OD2" Residue "L6 ARG 44": "NH1" <-> "NH2" Residue "L6 ARG 49": "NH1" <-> "NH2" Residue "L6 ARG 61": "NH1" <-> "NH2" Residue "L6 ARG 88": "NH1" <-> "NH2" Residue "L6 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L6 ARG 102": "NH1" <-> "NH2" Residue "L6 GLU 111": "OE1" <-> "OE2" Residue "L6 ASP 145": "OD1" <-> "OD2" Residue "L6 GLU 152": "OE1" <-> "OE2" Residue "L6 ARG 162": "NH1" <-> "NH2" Residue "L6 ARG 170": "NH1" <-> "NH2" Residue "L6 ASP 184": "OD1" <-> "OD2" Residue "L6 GLU 197": "OE1" <-> "OE2" Residue "LE TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE ASP 46": "OD1" <-> "OD2" Residue "LE ASP 63": "OD1" <-> "OD2" Residue "LE PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE GLU 107": "OE1" <-> "OE2" Residue "LE ASP 120": "OD1" <-> "OD2" Residue "LE GLU 122": "OE1" <-> "OE2" Residue "LE GLU 140": "OE1" <-> "OE2" Residue "LE ASP 141": "OD1" <-> "OD2" Residue "L7 ASP 9": "OD1" <-> "OD2" Residue "L7 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 GLU 41": "OE1" <-> "OE2" Residue "L7 ASP 45": "OD1" <-> "OD2" Residue "L7 ASP 50": "OD1" <-> "OD2" Residue "L7 ARG 70": "NH1" <-> "NH2" Residue "L7 PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 ARG 79": "NH1" <-> "NH2" Residue "L7 TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 ARG 91": "NH1" <-> "NH2" Residue "L7 GLU 93": "OE1" <-> "OE2" Residue "L7 PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 GLU 100": "OE1" <-> "OE2" Residue "L7 ARG 101": "NH1" <-> "NH2" Residue "L7 ARG 109": "NH1" <-> "NH2" Residue "L7 ARG 111": "NH1" <-> "NH2" Residue "L7 ASP 112": "OD1" <-> "OD2" Residue "L7 ARG 114": "NH1" <-> "NH2" Residue "L7 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 ARG 132": "NH1" <-> "NH2" Residue "L7 GLU 133": "OE1" <-> "OE2" Residue "L7 PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 GLU 139": "OE1" <-> "OE2" Residue "L7 TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 ASP 146": "OD1" <-> "OD2" Residue "L7 GLU 164": "OE1" <-> "OE2" Residue "L7 ASP 173": "OD1" <-> "OD2" Residue "L8 ARG 2": "NH1" <-> "NH2" Residue "L8 ASP 15": "OD1" <-> "OD2" Residue "L8 ASP 38": "OD1" <-> "OD2" Residue "L8 GLU 41": "OE1" <-> "OE2" Residue "L8 ASP 46": "OD1" <-> "OD2" Residue "L8 GLU 80": "OE1" <-> "OE2" Residue "L8 ASP 113": "OD1" <-> "OD2" Residue "L8 GLU 123": "OE1" <-> "OE2" Residue "L8 TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L8 ARG 152": "NH1" <-> "NH2" Residue "L8 GLU 154": "OE1" <-> "OE2" Residue "L8 TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L8 ARG 162": "NH1" <-> "NH2" Residue "L8 TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L8 GLU 166": "OE1" <-> "OE2" Residue "L8 ARG 169": "NH1" <-> "NH2" Residue "L8 GLU 172": "OE1" <-> "OE2" Residue "L9 ASP 17": "OD1" <-> "OD2" Residue "L9 TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 ARG 27": "NH1" <-> "NH2" Residue "L9 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 GLU 53": "OE1" <-> "OE2" Residue "L9 GLU 55": "OE1" <-> "OE2" Residue "L9 GLU 70": "OE1" <-> "OE2" Residue "L9 ASP 86": "OD1" <-> "OD2" Residue "L9 ASP 98": "OD1" <-> "OD2" Residue "L9 GLU 114": "OE1" <-> "OE2" Residue "L9 GLU 129": "OE1" <-> "OE2" Residue "L9 PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 GLU 149": "OE1" <-> "OE2" Residue "LF ARG 13": "NH1" <-> "NH2" Residue "LF ASP 14": "OD1" <-> "OD2" Residue "LF GLU 31": "OE1" <-> "OE2" Residue "LF ARG 37": "NH1" <-> "NH2" Residue "LF ASP 49": "OD1" <-> "OD2" Residue "LF ASP 52": "OD1" <-> "OD2" Residue "LF ASP 60": "OD1" <-> "OD2" Residue "LF ASP 71": "OD1" <-> "OD2" Residue "LF TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF GLU 90": "OE1" <-> "OE2" Residue "LF ARG 96": "NH1" <-> "NH2" Residue "LF GLU 98": "OE1" <-> "OE2" Residue "LF PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF ARG 120": "NH1" <-> "NH2" Residue "LF TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG GLU 4": "OE1" <-> "OE2" Residue "LG ASP 73": "OD1" <-> "OD2" Residue "LG PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG GLU 110": "OE1" <-> "OE2" Residue "LH GLU 10": "OE1" <-> "OE2" Residue "LH PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH GLU 51": "OE1" <-> "OE2" Residue "LH TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH ASP 81": "OD1" <-> "OD2" Residue "LH GLU 86": "OE1" <-> "OE2" Residue "LH GLU 115": "OE1" <-> "OE2" Residue "LH GLU 143": "OE1" <-> "OE2" Residue "LH GLU 144": "OE1" <-> "OE2" Residue "LI ARG 10": "NH1" <-> "NH2" Residue "LI ARG 18": "NH1" <-> "NH2" Residue "LI ARG 40": "NH1" <-> "NH2" Residue "LI ARG 44": "NH1" <-> "NH2" Residue "LI GLU 47": "OE1" <-> "OE2" Residue "LI ARG 50": "NH1" <-> "NH2" Residue "LI ARG 51": "NH1" <-> "NH2" Residue "LI ARG 55": "NH1" <-> "NH2" Residue "LI ARG 59": "NH1" <-> "NH2" Residue "LI GLU 90": "OE1" <-> "OE2" Residue "LI TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LI TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LI GLU 110": "OE1" <-> "OE2" Residue "LI ARG 114": "NH1" <-> "NH2" Residue "LJ PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ GLU 43": "OE1" <-> "OE2" Residue "LJ ASP 72": "OD1" <-> "OD2" Residue "LJ ASP 106": "OD1" <-> "OD2" Residue "LJ GLU 114": "OE1" <-> "OE2" Residue "LJ GLU 120": "OE1" <-> "OE2" Residue "LJ GLU 127": "OE1" <-> "OE2" Residue "LK GLU 20": "OE1" <-> "OE2" Residue "LK TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LK ASP 69": "OD1" <-> "OD2" Residue "LK GLU 80": "OE1" <-> "OE2" Residue "LK GLU 84": "OE1" <-> "OE2" Residue "LK ASP 89": "OD1" <-> "OD2" Residue "LK TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LK GLU 112": "OE1" <-> "OE2" Residue "LK PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ ASP 50": "OD1" <-> "OD2" Residue "LZ PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 156714 Number of models: 1 Model: "" Number of chains: 59 Chain: "SA" Number of atoms: 33076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1542, 33076 Classifications: {'RNA': 1542} Modifications used: {'5*END': 1, 'rna2p_pur': 123, 'rna3p_pur': 753, 'rna2p_pyr': 83, 'rna3p_pyr': 583} Link IDs: {'rna3p': 1336, 'rna2p': 205} Chain: "S6" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1639 Classifications: {'RNA': 77} Modifications used: {'rna3p_pyr': 30, 'rna2p_pur': 6, 'rna3p_pur': 33, 'rna2p_pyr': 8, '5*END': 1} Link IDs: {'rna3p': 63, 'rna2p': 13} Chain: "S7" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1577 Classifications: {'RNA': 74} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 35, 'rna2p_pyr': 9, 'rna3p_pyr': 27} Link IDs: {'rna3p': 61, 'rna2p': 12} Chain: "SJ" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 825 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "SK" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 965 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain: "SL" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "SM" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "SN" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "SO" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 716 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "SP" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "SQ" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 672 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "SR" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 626 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "SS" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 727 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain: "SB" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1872 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 232} Chain: "ST" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "SU" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 590 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "SC" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1822 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain: "SD" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "SE" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1225 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "SF" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1101 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "SG" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1400 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "SH" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "SI" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1036 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "S1" Number of atoms: 5431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5431 Classifications: {'peptide': 702} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 668} Chain: "LA" Number of atoms: 62333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2904, 62333 Classifications: {'RNA': 2904} Modifications used: {'5*END': 1, 'rna2p_pur': 271, 'rna3p_pur': 1401, 'rna2p_pyr': 146, 'rna3p_pyr': 1086} Link IDs: {'rna3p': 2486, 'rna2p': 417} Chain: "LB" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2566 Classifications: {'RNA': 120} Modifications used: {'rna3p_pyr': 52, 'rna2p_pur': 6, 'rna3p_pur': 58, 'rna2p_pyr': 4, '5*END': 1} Link IDs: {'rna3p': 109, 'rna2p': 10} Chain: "LC" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1733 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 226, 'PCIS': 1} Chain: "LM" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "LN" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2092 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "LO" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "LP" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "LQ" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "LR" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 787 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "LS" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 789 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "LT" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "LU" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 634 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "LV" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "LD" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1233 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain: "LW" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "LX" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "LY" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "L1" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "L2" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 441 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "L3" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "L4" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "L5" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "L6" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'CIS': 1, 'TRANS': 194} Chain: "LE" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "L7" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1420 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "L8" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "L9" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "LF" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "LG" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 947 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "LH" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "LI" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "LJ" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1008 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "LK" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "LZ" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 549 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "S1" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 63.02, per 1000 atoms: 0.40 Number of scatterers: 156714 At special positions: 0 Unit cell: (279.3, 266.7, 281.4, 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 195 16.00 P 4715 15.00 O 42815 8.00 N 29104 7.00 C 79885 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 57.25 Conformation dependent library (CDL) restraints added in 6.6 seconds 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13096 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 216 helices and 84 sheets defined 38.1% alpha, 18.9% beta 1461 base pairs and 2269 stacking pairs defined. Time for finding SS restraints: 66.53 Creating SS restraints... Processing helix chain 'SJ' and resid 14 through 33 Processing helix chain 'SJ' and resid 82 through 90 removed outlier: 3.635A pdb=" N ALASJ 86 " --> pdb=" O LYSSJ 82 " (cutoff:3.500A) Processing helix chain 'SK' and resid 45 through 50 removed outlier: 3.691A pdb=" N GLYSK 50 " --> pdb=" O ALASK 46 " (cutoff:3.500A) Processing helix chain 'SK' and resid 53 through 58 removed outlier: 4.983A pdb=" N SERSK 57 " --> pdb=" O GLYSK 53 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THRSK 58 " --> pdb=" O SERSK 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'SK' and resid 53 through 58' Processing helix chain 'SK' and resid 59 through 75 removed outlier: 3.516A pdb=" N ALASK 72 " --> pdb=" O ARGSK 68 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYSSK 74 " --> pdb=" O ALASK 70 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLUSK 75 " --> pdb=" O ASPSK 71 " (cutoff:3.500A) Processing helix chain 'SK' and resid 91 through 103 removed outlier: 4.769A pdb=" N ILESK 96 " --> pdb=" O ARGSK 92 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLYSK 103 " --> pdb=" O LEUSK 99 " (cutoff:3.500A) Processing helix chain 'SL' and resid 2 through 10 Proline residue: SL 10 - end of helix Processing helix chain 'SL' and resid 112 through 117 removed outlier: 4.829A pdb=" N TYRSL 116 " --> pdb=" O ALASL 112 " (cutoff:3.500A) Processing helix chain 'SM' and resid 13 through 22 removed outlier: 3.695A pdb=" N LEUSM 18 " --> pdb=" O ALASM 14 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THRSM 19 " --> pdb=" O VALSM 15 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SERSM 20 " --> pdb=" O ILESM 16 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILESM 21 " --> pdb=" O ALASM 17 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYRSM 22 " --> pdb=" O LEUSM 18 " (cutoff:3.500A) Processing helix chain 'SM' and resid 25 through 37 Processing helix chain 'SM' and resid 48 through 63 removed outlier: 3.503A pdb=" N GLUSM 58 " --> pdb=" O THRSM 54 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYSSM 61 " --> pdb=" O ASPSM 57 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHESM 62 " --> pdb=" O GLUSM 58 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VALSM 63 " --> pdb=" O VALSM 59 " (cutoff:3.500A) Processing helix chain 'SM' and resid 65 through 83 removed outlier: 3.985A pdb=" N ARGSM 70 " --> pdb=" O GLYSM 66 " (cutoff:3.500A) Processing helix chain 'SM' and resid 84 through 93 Processing helix chain 'SM' and resid 105 through 110 Processing helix chain 'SN' and resid 2 through 24 removed outlier: 3.847A pdb=" N ALASN 21 " --> pdb=" O ASPSN 17 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYSSN 22 " --> pdb=" O LYSSN 18 " (cutoff:3.500A) Processing helix chain 'SN' and resid 25 through 30 Processing helix chain 'SN' and resid 34 through 39 removed outlier: 4.587A pdb=" N GLUSN 38 " --> pdb=" O ASNSN 34 " (cutoff:3.500A) Processing helix chain 'SN' and resid 42 through 48 removed outlier: 4.618A pdb=" N LYSSN 46 " --> pdb=" O ASNSN 42 " (cutoff:3.500A) Processing helix chain 'SN' and resid 80 through 90 removed outlier: 3.974A pdb=" N GLUSN 85 " --> pdb=" O ILESN 81 " (cutoff:3.500A) Processing helix chain 'SO' and resid 3 through 15 Processing helix chain 'SO' and resid 23 through 45 removed outlier: 3.711A pdb=" N ALASO 43 " --> pdb=" O GLNSO 39 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLUSO 44 " --> pdb=" O GLYSO 40 " (cutoff:3.500A) Processing helix chain 'SO' and resid 48 through 73 removed outlier: 4.030A pdb=" N GLYSO 54 " --> pdb=" O HISSO 50 " (cutoff:3.500A) Processing helix chain 'SO' and resid 74 through 85 removed outlier: 3.645A pdb=" N GLUSO 82 " --> pdb=" O THRSO 78 " (cutoff:3.500A) Processing helix chain 'SP' and resid 53 through 64 Processing helix chain 'SP' and resid 68 through 79 Processing helix chain 'SR' and resid 24 through 33 removed outlier: 3.658A pdb=" N ASNSR 30 " --> pdb=" O ALASR 26 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYRSR 31 " --> pdb=" O THRSR 27 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILESR 32 " --> pdb=" O LEUSR 28 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N THRSR 33 " --> pdb=" O LYSSR 29 " (cutoff:3.500A) Processing helix chain 'SR' and resid 40 through 45 Processing helix chain 'SR' and resid 47 through 65 Processing helix chain 'SS' and resid 13 through 25 removed outlier: 3.619A pdb=" N LYSSS 17 " --> pdb=" O HISSS 13 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SERSS 24 " --> pdb=" O LYSSS 20 " (cutoff:3.500A) Processing helix chain 'SS' and resid 69 through 75 removed outlier: 4.480A pdb=" N PHESS 73 " --> pdb=" O LYSSS 69 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALASS 74 " --> pdb=" O LEUSS 70 " (cutoff:3.500A) Proline residue: SS 75 - end of helix No H-bonds generated for 'chain 'SS' and resid 69 through 75' Processing helix chain 'SB' and resid 3 through 15 removed outlier: 4.584A pdb=" N VALSB 13 " --> pdb=" O LEUSB 9 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N HISSB 14 " --> pdb=" O LYSSB 10 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N PHESB 15 " --> pdb=" O ALASB 11 " (cutoff:3.500A) Processing helix chain 'SB' and resid 26 through 31 removed outlier: 3.881A pdb=" N ILESB 30 " --> pdb=" O METSB 26 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N PHESB 31 " --> pdb=" O LYSSB 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'SB' and resid 26 through 31' Processing helix chain 'SB' and resid 43 through 63 Proline residue: SB 47 - end of helix removed outlier: 3.885A pdb=" N GLUSB 55 " --> pdb=" O GLUSB 51 " (cutoff:3.500A) Processing helix chain 'SB' and resid 75 through 85 removed outlier: 4.437A pdb=" N VALSB 79 " --> pdb=" O ALASB 75 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEUSB 84 " --> pdb=" O LYSSB 80 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N SERSB 85 " --> pdb=" O ASPSB 81 " (cutoff:3.500A) Processing helix chain 'SB' and resid 102 through 123 removed outlier: 3.510A pdb=" N GLNSB 108 " --> pdb=" O LYSSB 104 " (cutoff:3.500A) Processing helix chain 'SB' and resid 124 through 129 removed outlier: 3.664A pdb=" N LEUSB 128 " --> pdb=" O THRSB 124 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THRSB 129 " --> pdb=" O PHESB 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'SB' and resid 124 through 129' Processing helix chain 'SB' and resid 130 through 148 Processing helix chain 'SB' and resid 168 through 179 removed outlier: 3.735A pdb=" N ILESB 172 " --> pdb=" O GLUSB 168 " (cutoff:3.500A) Processing helix chain 'SB' and resid 205 through 239 removed outlier: 3.985A pdb=" N VALSB 209 " --> pdb=" O ALASB 205 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARGSB 224 " --> pdb=" O VALSB 220 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SERSB 225 " --> pdb=" O ARGSB 221 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLUSB 238 " --> pdb=" O GLUSB 234 " (cutoff:3.500A) Processing helix chain 'ST' and resid 6 through 41 removed outlier: 4.342A pdb=" N ALAST 10 " --> pdb=" O ALAST 6 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILEST 11 " --> pdb=" O LYSST 7 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VALST 34 " --> pdb=" O PHEST 30 " (cutoff:3.500A) Processing helix chain 'ST' and resid 43 through 64 Proline residue: ST 55 - end of helix Processing helix chain 'ST' and resid 68 through 86 removed outlier: 4.421A pdb=" N ALAST 72 " --> pdb=" O LYSST 68 " (cutoff:3.500A) Processing helix chain 'SU' and resid 15 through 20 Processing helix chain 'SU' and resid 38 through 44 removed outlier: 5.228A pdb=" N THRSU 42 " --> pdb=" O GLUSU 38 " (cutoff:3.500A) Processing helix chain 'SU' and resid 46 through 68 removed outlier: 4.569A pdb=" N GLUSU 62 " --> pdb=" O LYSSU 58 " (cutoff:3.500A) Processing helix chain 'SU' and resid 26 through 31 removed outlier: 4.168A pdb=" N GLUSU 30 " --> pdb=" O VALSU 27 " (cutoff:3.500A) Processing helix chain 'SC' and resid 5 through 11 removed outlier: 4.089A pdb=" N ARGSC 10 " --> pdb=" O PROSC 6 " (cutoff:3.500A) Processing helix chain 'SC' and resid 24 through 47 removed outlier: 4.414A pdb=" N ALASC 29 " --> pdb=" O THRSC 25 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ASPSC 30 " --> pdb=" O LYSSC 26 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLUSC 45 " --> pdb=" O TYRSC 41 " (cutoff:3.500A) Processing helix chain 'SC' and resid 71 through 77 removed outlier: 4.266A pdb=" N VALSC 75 " --> pdb=" O ARGSC 71 " (cutoff:3.500A) Processing helix chain 'SC' and resid 80 through 95 removed outlier: 4.946A pdb=" N GLYSC 95 " --> pdb=" O ALASC 91 " (cutoff:3.500A) Processing helix chain 'SC' and resid 107 through 112 removed outlier: 3.881A pdb=" N ASPSC 111 " --> pdb=" O LYSSC 107 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALASC 112 " --> pdb=" O PROSC 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 107 through 112' Processing helix chain 'SC' and resid 113 through 126 removed outlier: 3.522A pdb=" N GLNSC 122 " --> pdb=" O SERSC 118 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARGSC 126 " --> pdb=" O GLNSC 122 " (cutoff:3.500A) Processing helix chain 'SC' and resid 128 through 144 removed outlier: 6.304A pdb=" N ALASC 132 " --> pdb=" O METSC 128 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYSSC 134 " --> pdb=" O ARGSC 130 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARGSC 135 " --> pdb=" O ARGSC 131 " (cutoff:3.500A) Processing helix chain 'SC' and resid 216 through 221 removed outlier: 4.214A pdb=" N ALASC 220 " --> pdb=" O PROSC 216 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ALASC 221 " --> pdb=" O GLUSC 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 216 through 221' Processing helix chain 'SD' and resid 6 through 15 removed outlier: 4.072A pdb=" N LEUSD 10 " --> pdb=" O PROSD 6 " (cutoff:3.500A) Processing helix chain 'SD' and resid 27 through 32 removed outlier: 7.302A pdb=" N CYSSD 31 " --> pdb=" O ILESD 27 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LYSSD 32 " --> pdb=" O ASPSD 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'SD' and resid 27 through 32' Processing helix chain 'SD' and resid 48 through 65 removed outlier: 4.237A pdb=" N GLNSD 53 " --> pdb=" O ASPSD 49 " (cutoff:3.500A) Processing helix chain 'SD' and resid 67 through 82 removed outlier: 4.285A pdb=" N LYSSD 82 " --> pdb=" O ALASD 78 " (cutoff:3.500A) Processing helix chain 'SD' and resid 84 through 96 removed outlier: 3.901A pdb=" N ARGSD 96 " --> pdb=" O LEUSD 92 " (cutoff:3.500A) Processing helix chain 'SD' and resid 97 through 105 Processing helix chain 'SD' and resid 109 through 120 removed outlier: 3.607A pdb=" N LYSSD 120 " --> pdb=" O LEUSD 116 " (cutoff:3.500A) Processing helix chain 'SD' and resid 145 through 151 removed outlier: 3.672A pdb=" N LYSSD 149 " --> pdb=" O ARGSD 145 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LYSSD 150 " --> pdb=" O GLUSD 146 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLNSD 151 " --> pdb=" O LYSSD 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'SD' and resid 145 through 151' Processing helix chain 'SD' and resid 152 through 163 removed outlier: 5.545A pdb=" N GLNSD 163 " --> pdb=" O GLUSD 159 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 191 removed outlier: 4.451A pdb=" N SERSD 191 " --> pdb=" O ARGSD 187 " (cutoff:3.500A) Processing helix chain 'SD' and resid 195 through 204 removed outlier: 3.919A pdb=" N VALSD 200 " --> pdb=" O GLUSD 196 " (cutoff:3.500A) Processing helix chain 'SE' and resid 54 through 70 removed outlier: 4.027A pdb=" N ARGSE 68 " --> pdb=" O GLUSE 64 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASNSE 69 " --> pdb=" O LYSSE 65 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N METSE 70 " --> pdb=" O ALASE 66 " (cutoff:3.500A) Processing helix chain 'SE' and resid 108 through 118 removed outlier: 4.703A pdb=" N ALASE 112 " --> pdb=" O GLYSE 108 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VALSE 113 " --> pdb=" O ALASE 109 " (cutoff:3.500A) Processing helix chain 'SE' and resid 132 through 146 removed outlier: 4.038A pdb=" N VALSE 136 " --> pdb=" O PROSE 132 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARGSE 137 " --> pdb=" O ILESE 133 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N METSE 146 " --> pdb=" O GLYSE 142 " (cutoff:3.500A) Processing helix chain 'SE' and resid 156 through 164 Processing helix chain 'SF' and resid 14 through 33 removed outlier: 4.136A pdb=" N VALSF 18 " --> pdb=" O GLNSF 14 " (cutoff:3.500A) Proline residue: SF 19 - end of helix removed outlier: 3.618A pdb=" N ALASF 27 " --> pdb=" O GLUSF 23 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALASF 32 " --> pdb=" O ALASF 28 " (cutoff:3.500A) Processing helix chain 'SF' and resid 67 through 81 removed outlier: 3.710A pdb=" N ILESF 71 " --> pdb=" O PROSF 67 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THRSF 77 " --> pdb=" O GLUSF 73 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASNSF 81 " --> pdb=" O THRSF 77 " (cutoff:3.500A) Processing helix chain 'SF' and resid 94 through 112 removed outlier: 4.450A pdb=" N GLUSF 98 " --> pdb=" O HISSF 94 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALASF 99 " --> pdb=" O ALASF 95 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SERSF 100 " --> pdb=" O VALSF 96 " (cutoff:3.500A) Proline residue: SF 101 - end of helix removed outlier: 4.792A pdb=" N LYSSF 104 " --> pdb=" O SERSF 100 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALASF 105 " --> pdb=" O PROSF 101 " (cutoff:3.500A) Processing helix chain 'SF' and resid 117 through 126 removed outlier: 4.176A pdb=" N ALASF 121 " --> pdb=" O ALASF 117 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ALASF 126 " --> pdb=" O ASPSF 122 " (cutoff:3.500A) Processing helix chain 'SG' and resid 19 through 30 removed outlier: 3.826A pdb=" N ALASG 23 " --> pdb=" O SERSG 19 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASNSG 27 " --> pdb=" O ALASG 23 " (cutoff:3.500A) Processing helix chain 'SG' and resid 34 through 53 removed outlier: 3.556A pdb=" N SERSG 40 " --> pdb=" O SERSG 36 " (cutoff:3.500A) Processing helix chain 'SG' and resid 56 through 69 removed outlier: 4.281A pdb=" N ALASG 60 " --> pdb=" O SERSG 56 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHESG 61 " --> pdb=" O GLUSG 57 " (cutoff:3.500A) Processing helix chain 'SG' and resid 91 through 111 removed outlier: 3.504A pdb=" N ILESG 103 " --> pdb=" O ALASG 99 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VALSG 104 " --> pdb=" O METSG 100 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYSSG 109 " --> pdb=" O GLUSG 105 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLYSG 111 " --> pdb=" O ALASG 107 " (cutoff:3.500A) Processing helix chain 'SG' and resid 114 through 129 removed outlier: 3.567A pdb=" N GLUSG 128 " --> pdb=" O SERSG 124 " (cutoff:3.500A) Processing helix chain 'SG' and resid 131 through 148 removed outlier: 3.569A pdb=" N LYSSG 136 " --> pdb=" O THRSG 132 " (cutoff:3.500A) Processing helix chain 'SG' and resid 153 through 165 Processing helix chain 'SH' and resid 4 through 20 Processing helix chain 'SH' and resid 29 through 43 Processing helix chain 'SH' and resid 111 through 119 Processing helix chain 'SI' and resid 33 through 39 removed outlier: 3.618A pdb=" N GLYSI 39 " --> pdb=" O GLUSI 35 " (cutoff:3.500A) Processing helix chain 'SI' and resid 42 through 55 Proline residue: SI 50 - end of helix Processing helix chain 'SI' and resid 70 through 91 removed outlier: 3.969A pdb=" N THRSI 83 " --> pdb=" O ARGSI 79 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLUSI 88 " --> pdb=" O ARGSI 84 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYRSI 89 " --> pdb=" O ALASI 85 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASPSI 90 " --> pdb=" O LEUSI 86 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLUSI 91 " --> pdb=" O METSI 87 " (cutoff:3.500A) Processing helix chain 'SI' and resid 92 through 101 removed outlier: 3.643A pdb=" N GLUSI 96 " --> pdb=" O SERSI 92 " (cutoff:3.500A) Processing helix chain 'S1' and resid 5 through 10 removed outlier: 6.860A pdb=" N TYRS1 9 " --> pdb=" O PROS1 5 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ARGS1 10 " --> pdb=" O ILES1 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'S1' and resid 5 through 10' Processing helix chain 'S1' and resid 21 through 37 removed outlier: 4.414A pdb=" N VALS1 35 " --> pdb=" O PHES1 31 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASNS1 36 " --> pdb=" O TYRS1 32 " (cutoff:3.500A) Processing helix chain 'S1' and resid 52 through 59 removed outlier: 3.996A pdb=" N GLNS1 56 " --> pdb=" O METS1 52 " (cutoff:3.500A) Processing helix chain 'S1' and resid 94 through 105 removed outlier: 4.081A pdb=" N VALS1 98 " --> pdb=" O PHES1 94 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARGS1 103 " --> pdb=" O GLUS1 99 " (cutoff:3.500A) Processing helix chain 'S1' and resid 119 through 133 removed outlier: 3.649A pdb=" N VALS1 125 " --> pdb=" O GLNS1 121 " (cutoff:3.500A) Processing helix chain 'S1' and resid 149 through 160 removed outlier: 4.198A pdb=" N VALS1 153 " --> pdb=" O ASNS1 149 " (cutoff:3.500A) Processing helix chain 'S1' and resid 194 through 201 removed outlier: 5.087A pdb=" N GLYS1 198 " --> pdb=" O ASPS1 194 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VALS1 199 " --> pdb=" O ALAS1 195 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THRS1 200 " --> pdb=" O ASPS1 196 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N PHES1 201 " --> pdb=" O GLNS1 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'S1' and resid 194 through 201' Processing helix chain 'S1' and resid 211 through 228 removed outlier: 3.840A pdb=" N GLUS1 216 " --> pdb=" O GLUS1 212 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLUS1 227 " --> pdb=" O GLUS1 223 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALAS1 228 " --> pdb=" O SERS1 224 " (cutoff:3.500A) Processing helix chain 'S1' and resid 229 through 239 removed outlier: 3.642A pdb=" N GLYS1 239 " --> pdb=" O LYSS1 235 " (cutoff:3.500A) Processing helix chain 'S1' and resid 243 through 258 Processing helix chain 'S1' and resid 273 through 284 removed outlier: 3.577A pdb=" N ASPS1 283 " --> pdb=" O ASPS1 279 " (cutoff:3.500A) Processing helix chain 'S1' and resid 426 through 442 Proline residue: S1 442 - end of helix Processing helix chain 'S1' and resid 461 through 475 Processing helix chain 'S1' and resid 548 through 563 removed outlier: 3.803A pdb=" N ILES1 556 " --> pdb=" O VALS1 552 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYSS1 561 " --> pdb=" O GLNS1 557 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALAS1 562 " --> pdb=" O GLUS1 558 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLYS1 563 " --> pdb=" O GLNS1 559 " (cutoff:3.500A) Processing helix chain 'S1' and resid 588 through 608 removed outlier: 3.686A pdb=" N LYSS1 605 " --> pdb=" O LYSS1 601 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYSS1 608 " --> pdb=" O PHES1 604 " (cutoff:3.500A) Processing helix chain 'S1' and resid 623 through 638 removed outlier: 3.841A pdb=" N THRS1 627 " --> pdb=" O PROS1 623 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLYS1 628 " --> pdb=" O GLUS1 624 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASPS1 629 " --> pdb=" O GLUS1 625 " (cutoff:3.500A) Processing helix chain 'S1' and resid 658 through 663 removed outlier: 4.296A pdb=" N METS1 662 " --> pdb=" O PROS1 658 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHES1 663 " --> pdb=" O LEUS1 659 " (cutoff:3.500A) No H-bonds generated for 'chain 'S1' and resid 658 through 663' Processing helix chain 'S1' and resid 664 through 674 Processing helix chain 'S1' and resid 691 through 702 removed outlier: 4.372A pdb=" N GLNS1 695 " --> pdb=" O SERS1 691 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALAS1 696 " --> pdb=" O ASNS1 692 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILES1 698 " --> pdb=" O ALAS1 694 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLUS1 699 " --> pdb=" O GLNS1 695 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARGS1 701 " --> pdb=" O VALS1 697 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLYS1 702 " --> pdb=" O ILES1 698 " (cutoff:3.500A) Processing helix chain 'LC' and resid 5 through 16 removed outlier: 3.739A pdb=" N VALLC 10 " --> pdb=" O LYSLC 6 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASPLC 16 " --> pdb=" O ARGLC 12 " (cutoff:3.500A) Processing helix chain 'LC' and resid 23 through 34 removed outlier: 3.872A pdb=" N GLULC 32 " --> pdb=" O ALALC 28 " (cutoff:3.500A) Processing helix chain 'LC' and resid 84 through 91 removed outlier: 5.013A pdb=" N GLYLC 91 " --> pdb=" O ALALC 87 " (cutoff:3.500A) Processing helix chain 'LC' and resid 96 through 107 removed outlier: 6.299A pdb=" N LEULC 100 " --> pdb=" O GLYLC 96 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYSLC 105 " --> pdb=" O ALALC 101 " (cutoff:3.500A) Processing helix chain 'LC' and resid 117 through 125 removed outlier: 3.739A pdb=" N METLC 121 " --> pdb=" O SERLC 117 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VALLC 123 " --> pdb=" O ASPLC 119 " (cutoff:3.500A) Processing helix chain 'LC' and resid 148 through 159 Processing helix chain 'LC' and resid 181 through 199 Processing helix chain 'LM' and resid 1 through 12 removed outlier: 4.518A pdb=" N LYSLM 5 " --> pdb=" O SERLM 1 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEULM 7 " --> pdb=" O ILELM 3 " (cutoff:3.500A) Processing helix chain 'LM' and resid 103 through 108 removed outlier: 4.580A pdb=" N ARGLM 108 " --> pdb=" O GLYLM 104 " (cutoff:3.500A) Processing helix chain 'LM' and resid 96 through 102 removed outlier: 3.582A pdb=" N ARGLM 100 " --> pdb=" O TYRLM 97 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLULM 101 " --> pdb=" O TYRLM 98 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARGLM 102 " --> pdb=" O LEULM 99 " (cutoff:3.500A) Processing helix chain 'LN' and resid 9 through 14 removed outlier: 3.793A pdb=" N ARGLN 13 " --> pdb=" O SERLN 9 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N HISLN 14 " --> pdb=" O PROLN 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 9 through 14' Processing helix chain 'LN' and resid 130 through 135 removed outlier: 4.152A pdb=" N ILELN 134 " --> pdb=" O PROLN 130 " (cutoff:3.500A) Proline residue: LN 135 - end of helix No H-bonds generated for 'chain 'LN' and resid 130 through 135' Processing helix chain 'LN' and resid 206 through 214 removed outlier: 3.810A pdb=" N ALALN 210 " --> pdb=" O LYSLN 206 " (cutoff:3.500A) Processing helix chain 'LN' and resid 220 through 225 removed outlier: 4.011A pdb=" N METLN 224 " --> pdb=" O ARGLN 220 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASNLN 225 " --> pdb=" O GLYLN 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 220 through 225' Processing helix chain 'LN' and resid 259 through 267 removed outlier: 6.254A pdb=" N ASPLN 263 " --> pdb=" O ASNLN 259 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LYSLN 264 " --> pdb=" O LYSLN 260 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N PHELN 265 " --> pdb=" O ARGLN 261 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILELN 266 " --> pdb=" O THRLN 262 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VALLN 267 " --> pdb=" O ASPLN 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 259 through 267' Processing helix chain 'LO' and resid 5 through 21 removed outlier: 4.191A pdb=" N ALALO 11 " --> pdb=" O VALLO 7 " (cutoff:3.500A) Processing helix chain 'LO' and resid 25 through 30 removed outlier: 4.448A pdb=" N ARGLO 29 " --> pdb=" O GLYLO 25 " (cutoff:3.500A) Processing helix chain 'LO' and resid 35 through 56 removed outlier: 3.987A pdb=" N ARGLO 50 " --> pdb=" O TYRLO 46 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYSLO 53 " --> pdb=" O ARGLO 49 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARGLO 54 " --> pdb=" O ARGLO 50 " (cutoff:3.500A) Processing helix chain 'LO' and resid 58 through 72 Processing helix chain 'LO' and resid 74 through 85 Processing helix chain 'LO' and resid 94 through 101 removed outlier: 4.904A pdb=" N ALALO 98 " --> pdb=" O LEULO 94 " (cutoff:3.500A) Processing helix chain 'LO' and resid 102 through 116 removed outlier: 3.783A pdb=" N ALALO 107 " --> pdb=" O VALLO 103 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEULO 108 " --> pdb=" O ALALO 104 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 13 through 25 removed outlier: 3.631A pdb=" N LEULQ 19 " --> pdb=" O GLNLQ 15 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VALLQ 20 " --> pdb=" O LYSLQ 16 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEULQ 23 " --> pdb=" O LEULQ 19 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILELQ 24 " --> pdb=" O VALLQ 20 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARGLQ 25 " --> pdb=" O ALALQ 21 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 28 through 40 removed outlier: 3.621A pdb=" N ASPLQ 34 " --> pdb=" O SERLQ 30 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASNLQ 40 " --> pdb=" O LEULQ 36 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 41 through 61 removed outlier: 3.702A pdb=" N VALLQ 45 " --> pdb=" O LYSLQ 41 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASNLQ 61 " --> pdb=" O ASNLQ 57 " (cutoff:3.500A) Processing helix chain 'LR' and resid 4 through 9 removed outlier: 4.245A pdb=" N LYSLR 9 " --> pdb=" O GLULR 5 " (cutoff:3.500A) Processing helix chain 'LR' and resid 19 through 28 Processing helix chain 'LR' and resid 39 through 51 removed outlier: 3.743A pdb=" N GLNLR 48 " --> pdb=" O LYSLR 44 " (cutoff:3.500A) Processing helix chain 'LS' and resid 65 through 70 removed outlier: 3.821A pdb=" N VALLS 69 " --> pdb=" O GLNLS 65 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ALALS 70 " --> pdb=" O VALLS 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'LS' and resid 65 through 70' Processing helix chain 'LT' and resid 13 through 24 removed outlier: 3.563A pdb=" N ALALT 23 " --> pdb=" O ARGLT 19 " (cutoff:3.500A) Processing helix chain 'LT' and resid 43 through 52 removed outlier: 3.656A pdb=" N VALLT 47 " --> pdb=" O ASPLT 43 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASNLT 49 " --> pdb=" O ASPLT 45 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N METLT 50 " --> pdb=" O LYSLT 46 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLNLT 51 " --> pdb=" O VALLT 47 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALALT 52 " --> pdb=" O METLT 48 " (cutoff:3.500A) Processing helix chain 'LT' and resid 53 through 59 removed outlier: 4.277A pdb=" N TYRLT 57 " --> pdb=" O LYSLT 53 " (cutoff:3.500A) Processing helix chain 'LU' and resid 39 through 44 removed outlier: 6.958A pdb=" N LYSLU 43 " --> pdb=" O GLNLU 39 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHELU 44 " --> pdb=" O ARGLU 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'LU' and resid 39 through 44' Processing helix chain 'LV' and resid 51 through 62 Processing helix chain 'LV' and resid 63 through 74 Processing helix chain 'LD' and resid 4 through 21 removed outlier: 4.753A pdb=" N GLNLD 8 " --> pdb=" O LEULD 4 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VALLD 11 " --> pdb=" O LYSLD 7 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALALD 12 " --> pdb=" O GLNLD 8 " (cutoff:3.500A) Processing helix chain 'LD' and resid 33 through 48 removed outlier: 3.571A pdb=" N METLD 37 " --> pdb=" O THRLD 33 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEULD 40 " --> pdb=" O LYSLD 36 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLULD 46 " --> pdb=" O LYSLD 42 " (cutoff:3.500A) Processing helix chain 'LD' and resid 55 through 66 removed outlier: 3.546A pdb=" N THRLD 66 " --> pdb=" O ALALD 62 " (cutoff:3.500A) Processing helix chain 'LD' and resid 89 through 102 removed outlier: 3.892A pdb=" N ARGLD 93 " --> pdb=" O GLYLD 89 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHELD 95 " --> pdb=" O ALALD 91 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYSLD 100 " --> pdb=" O LYSLD 96 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALALD 101 " --> pdb=" O GLULD 97 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASNLD 102 " --> pdb=" O PHELD 98 " (cutoff:3.500A) Processing helix chain 'LD' and resid 119 through 127 removed outlier: 4.013A pdb=" N ASPLD 123 " --> pdb=" O ALALD 119 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARGLD 124 " --> pdb=" O SERLD 120 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEULD 125 " --> pdb=" O GLNLD 121 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THRLD 127 " --> pdb=" O ASPLD 123 " (cutoff:3.500A) Processing helix chain 'LD' and resid 130 through 147 removed outlier: 3.559A pdb=" N METLD 142 " --> pdb=" O LEULD 138 " (cutoff:3.500A) Processing helix chain 'LD' and resid 148 through 164 removed outlier: 3.714A pdb=" N ALALD 164 " --> pdb=" O ALALD 160 " (cutoff:3.500A) Processing helix chain 'LW' and resid 2 through 7 removed outlier: 4.729A pdb=" N LEULW 6 " --> pdb=" O LYSLW 2 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARGLW 7 " --> pdb=" O ALALW 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'LW' and resid 2 through 7' Processing helix chain 'LW' and resid 9 through 35 removed outlier: 4.170A pdb=" N LEULW 21 " --> pdb=" O GLULW 17 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLULW 24 " --> pdb=" O ASNLW 20 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLNLW 25 " --> pdb=" O LEULW 21 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N PHELW 26 " --> pdb=" O LEULW 22 " (cutoff:3.500A) Processing helix chain 'LW' and resid 39 through 57 removed outlier: 4.244A pdb=" N ARGLW 47 " --> pdb=" O LEULW 43 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VALLW 50 " --> pdb=" O VALLW 46 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEULW 57 " --> pdb=" O VALLW 53 " (cutoff:3.500A) Processing helix chain 'LX' and resid 56 through 61 removed outlier: 6.755A pdb=" N VALLX 60 " --> pdb=" O LYSLX 56 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THRLX 61 " --> pdb=" O ALALX 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'LX' and resid 56 through 61' Processing helix chain 'LX' and resid 62 through 72 removed outlier: 3.603A pdb=" N HISLX 67 " --> pdb=" O PROLX 63 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALALX 71 " --> pdb=" O HISLX 67 " (cutoff:3.500A) Processing helix chain 'LX' and resid 97 through 102 removed outlier: 4.675A pdb=" N PHELX 101 " --> pdb=" O SERLX 97 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALALX 102 " --> pdb=" O VALLX 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'LX' and resid 97 through 102' Processing helix chain 'LX' and resid 120 through 125 Processing helix chain 'LY' and resid 16 through 27 Processing helix chain 'LY' and resid 40 through 51 removed outlier: 4.340A pdb=" N METLY 46 " --> pdb=" O ALALY 42 " (cutoff:3.500A) Processing helix chain 'L1' and resid 8 through 18 removed outlier: 3.503A pdb=" N SERL1 17 " --> pdb=" O GLYL1 13 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N HISL1 18 " --> pdb=" O METL1 14 " (cutoff:3.500A) Processing helix chain 'L3' and resid 8 through 16 Processing helix chain 'L3' and resid 17 through 25 removed outlier: 4.409A pdb=" N ARGL3 21 " --> pdb=" O GLYL3 17 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N THRL3 24 " --> pdb=" O ALAL3 20 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LYSL3 25 " --> pdb=" O ARGL3 21 " (cutoff:3.500A) Processing helix chain 'L3' and resid 26 through 38 Processing helix chain 'L4' and resid 6 through 14 removed outlier: 3.551A pdb=" N LYSL4 11 " --> pdb=" O ARGL4 7 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARGL4 12 " --> pdb=" O GLYL4 8 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHEL4 13 " --> pdb=" O ALAL4 9 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYSL4 14 " --> pdb=" O ALAL4 10 " (cutoff:3.500A) Processing helix chain 'L4' and resid 36 through 45 Proline residue: L4 45 - end of helix Processing helix chain 'L4' and resid 51 through 62 removed outlier: 6.244A pdb=" N GLYL4 55 " --> pdb=" O LYSL4 51 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEUL4 56 " --> pdb=" O GLYL4 52 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALAL4 59 " --> pdb=" O GLYL4 55 " (cutoff:3.500A) Proline residue: L4 62 - end of helix Processing helix chain 'L6' and resid 15 through 20 Processing helix chain 'L6' and resid 24 through 41 removed outlier: 5.690A pdb=" N GLNL6 41 " --> pdb=" O ALAL6 37 " (cutoff:3.500A) Processing helix chain 'L6' and resid 97 through 116 removed outlier: 3.501A pdb=" N ASPL6 116 " --> pdb=" O LEUL6 112 " (cutoff:3.500A) Processing helix chain 'L6' and resid 130 through 142 removed outlier: 3.548A pdb=" N LEUL6 134 " --> pdb=" O LYSL6 130 " (cutoff:3.500A) Processing helix chain 'L6' and resid 154 through 162 removed outlier: 4.116A pdb=" N ALAL6 161 " --> pdb=" O LEUL6 157 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARGL6 162 " --> pdb=" O PHEL6 158 " (cutoff:3.500A) Processing helix chain 'L6' and resid 176 through 183 removed outlier: 4.850A pdb=" N PHEL6 183 " --> pdb=" O SERL6 179 " (cutoff:3.500A) Processing helix chain 'L6' and resid 189 through 201 Processing helix chain 'LE' and resid 19 through 24 Processing helix chain 'LE' and resid 25 through 31 Processing helix chain 'LE' and resid 33 through 46 removed outlier: 3.692A pdb=" N ALALE 43 " --> pdb=" O LYSLE 39 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYSLE 44 " --> pdb=" O ALALE 40 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THRLE 45 " --> pdb=" O PHELE 41 " (cutoff:3.500A) Processing helix chain 'LE' and resid 74 through 84 Processing helix chain 'LE' and resid 101 through 113 Processing helix chain 'LE' and resid 120 through 136 removed outlier: 3.603A pdb=" N GLYLE 130 " --> pdb=" O ARGLE 126 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THRLE 131 " --> pdb=" O SERLE 127 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLYLE 136 " --> pdb=" O ALALE 132 " (cutoff:3.500A) Processing helix chain 'LE' and resid 91 through 96 removed outlier: 3.918A pdb=" N LYSLE 96 " --> pdb=" O LYSLE 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 91 through 96' Processing helix chain 'L7' and resid 1 through 20 removed outlier: 3.896A pdb=" N ASPL7 5 " --> pdb=" O ALAL7 1 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VALL7 12 " --> pdb=" O LYSL7 8 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYSL7 13 " --> pdb=" O ASPL7 9 " (cutoff:3.500A) Processing helix chain 'L7' and resid 46 through 61 removed outlier: 5.347A pdb=" N ASPL7 50 " --> pdb=" O LYSL7 46 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALAL7 54 " --> pdb=" O ASPL7 50 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALAL7 58 " --> pdb=" O ALAL7 54 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILEL7 59 " --> pdb=" O ASPL7 55 " (cutoff:3.500A) Processing helix chain 'L7' and resid 92 through 111 removed outlier: 4.475A pdb=" N ILEL7 103 " --> pdb=" O PHEL7 99 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THRL7 104 " --> pdb=" O GLUL7 100 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ALAL7 106 " --> pdb=" O LEUL7 102 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VALL7 107 " --> pdb=" O ILEL7 103 " (cutoff:3.500A) Proline residue: L7 108 - end of helix removed outlier: 5.655A pdb=" N ARGL7 111 " --> pdb=" O VALL7 107 " (cutoff:3.500A) Processing helix chain 'L7' and resid 161 through 172 removed outlier: 3.876A pdb=" N ALAL7 167 " --> pdb=" O GLUL7 163 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEUL7 168 " --> pdb=" O GLUL7 164 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEUL7 169 " --> pdb=" O GLYL7 165 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALAL7 170 " --> pdb=" O ARGL7 166 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHEL7 172 " --> pdb=" O LEUL7 168 " (cutoff:3.500A) Processing helix chain 'L8' and resid 1 through 7 removed outlier: 4.702A pdb=" N LYSL8 5 " --> pdb=" O SERL8 1 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALAL8 6 " --> pdb=" O ARGL8 2 " (cutoff:3.500A) Proline residue: L8 7 - end of helix No H-bonds generated for 'chain 'L8' and resid 1 through 7' Processing helix chain 'L8' and resid 58 through 80 removed outlier: 5.030A pdb=" N ALAL8 62 " --> pdb=" O ALAL8 58 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLNL8 63 " --> pdb=" O ASPL8 59 " (cutoff:3.500A) Processing helix chain 'L8' and resid 136 through 152 removed outlier: 3.928A pdb=" N TYRL8 150 " --> pdb=" O ASPL8 146 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARGL8 151 " --> pdb=" O LEUL8 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARGL8 152 " --> pdb=" O ARGL8 148 " (cutoff:3.500A) Processing helix chain 'L9' and resid 22 through 29 removed outlier: 4.320A pdb=" N ALAL9 26 " --> pdb=" O LYSL9 22 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARGL9 27 " --> pdb=" O ALAL9 23 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASNL9 28 " --> pdb=" O GLYL9 24 " (cutoff:3.500A) Processing helix chain 'L9' and resid 40 through 51 removed outlier: 5.491A pdb=" N GLUL9 45 " --> pdb=" O LYSL9 41 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N PHEL9 46 " --> pdb=" O LYSL9 42 " (cutoff:3.500A) Processing helix chain 'L9' and resid 52 through 73 removed outlier: 4.578A pdb=" N LEUL9 62 " --> pdb=" O LEUL9 58 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALAL9 63 " --> pdb=" O ALAL9 59 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALAL9 64 " --> pdb=" O GLUL9 60 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALAL9 65 " --> pdb=" O VALL9 61 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALAL9 67 " --> pdb=" O ALAL9 63 " (cutoff:3.500A) Processing helix chain 'L9' and resid 97 through 107 removed outlier: 4.711A pdb=" N ASPL9 101 " --> pdb=" O ARGL9 97 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALAL9 102 " --> pdb=" O ASPL9 98 " (cutoff:3.500A) Processing helix chain 'L9' and resid 117 through 122 removed outlier: 4.055A pdb=" N VALL9 121 " --> pdb=" O LEUL9 117 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEUL9 122 " --> pdb=" O PROL9 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'L9' and resid 117 through 122' Processing helix chain 'LF' and resid 24 through 38 removed outlier: 3.517A pdb=" N GLULF 31 " --> pdb=" O ARGLF 27 " (cutoff:3.500A) Processing helix chain 'LF' and resid 58 through 63 removed outlier: 4.530A pdb=" N VALLF 62 " --> pdb=" O ASNLF 58 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALALF 63 " --> pdb=" O ALALF 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'LF' and resid 58 through 63' Processing helix chain 'LF' and resid 88 through 96 Processing helix chain 'LF' and resid 97 through 110 removed outlier: 3.941A pdb=" N ILELF 101 " --> pdb=" O PROLF 97 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLYLF 107 " --> pdb=" O ILELF 103 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N METLF 108 " --> pdb=" O ALALF 104 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEULF 109 " --> pdb=" O VALLF 105 " (cutoff:3.500A) Proline residue: LF 110 - end of helix Processing helix chain 'LF' and resid 112 through 123 removed outlier: 3.856A pdb=" N LYSLF 121 " --> pdb=" O ALALF 117 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEULF 122 " --> pdb=" O METLF 118 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYSLF 123 " --> pdb=" O PHELF 119 " (cutoff:3.500A) Processing helix chain 'LG' and resid 112 through 117 removed outlier: 6.281A pdb=" N SERLG 117 " --> pdb=" O METLG 113 " (cutoff:3.500A) Processing helix chain 'LH' and resid 1 through 6 removed outlier: 4.868A pdb=" N THRLH 5 " --> pdb=" O METLH 1 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEULH 6 " --> pdb=" O ARGLH 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'LH' and resid 1 through 6' Processing helix chain 'LH' and resid 37 through 42 removed outlier: 3.779A pdb=" N ARGLH 41 " --> pdb=" O GLYLH 37 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N SERLH 42 " --> pdb=" O GLNLH 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'LH' and resid 37 through 42' Processing helix chain 'LH' and resid 56 through 62 Proline residue: LH 62 - end of helix Processing helix chain 'LH' and resid 68 through 75 removed outlier: 4.434A pdb=" N ALALH 72 " --> pdb=" O SERLH 68 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILELH 73 " --> pdb=" O ARGLH 69 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ALALH 75 " --> pdb=" O ALALH 71 " (cutoff:3.500A) Processing helix chain 'LH' and resid 78 through 85 removed outlier: 3.549A pdb=" N VALLH 85 " --> pdb=" O ASPLH 81 " (cutoff:3.500A) Processing helix chain 'LH' and resid 91 through 99 removed outlier: 3.549A pdb=" N LYSLH 96 " --> pdb=" O LEULH 92 " (cutoff:3.500A) Processing helix chain 'LH' and resid 128 through 139 removed outlier: 3.557A pdb=" N ALALH 133 " --> pdb=" O LYSLH 129 " (cutoff:3.500A) Processing helix chain 'LI' and resid 42 through 58 removed outlier: 5.970A pdb=" N ILELI 46 " --> pdb=" O THRLI 42 " (cutoff:3.500A) Processing helix chain 'LI' and resid 109 through 125 removed outlier: 3.797A pdb=" N LYSLI 123 " --> pdb=" O LEULI 119 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEULI 124 " --> pdb=" O ALALI 120 " (cutoff:3.500A) Proline residue: LI 125 - end of helix Processing helix chain 'LJ' and resid 13 through 32 Processing helix chain 'LJ' and resid 38 through 57 removed outlier: 3.569A pdb=" N GLULJ 49 " --> pdb=" O ARGLJ 45 " (cutoff:3.500A) Proline residue: LJ 50 - end of helix removed outlier: 4.373A pdb=" N THRLJ 57 " --> pdb=" O THRLJ 53 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 59 through 71 removed outlier: 3.836A pdb=" N ARGLJ 71 " --> pdb=" O PHELJ 67 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 72 through 81 removed outlier: 3.563A pdb=" N VALLJ 76 " --> pdb=" O ASPLJ 72 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHELJ 80 " --> pdb=" O VALLJ 76 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASNLJ 81 " --> pdb=" O ALALJ 77 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 82 through 88 removed outlier: 4.194A pdb=" N ARGLJ 86 " --> pdb=" O GLULJ 82 " (cutoff:3.500A) Processing helix chain 'LK' and resid 1 through 20 removed outlier: 4.549A pdb=" N SERLK 5 " --> pdb=" O METLK 1 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARGLK 9 " --> pdb=" O SERLK 5 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ARGLK 13 " --> pdb=" O ARGLK 9 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALALK 14 " --> pdb=" O ARGLK 10 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYSLK 17 " --> pdb=" O ARGLK 13 " (cutoff:3.500A) Processing helix chain 'LK' and resid 67 through 86 removed outlier: 4.202A pdb=" N GLULK 80 " --> pdb=" O LYSLK 76 " (cutoff:3.500A) Processing helix chain 'LK' and resid 101 through 114 Processing helix chain 'LZ' and resid 8 through 14 Processing helix chain 'LZ' and resid 41 through 46 removed outlier: 7.216A pdb=" N GLYLZ 46 " --> pdb=" O PROLZ 42 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 28 through 33 removed outlier: 6.340A pdb=" N ASPLZ 31 " --> pdb=" O VALLZ 28 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEULZ 32 " --> pdb=" O GLYLZ 29 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASNLZ 33 " --> pdb=" O HISLZ 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'LZ' and resid 28 through 33' Processing sheet with id= 1, first strand: chain 'SJ' and resid 39 through 42 removed outlier: 4.497A pdb=" N LEUSJ 71 " --> pdb=" O LEUSJ 42 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILESJ 8 " --> pdb=" O VALSJ 74 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILESJ 76 " --> pdb=" O ILESJ 6 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILESJ 6 " --> pdb=" O ILESJ 76 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ARGSJ 7 " --> pdb=" O SERSJ 101 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SERSJ 101 " --> pdb=" O ARGSJ 7 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'SJ' and resid 44 through 52 Processing sheet with id= 3, first strand: chain 'SK' and resid 41 through 44 removed outlier: 3.611A pdb=" N GLYSK 42 " --> pdb=" O ILESK 33 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASNSK 28 " --> pdb=" O SERSK 25 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VALSK 83 " --> pdb=" O THRSK 107 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'SK' and resid 83 through 87 removed outlier: 7.151A pdb=" N GLYSK 87 " --> pdb=" O VALSK 112 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'SL' and resid 28 through 31 removed outlier: 5.087A pdb=" N LEUSL 80 " --> pdb=" O VALSL 97 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'SL' and resid 35 through 40 removed outlier: 5.133A pdb=" N LYSSL 50 " --> pdb=" O ILESL 66 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'SP' and resid 4 through 10 removed outlier: 3.757A pdb=" N GLYSP 37 " --> pdb=" O VALSP 19 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLYSP 49 " --> pdb=" O ASNSP 40 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'SQ' and resid 6 through 10 removed outlier: 6.716A pdb=" N GLUSQ 59 " --> pdb=" O VALSQ 75 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'SQ' and resid 18 through 29 No H-bonds generated for sheet with id= 9 Processing sheet with id= 10, first strand: chain 'SS' and resid 29 through 32 removed outlier: 4.537A pdb=" N LEUSS 46 " --> pdb=" O VALSS 61 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLNSS 55 " --> pdb=" O ASNSS 52 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'SB' and resid 88 through 91 removed outlier: 5.906A pdb=" N GLYSB 70 " --> pdb=" O VALSB 91 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHESB 197 " --> pdb=" O VALSB 182 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'SC' and resid 53 through 58 removed outlier: 3.548A pdb=" N ARGSC 53 " --> pdb=" O HISSC 68 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'SC' and resid 163 through 169 Processing sheet with id= 14, first strand: chain 'SD' and resid 140 through 143 removed outlier: 3.794A pdb=" N ASPSD 140 " --> pdb=" O PHESD 181 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'SE' and resid 11 through 15 removed outlier: 4.226A pdb=" N GLYSE 39 " --> pdb=" O GLNSE 11 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYSSE 13 " --> pdb=" O VALSE 37 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEUSE 35 " --> pdb=" O ILESE 15 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALASE 16 " --> pdb=" O LEUSE 35 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'SE' and resid 83 through 87 Processing sheet with id= 17, first strand: chain 'SE' and resid 32 through 39 Processing sheet with id= 18, first strand: chain 'SF' and resid 34 through 37 removed outlier: 6.554A pdb=" N ASNSF 63 " --> pdb=" O HISSF 37 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARGSF 86 " --> pdb=" O METSF 9 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'SF' and resid 38 through 42 removed outlier: 3.699A pdb=" N ARGSF 38 " --> pdb=" O ASNSF 63 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYRSF 59 " --> pdb=" O TRPSF 42 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'SF' and resid 43 through 46 removed outlier: 3.633A pdb=" N GLYSF 43 " --> pdb=" O TYRSF 59 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'SG' and resid 71 through 76 removed outlier: 6.634A pdb=" N THRSG 71 " --> pdb=" O VALSG 90 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'SH' and resid 22 through 28 removed outlier: 6.377A pdb=" N ALASH 22 " --> pdb=" O LEUSH 62 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SERSH 28 " --> pdb=" O PROSH 56 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASPSH 47 " --> pdb=" O THRSH 61 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'SH' and resid 73 through 76 removed outlier: 3.757A pdb=" N CYSSH 126 " --> pdb=" O VALSH 102 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VALSH 102 " --> pdb=" O ILESH 125 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'SI' and resid 4 through 10 removed outlier: 5.417A pdb=" N LYSSI 59 " --> pdb=" O GLYSI 23 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYSSI 26 " --> pdb=" O LEUSI 60 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'S1' and resid 64 through 70 removed outlier: 4.993A pdb=" N ALAS1 16 " --> pdb=" O THRS1 88 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARGS1 136 " --> pdb=" O ILES1 260 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEUS1 262 " --> pdb=" O ARGS1 136 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N CYSS1 265 " --> pdb=" O LEUS1 168 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'S1' and resid 169 through 172 removed outlier: 3.712A pdb=" N GLYS1 180 " --> pdb=" O ILES1 172 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'S1' and resid 294 through 297 removed outlier: 3.892A pdb=" N ILES1 294 " --> pdb=" O ARGS1 308 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'S1' and resid 322 through 326 removed outlier: 3.926A pdb=" N ASPS1 326 " --> pdb=" O GLYS1 330 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHES1 334 " --> pdb=" O PHES1 321 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHES1 316 " --> pdb=" O ASPS1 398 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASPS1 394 " --> pdb=" O ALAS1 320 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'S1' and resid 340 through 343 removed outlier: 7.838A pdb=" N GLYS1 340 " --> pdb=" O ALAS1 378 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'S1' and resid 347 through 350 Processing sheet with id= 31, first strand: chain 'S1' and resid 369 through 372 removed outlier: 3.552A pdb=" N ARGS1 361 " --> pdb=" O ILES1 385 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'S1' and resid 444 through 449 removed outlier: 5.080A pdb=" N GLNS1 454 " --> pdb=" O ASPS1 449 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THRS1 455 " --> pdb=" O VALS1 419 " (cutoff:3.500A) removed outlier: 9.933A pdb=" N SERS1 416 " --> pdb=" O PROS1 485 " (cutoff:3.500A) removed outlier: 36.943A pdb=" N ALAS1 480 " --> pdb=" O THRS1 622 " (cutoff:3.500A) removed outlier: 32.811A pdb=" N THRS1 622 " --> pdb=" O ALAS1 480 " (cutoff:3.500A) removed outlier: 29.675A pdb=" N VALS1 482 " --> pdb=" O VALS1 620 " (cutoff:3.500A) removed outlier: 26.048A pdb=" N VALS1 620 " --> pdb=" O VALS1 482 " (cutoff:3.500A) removed outlier: 21.849A pdb=" N LYSS1 484 " --> pdb=" O VALS1 618 " (cutoff:3.500A) removed outlier: 20.185A pdb=" N VALS1 618 " --> pdb=" O LYSS1 484 " (cutoff:3.500A) removed outlier: 17.201A pdb=" N GLNS1 486 " --> pdb=" O METS1 616 " (cutoff:3.500A) removed outlier: 12.457A pdb=" N METS1 616 " --> pdb=" O GLNS1 486 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ALAS1 488 " --> pdb=" O PROS1 614 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'S1' and resid 497 through 506 removed outlier: 4.814A pdb=" N GLYS1 515 " --> pdb=" O HISS1 504 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYSS1 506 " --> pdb=" O GLNS1 513 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLNS1 513 " --> pdb=" O LYSS1 506 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VALS1 518 " --> pdb=" O HISS1 578 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'S1' and resid 332 through 337 removed outlier: 3.970A pdb=" N ASPS1 380 " --> pdb=" O VALS1 337 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S1' and resid 616 through 622 Processing sheet with id= 36, first strand: chain 'S1' and resid 612 through 616 No H-bonds generated for sheet with id= 36 Processing sheet with id= 37, first strand: chain 'LC' and resid 17 through 22 removed outlier: 6.554A pdb=" N GLYLC 221 " --> pdb=" O ALALC 17 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LYSLC 19 " --> pdb=" O GLYLC 221 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALALC 223 " --> pdb=" O LYSLC 19 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASPLC 225 " --> pdb=" O TYRLC 21 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALALC 220 " --> pdb=" O THRLC 216 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VALLC 212 " --> pdb=" O VALLC 224 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYSLC 211 " --> pdb=" O ASNLC 47 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VALLC 42 " --> pdb=" O ILELC 175 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLYLC 169 " --> pdb=" O LEULC 48 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'LC' and resid 60 through 64 Processing sheet with id= 39, first strand: chain 'LC' and resid 74 through 78 removed outlier: 4.667A pdb=" N VALLC 113 " --> pdb=" O ARGLC 74 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'LM' and resid 67 through 75 removed outlier: 4.185A pdb=" N GLULM 67 " --> pdb=" O SERLM 64 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N SERLM 56 " --> pdb=" O THRLM 75 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THRLM 59 " --> pdb=" O ILELM 47 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILELM 63 " --> pdb=" O GLULM 43 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N GLULM 43 " --> pdb=" O ILELM 63 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLYLM 44 " --> pdb=" O VALLM 25 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VALLM 25 " --> pdb=" O GLYLM 44 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'LN' and resid 32 through 35 No H-bonds generated for sheet with id= 41 Processing sheet with id= 42, first strand: chain 'LN' and resid 79 through 82 removed outlier: 3.835A pdb=" N ARGLN 79 " --> pdb=" O LEULN 92 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEULN 92 " --> pdb=" O GLULN 78 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEULN 94 " --> pdb=" O VALLN 76 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VALLN 77 " --> pdb=" O ALALN 111 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ALALN 111 " --> pdb=" O VALLN 77 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'LN' and resid 126 through 129 removed outlier: 4.829A pdb=" N ASNLN 127 " --> pdb=" O LEULN 191 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEULN 191 " --> pdb=" O ASNLN 127 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'LN' and resid 137 through 141 removed outlier: 3.807A pdb=" N SERLN 138 " --> pdb=" O ILELN 163 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VALLN 140 " --> pdb=" O VALLN 161 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THRLN 172 " --> pdb=" O VALLN 164 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ALALN 169 " --> pdb=" O ALALN 185 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLULN 179 " --> pdb=" O LEULN 175 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'LN' and resid 90 through 95 removed outlier: 5.964A pdb=" N ARGLN 101 " --> pdb=" O VALLN 93 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLULN 99 " --> pdb=" O TYRLN 95 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'LP' and resid 11 through 15 removed outlier: 5.501A pdb=" N TYRLP 2 " --> pdb=" O ALALP 42 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'LP' and resid 18 through 23 removed outlier: 4.288A pdb=" N GLNLP 18 " --> pdb=" O ILELP 98 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASPLP 95 " --> pdb=" O VALLP 64 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LYSLP 60 " --> pdb=" O THRLP 99 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLULP 31 " --> pdb=" O VALLP 63 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'LP' and resid 65 through 68 Processing sheet with id= 49, first strand: chain 'LP' and resid 71 through 78 removed outlier: 4.163A pdb=" N TYRLP 83 " --> pdb=" O ARGLP 78 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'LQ' and resid 2 through 8 removed outlier: 6.803A pdb=" N VALLQ 106 " --> pdb=" O THRLQ 72 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'LQ' and resid 73 through 78 Processing sheet with id= 52, first strand: chain 'LR' and resid 29 through 34 removed outlier: 6.185A pdb=" N LYSLR 81 " --> pdb=" O VALLR 34 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARGLR 73 " --> pdb=" O HISLR 70 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N HISLR 70 " --> pdb=" O ARGLR 73 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLYLR 75 " --> pdb=" O LYSLR 68 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARGLR 77 " --> pdb=" O LYSLR 66 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYSLR 66 " --> pdb=" O ARGLR 77 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASPLR 79 " --> pdb=" O LYSLR 64 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LYSLR 64 " --> pdb=" O ASPLR 79 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYSLR 81 " --> pdb=" O VALLR 62 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VALLR 62 " --> pdb=" O LYSLR 81 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALALR 83 " --> pdb=" O THRLR 60 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THRLR 60 " --> pdb=" O ALALR 83 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VALLR 85 " --> pdb=" O VALLR 58 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VALLR 58 " --> pdb=" O VALLR 85 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'LS' and resid 39 through 45 removed outlier: 5.168A pdb=" N ASNLS 39 " --> pdb=" O ALALS 62 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'LS' and resid 82 through 85 removed outlier: 3.868A pdb=" N ARGLS 85 " --> pdb=" O VALLS 92 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VALLS 92 " --> pdb=" O ARGLS 85 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'LT' and resid 2 through 6 removed outlier: 4.656A pdb=" N PHELT 2 " --> pdb=" O VALLT 60 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILELT 63 " --> pdb=" O ILELT 70 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'LT' and resid 34 through 42 removed outlier: 6.032A pdb=" N GLYLT 33 " --> pdb=" O LYSLT 34 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ALALT 36 " --> pdb=" O TYRLT 31 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYRLT 31 " --> pdb=" O ALALT 36 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEULT 38 " --> pdb=" O ILELT 29 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILELT 29 " --> pdb=" O LEULT 38 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILELT 40 " --> pdb=" O PROLT 27 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEULT 42 " --> pdb=" O LYSLT 25 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYSLT 25 " --> pdb=" O LEULT 42 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLNLT 87 " --> pdb=" O LYSLT 25 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLYLT 33 " --> pdb=" O ARGLT 93 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASPLT 76 " --> pdb=" O ASPLT 90 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'LU' and resid 63 through 70 No H-bonds generated for sheet with id= 57 Processing sheet with id= 58, first strand: chain 'LV' and resid 10 through 17 No H-bonds generated for sheet with id= 58 Processing sheet with id= 59, first strand: chain 'LV' and resid 33 through 40 Processing sheet with id= 60, first strand: chain 'LD' and resid 49 through 53 removed outlier: 4.150A pdb=" N SERLD 23 " --> pdb=" O SERLD 84 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'LX' and resid 3 through 9 removed outlier: 3.963A pdb=" N SERLX 199 " --> pdb=" O LYSLX 8 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASPLX 200 " --> pdb=" O THRLX 112 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N THRLX 112 " --> pdb=" O ASPLX 200 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VALLX 109 " --> pdb=" O VALLX 172 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VALLX 170 " --> pdb=" O GLYLX 111 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'LX' and resid 10 through 16 removed outlier: 4.268A pdb=" N VALLX 20 " --> pdb=" O THRLX 16 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'LX' and resid 32 through 35 removed outlier: 6.663A pdb=" N GLNLX 49 " --> pdb=" O THRLX 35 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'LX' and resid 46 through 51 removed outlier: 5.260A pdb=" N ARGLX 46 " --> pdb=" O LEULX 84 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'LY' and resid 33 through 38 removed outlier: 4.787A pdb=" N HISLY 33 " --> pdb=" O GLNLY 8 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLNLY 8 " --> pdb=" O HISLY 33 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N METLY 53 " --> pdb=" O THRLY 9 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'L2' and resid 18 through 23 removed outlier: 6.186A pdb=" N HISL2 18 " --> pdb=" O SERL2 12 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILEL2 47 " --> pdb=" O SERL2 13 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEUL2 35 " --> pdb=" O TYRL2 48 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'L4' and resid 21 through 24 removed outlier: 5.501A pdb=" N PHEL4 21 " --> pdb=" O VALL4 49 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'L5' and resid 14 through 19 Processing sheet with id= 69, first strand: chain 'L6' and resid 1 through 5 removed outlier: 6.499A pdb=" N LEUL6 3 " --> pdb=" O LEUL6 12 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SERL6 10 " --> pdb=" O LEUL6 5 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'L6' and resid 117 through 120 removed outlier: 5.732A pdb=" N ARGL6 117 " --> pdb=" O ASPL6 184 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYSL6 185 " --> pdb=" O ASPL6 145 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VALL6 146 " --> pdb=" O LYSL6 166 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'LE' and resid 7 through 12 removed outlier: 3.617A pdb=" N LYSLE 71 " --> pdb=" O PROLE 55 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'L7' and resid 28 through 31 removed outlier: 3.762A pdb=" N THRL7 156 " --> pdb=" O GLUL7 31 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASNL7 36 " --> pdb=" O ASPL7 152 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N THRL7 154 " --> pdb=" O THRL7 34 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LYSL7 32 " --> pdb=" O THRL7 156 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEUL7 35 " --> pdb=" O VALL7 88 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VALL7 88 " --> pdb=" O LEUL7 35 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N METL7 37 " --> pdb=" O CYSL7 86 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N CYSL7 86 " --> pdb=" O METL7 37 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N TYRL7 82 " --> pdb=" O ALAL7 69 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N THRL7 67 " --> pdb=" O ILEL7 84 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N CYSL7 86 " --> pdb=" O LEUL7 65 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'L7' and resid 126 through 131 Processing sheet with id= 74, first strand: chain 'L8' and resid 14 through 18 removed outlier: 6.248A pdb=" N GLYL8 27 " --> pdb=" O GLUL8 31 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLUL8 31 " --> pdb=" O GLYL8 27 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'L8' and resid 40 through 44 Processing sheet with id= 76, first strand: chain 'L8' and resid 84 through 88 removed outlier: 4.074A pdb=" N LYSL8 84 " --> pdb=" O LEUL8 132 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N THRL8 128 " --> pdb=" O LEUL8 88 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLUL8 129 " --> pdb=" O PROL8 125 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'L8' and resid 94 through 97 Processing sheet with id= 78, first strand: chain 'L9' and resid 3 through 6 removed outlier: 6.034A pdb=" N LYSL9 35 " --> pdb=" O LEUL9 6 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'L9' and resid 77 through 82 Processing sheet with id= 80, first strand: chain 'LF' and resid 15 through 18 Processing sheet with id= 81, first strand: chain 'LG' and resid 56 through 60 removed outlier: 4.644A pdb=" N ASPLG 56 " --> pdb=" O ILELG 43 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYSLG 40 " --> pdb=" O ILELG 22 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THRLG 6 " --> pdb=" O CYSLG 21 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASNLG 82 " --> pdb=" O METLG 7 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLYLG 81 " --> pdb=" O LYSLG 66 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'LI' and resid 99 through 102 removed outlier: 3.927A pdb=" N LYSLI 100 " --> pdb=" O ALALI 35 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEULI 33 " --> pdb=" O LEULI 102 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N SERLI 30 " --> pdb=" O LYSLI 133 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYSLI 127 " --> pdb=" O VALLI 36 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'LJ' and resid 33 through 37 removed outlier: 5.928A pdb=" N ALALJ 108 " --> pdb=" O PHELJ 102 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHELJ 102 " --> pdb=" O ALALJ 108 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N METLJ 110 " --> pdb=" O CYSLJ 100 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'LK' and resid 48 through 53 removed outlier: 6.086A pdb=" N ILELK 35 " --> pdb=" O THRLK 53 " (cutoff:3.500A) 2186 hydrogen bonds defined for protein. 6453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3658 hydrogen bonds 5936 hydrogen bond angles 0 basepair planarities 1461 basepair parallelities 2269 stacking parallelities Total time for adding SS restraints: 254.41 Time building geometry restraints manager: 63.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 27140 1.33 - 1.46: 74445 1.46 - 1.59: 65619 1.59 - 1.72: 2061 1.72 - 1.84: 355 Bond restraints: 169620 Sorted by residual: bond pdb=" O3B GTPS1 801 " pdb=" PB GTPS1 801 " ideal model delta sigma weight residual 1.610 1.808 -0.198 2.00e-02 2.50e+03 9.84e+01 bond pdb=" O3' ULA2571 " pdb=" P ALA2572 " ideal model delta sigma weight residual 1.607 1.485 0.122 1.50e-02 4.44e+03 6.60e+01 bond pdb=" O3B GTPS1 801 " pdb=" PG GTPS1 801 " ideal model delta sigma weight residual 1.610 1.763 -0.153 2.00e-02 2.50e+03 5.89e+01 bond pdb=" CA PHEL3 18 " pdb=" C PHEL3 18 " ideal model delta sigma weight residual 1.524 1.473 0.052 7.00e-03 2.04e+04 5.50e+01 bond pdb=" O3' ASA 51 " pdb=" P CSA 52 " ideal model delta sigma weight residual 1.607 1.498 0.109 1.50e-02 4.44e+03 5.32e+01 ... (remaining 169615 not shown) Histogram of bond angle deviations from ideal: 85.96 - 98.94: 1353 98.94 - 111.92: 102498 111.92 - 124.90: 127420 124.90 - 137.89: 21072 137.89 - 150.87: 29 Bond angle restraints: 252372 Sorted by residual: angle pdb=" C3' ALA1900 " pdb=" O3' ALA1900 " pdb=" P ALA1901 " ideal model delta sigma weight residual 120.20 150.87 -30.67 1.50e+00 4.44e-01 4.18e+02 angle pdb=" C3' ASA 51 " pdb=" O3' ASA 51 " pdb=" P CSA 52 " ideal model delta sigma weight residual 120.20 149.97 -29.77 1.50e+00 4.44e-01 3.94e+02 angle pdb=" P CSA 810 " pdb=" O5' CSA 810 " pdb=" C5' CSA 810 " ideal model delta sigma weight residual 120.90 146.90 -26.00 1.50e+00 4.44e-01 3.01e+02 angle pdb=" C3' ALA1420 " pdb=" O3' ALA1420 " pdb=" P GLA1421 " ideal model delta sigma weight residual 120.20 142.71 -22.51 1.50e+00 4.44e-01 2.25e+02 angle pdb=" P ULA1409 " pdb=" O5' ULA1409 " pdb=" C5' ULA1409 " ideal model delta sigma weight residual 120.90 143.26 -22.36 1.50e+00 4.44e-01 2.22e+02 ... (remaining 252367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 87265 35.98 - 71.97: 3630 71.97 - 107.95: 392 107.95 - 143.93: 66 143.93 - 179.92: 130 Dihedral angle restraints: 91483 sinusoidal: 71175 harmonic: 20308 Sorted by residual: dihedral pdb=" C5' USA1498 " pdb=" C4' USA1498 " pdb=" C3' USA1498 " pdb=" O3' USA1498 " ideal model delta sinusoidal sigma weight residual 82.00 -140.61 -137.39 1 8.00e+00 1.56e-02 2.60e+02 dihedral pdb=" CA VALS1 585 " pdb=" C VALS1 585 " pdb=" N ASPS1 586 " pdb=" CA ASPS1 586 " ideal model delta harmonic sigma weight residual -180.00 -115.57 -64.43 0 5.00e+00 4.00e-02 1.66e+02 dihedral pdb=" C5' ALA2448 " pdb=" C4' ALA2448 " pdb=" C3' ALA2448 " pdb=" O3' ALA2448 " ideal model delta sinusoidal sigma weight residual 147.00 63.08 83.92 1 8.00e+00 1.56e-02 1.34e+02 ... (remaining 91480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.037: 32044 1.037 - 2.074: 2 2.074 - 3.111: 1 3.111 - 4.148: 0 4.148 - 5.185: 2 Chirality restraints: 32049 Sorted by residual: chirality pdb=" C4' USA1498 " pdb=" C5' USA1498 " pdb=" O4' USA1498 " pdb=" C3' USA1498 " both_signs ideal model delta sigma weight residual False -2.50 2.69 -5.19 2.00e-01 2.50e+01 6.72e+02 chirality pdb=" C3' USA1498 " pdb=" C4' USA1498 " pdb=" O3' USA1498 " pdb=" C2' USA1498 " both_signs ideal model delta sigma weight residual False -2.48 2.63 -5.11 2.00e-01 2.50e+01 6.52e+02 chirality pdb=" C1' GLA2251 " pdb=" O4' GLA2251 " pdb=" C2' GLA2251 " pdb=" N9 GLA2251 " both_signs ideal model delta sigma weight residual False 2.46 0.06 2.39 2.00e-01 2.50e+01 1.43e+02 ... (remaining 32046 not shown) Planarity restraints: 14531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GLA2445 " -0.785 2.00e-02 2.50e+03 4.01e-01 4.83e+03 pdb=" N9 GLA2445 " -0.126 2.00e-02 2.50e+03 pdb=" C8 GLA2445 " -0.079 2.00e-02 2.50e+03 pdb=" N7 GLA2445 " 0.346 2.00e-02 2.50e+03 pdb=" C5 GLA2445 " 0.474 2.00e-02 2.50e+03 pdb=" C6 GLA2445 " -0.141 2.00e-02 2.50e+03 pdb=" O6 GLA2445 " -0.453 2.00e-02 2.50e+03 pdb=" N1 GLA2445 " -0.354 2.00e-02 2.50e+03 pdb=" C2 GLA2445 " 0.054 2.00e-02 2.50e+03 pdb=" N2 GLA2445 " -0.025 2.00e-02 2.50e+03 pdb=" N3 GLA2445 " 0.572 2.00e-02 2.50e+03 pdb=" C4 GLA2445 " 0.516 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GLA 745 " -0.549 2.00e-02 2.50e+03 2.96e-01 2.63e+03 pdb=" N9 GLA 745 " -0.113 2.00e-02 2.50e+03 pdb=" C8 GLA 745 " -0.031 2.00e-02 2.50e+03 pdb=" N7 GLA 745 " 0.223 2.00e-02 2.50e+03 pdb=" C5 GLA 745 " 0.332 2.00e-02 2.50e+03 pdb=" C6 GLA 745 " -0.100 2.00e-02 2.50e+03 pdb=" O6 GLA 745 " -0.288 2.00e-02 2.50e+03 pdb=" N1 GLA 745 " -0.309 2.00e-02 2.50e+03 pdb=" C2 GLA 745 " 0.050 2.00e-02 2.50e+03 pdb=" N2 GLA 745 " -0.075 2.00e-02 2.50e+03 pdb=" N3 GLA 745 " 0.505 2.00e-02 2.50e+03 pdb=" C4 GLA 745 " 0.355 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GSA 730 " -0.375 2.00e-02 2.50e+03 2.52e-01 1.91e+03 pdb=" N9 GSA 730 " -0.018 2.00e-02 2.50e+03 pdb=" C8 GSA 730 " 0.019 2.00e-02 2.50e+03 pdb=" N7 GSA 730 " 0.242 2.00e-02 2.50e+03 pdb=" C5 GSA 730 " 0.261 2.00e-02 2.50e+03 pdb=" C6 GSA 730 " -0.080 2.00e-02 2.50e+03 pdb=" O6 GSA 730 " -0.123 2.00e-02 2.50e+03 pdb=" N1 GSA 730 " -0.540 2.00e-02 2.50e+03 pdb=" C2 GSA 730 " -0.087 2.00e-02 2.50e+03 pdb=" N2 GSA 730 " 0.322 2.00e-02 2.50e+03 pdb=" N3 GSA 730 " 0.192 2.00e-02 2.50e+03 pdb=" C4 GSA 730 " 0.187 2.00e-02 2.50e+03 ... (remaining 14528 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 30151 2.79 - 3.32: 147522 3.32 - 3.85: 321809 3.85 - 4.37: 388648 4.37 - 4.90: 522513 Nonbonded interactions: 1410643 Sorted by model distance: nonbonded pdb=" OD2 ASPS1 144 " pdb=" N1 GTPS1 801 " model vdw 2.267 2.520 nonbonded pdb=" OG1 THRS1 23 " pdb=" O2B GTPS1 801 " model vdw 2.276 2.440 nonbonded pdb=" N GLNLG 3 " pdb=" O GLNLG 3 " model vdw 2.277 2.496 nonbonded pdb=" N ARGLU 19 " pdb=" O ARGLU 19 " model vdw 2.332 2.496 nonbonded pdb=" N LYSLK 88 " pdb=" O LYSLK 88 " model vdw 2.336 2.496 ... (remaining 1410638 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 4715 5.49 5 S 195 5.16 5 C 79885 2.51 5 N 29104 2.21 5 O 42815 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.130 Extract box with map and model: 20.340 Check model and map are aligned: 1.680 Convert atoms to be neutral: 1.000 Process input model: 554.300 Find NCS groups from input model: 3.630 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 585.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3899 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 : 0.017 0.198 169620 Z= 1.033 Angle : 2.307 30.666 252372 Z= 1.492 Chirality : 0.159 5.185 32049 Planarity : 0.045 0.401 14531 Dihedral : 18.213 179.917 78387 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 3.29 % Allowed : 7.61 % Favored : 89.10 % Rotamer Outliers : 3.84 % Cbeta Deviations : 2.61 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.01 % Twisted Proline : 3.67 % Twisted General : 0.83 % 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: -2.82 (0.09), residues: 7019 helix: -1.60 (0.09), residues: 2137 sheet: -1.39 (0.14), residues: 1229 loop : -2.21 (0.09), residues: 3653 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2398 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 2176 time to evaluate : 7.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 222 outliers final: 48 residues processed: 2322 average time/residue: 1.5528 time to fit residues: 6053.8274 Evaluate side-chains 1210 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1162 time to evaluate : 7.103 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 2 residues processed: 48 average time/residue: 1.4087 time to fit residues: 127.2641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1159 random chunks: chunk 978 optimal weight: 1.9990 chunk 878 optimal weight: 2.9990 chunk 487 optimal weight: 0.9980 chunk 300 optimal weight: 5.9990 chunk 592 optimal weight: 5.9990 chunk 469 optimal weight: 2.9990 chunk 908 optimal weight: 10.0000 chunk 351 optimal weight: 6.9990 chunk 552 optimal weight: 0.8980 chunk 676 optimal weight: 0.8980 chunk 1052 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SJ 58 ASN SK 27 ASN SM 51 GLN SN 42 ASN SN 65 GLN SP 18 GLN SP 63 GLN SQ 30 HIS SQ 44 HIS SS 51 HIS SS 82 HIS SB 121 GLN SB 145 ASN ST 54 GLN SC 5 HIS SC 68 HIS SC 138 GLN ** SC 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 70 GLN SD 88 ASN SG 141 HIS ** SH 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 54 GLN ** S1 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 119 GLN S1 128 GLN S1 220 ASN S1 516 HIS ** S1 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 47 ASN LC 58 ASN ** LC 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 172 HIS ** LM 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 55 HIS LN 45 ASN LN 85 ASN LN 114 GLN LN 152 GLN ** LN 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LO 19 GLN LO 36 GLN LO 43 GLN LP 11 GLN LP 12 HIS LR 70 HIS LS 26 ASN LT 80 HIS LU 2 HIS LU 45 HIS LU 49 ASN LU 75 ASN LV 22 ASN LV 35 HIS LW 20 ASN ** LX 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 148 GLN LY 19 HIS L1 5 ASN L1 18 HIS L4 27 ASN L4 30 HIS L6 97 ASN ** L6 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L7 62 GLN L8 63 GLN L8 72 ASN L9 135 HIS ** LF 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LF 77 HIS ** LH 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 34 HIS LK 38 GLN LK 100 HIS Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4336 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.108 169620 Z= 0.221 Angle : 0.850 18.860 252372 Z= 0.434 Chirality : 0.044 0.622 32049 Planarity : 0.008 0.146 14531 Dihedral : 15.874 179.940 64492 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.95 % Allowed : 6.54 % Favored : 92.51 % Rotamer Outliers : 5.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.01 % Twisted Proline : 0.82 % Twisted General : 0.22 % 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: -1.84 (0.09), residues: 7019 helix: -0.31 (0.10), residues: 2233 sheet: -0.69 (0.15), residues: 1143 loop : -2.02 (0.09), residues: 3643 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1705 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1412 time to evaluate : 7.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 293 outliers final: 134 residues processed: 1574 average time/residue: 1.5531 time to fit residues: 4212.4891 Evaluate side-chains 1251 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1117 time to evaluate : 7.037 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 134 outliers final: 1 residues processed: 134 average time/residue: 1.3356 time to fit residues: 342.1400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1159 random chunks: chunk 584 optimal weight: 20.0000 chunk 326 optimal weight: 9.9990 chunk 875 optimal weight: 0.9990 chunk 716 optimal weight: 10.0000 chunk 290 optimal weight: 7.9990 chunk 1054 optimal weight: 10.0000 chunk 1139 optimal weight: 8.9990 chunk 939 optimal weight: 9.9990 chunk 1045 optimal weight: 1.9990 chunk 359 optimal weight: 10.0000 chunk 845 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SJ 56 HIS SJ 70 HIS ** SL 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SM 13 HIS SN 65 GLN SO 39 GLN SO 41 HIS SO 45 HIS SO 50 HIS ** SP 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SS 56 HIS SS 82 HIS ** ST 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 7 ASN ** SC 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 53 GLN ** SD 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 11 HIS ** SF 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 125 GLN S1 54 GLN ** S1 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 343 ASN S1 454 GLN ** S1 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 80 GLN ** LC 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 234 ASN ** LM 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LM 74 GLN LM 76 HIS ** LN 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 229 HIS LN 231 HIS LN 238 ASN ** LO 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 11 GLN ** LQ 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LQ 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LR 59 ASN LT 49 ASN ** LT 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LU 56 HIS ** LU 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 16 ASN LV 22 ASN ** LD 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LW 25 GLN LX 134 HIS ** LX 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 164 GLN LY 8 GLN ** LY 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 97 ASN ** L6 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 30 GLN L7 80 GLN ** L8 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 44 HIS L8 63 GLN L8 103 ASN ** LF 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LG 93 GLN LI 3 GLN LJ 3 HIS ** LJ 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.9374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.380 169620 Z= 0.477 Angle : 1.133 28.164 252372 Z= 0.578 Chirality : 0.056 0.636 32049 Planarity : 0.011 0.184 14531 Dihedral : 16.695 179.573 64492 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 27.69 Ramachandran Plot: Outliers : 0.94 % Allowed : 9.70 % Favored : 89.36 % Rotamer Outliers : 7.79 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.01 % Twisted Proline : 1.22 % Twisted General : 0.40 % 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: -2.74 (0.09), residues: 7019 helix: -1.25 (0.10), residues: 2222 sheet: -0.90 (0.15), residues: 1128 loop : -2.54 (0.09), residues: 3669 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2304 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 451 poor density : 1853 time to evaluate : 6.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 451 outliers final: 151 residues processed: 2090 average time/residue: 1.5204 time to fit residues: 5496.7128 Evaluate side-chains 1501 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1350 time to evaluate : 7.051 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 151 outliers final: 1 residues processed: 151 average time/residue: 1.3169 time to fit residues: 379.5088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1159 random chunks: chunk 1041 optimal weight: 7.9990 chunk 792 optimal weight: 7.9990 chunk 547 optimal weight: 10.0000 chunk 116 optimal weight: 30.0000 chunk 503 optimal weight: 10.0000 chunk 708 optimal weight: 10.0000 chunk 1058 optimal weight: 10.0000 chunk 1120 optimal weight: 5.9990 chunk 552 optimal weight: 10.0000 chunk 1002 optimal weight: 0.9980 chunk 301 optimal weight: 9.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SJ 58 ASN SL 28 GLN SO 19 ASN ** SO 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 44 HIS SB 177 ASN ST 20 ASN ** ST 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 54 GLN ** SC 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SD 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 53 GLN ** SD 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 11 HIS ** SF 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 129 ASN SG 141 HIS ** SI 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 81 HIS ** S1 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 368 ASN ** S1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LC 148 ASN ** LC 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LM 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LM 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LO 36 GLN LP 6 GLN ** LP 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LP 82 HIS LR 92 ASN ** LS 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LT 87 GLN LV 35 HIS LD 56 ASN ** LD 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LW 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 150 GLN LX 164 GLN ** LY 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 5 ASN ** L3 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L4 42 HIS L6 41 GLN L6 90 GLN L6 115 GLN ** L6 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 104 GLN L7 80 GLN L8 37 ASN L8 63 GLN L8 114 HIS L8 127 GLN L9 28 ASN ** LF 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LH 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LJ 3 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 1.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.293 169620 Z= 0.358 Angle : 0.841 16.948 252372 Z= 0.429 Chirality : 0.044 0.401 32049 Planarity : 0.008 0.152 14531 Dihedral : 15.990 179.986 64492 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.59 % Favored : 91.65 % Rotamer Outliers : 5.46 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.09), residues: 7019 helix: -0.72 (0.10), residues: 2214 sheet: -0.89 (0.15), residues: 1177 loop : -2.31 (0.09), residues: 3628 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1918 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1602 time to evaluate : 6.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 316 outliers final: 146 residues processed: 1774 average time/residue: 1.3999 time to fit residues: 4349.5230 Evaluate side-chains 1489 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1343 time to evaluate : 6.423 Switching outliers to nearest non-outliers outliers start: 146 outliers final: 0 residues processed: 146 average time/residue: 1.2766 time to fit residues: 358.4821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1159 random chunks: chunk 933 optimal weight: 0.9980 chunk 635 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 834 optimal weight: 6.9990 chunk 462 optimal weight: 10.0000 chunk 955 optimal weight: 9.9990 chunk 774 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 572 optimal weight: 20.0000 chunk 1005 optimal weight: 5.9990 chunk 282 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SK 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 5 GLN SN 59 GLN SO 41 HIS SQ 44 HIS SB 102 ASN ST 20 ASN ** ST 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 60 GLN ST 74 HIS SD 40 HIS SD 58 GLN ** SD 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 129 ASN SG 141 HIS SH 3 GLN ** SI 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 258 ASN ** S1 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 331 ASN ** S1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 80 GLN ** LC 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 51 ASN LM 74 GLN LN 44 ASN ** LN 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LN 225 ASN LN 238 ASN ** LP 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 2 HIS LV 33 HIS LV 35 HIS LD 56 ASN ** LD 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 5 ASN L3 26 ASN L4 23 HIS L6 41 GLN ** L6 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L7 80 GLN ** L8 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 63 GLN ** L9 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LZ 61 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 1.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.201 169620 Z= 0.357 Angle : 0.840 18.303 252372 Z= 0.429 Chirality : 0.044 0.423 32049 Planarity : 0.008 0.179 14531 Dihedral : 15.981 179.347 64492 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.73 % Allowed : 10.09 % Favored : 89.19 % Rotamer Outliers : 5.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.36 (0.09), residues: 7019 helix: -0.73 (0.10), residues: 2236 sheet: -1.02 (0.14), residues: 1220 loop : -2.35 (0.09), residues: 3563 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1938 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 1609 time to evaluate : 6.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 329 outliers final: 156 residues processed: 1773 average time/residue: 1.3066 time to fit residues: 4064.3419 Evaluate side-chains 1500 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1344 time to evaluate : 6.507 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 156 outliers final: 1 residues processed: 156 average time/residue: 1.1222 time to fit residues: 336.1227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1159 random chunks: chunk 376 optimal weight: 10.0000 chunk 1008 optimal weight: 9.9990 chunk 221 optimal weight: 6.9990 chunk 657 optimal weight: 30.0000 chunk 276 optimal weight: 10.0000 chunk 1121 optimal weight: 9.9990 chunk 930 optimal weight: 4.9990 chunk 519 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 370 optimal weight: 7.9990 chunk 588 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SK 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 39 ASN ** SP 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 102 ASN ** ST 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 60 GLN SC 31 ASN SD 40 HIS SD 58 GLN ** SD 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 163 GLN ** SE 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 141 HIS SH 75 GLN SI 109 GLN S1 77 GLN ** S1 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 504 HIS ** S1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 6 GLN ** LM 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 51 ASN ** LN 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 238 ASN LP 6 GLN ** LP 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LP 82 HIS LQ 57 ASN LT 51 GLN ** LT 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LV 22 ASN ** LD 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LW 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 32 ASN ** LX 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L6 41 GLN ** L6 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 93 ASN LE 104 GLN ** L9 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L9 28 ASN ** LK 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 104 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 1.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.157 169620 Z= 0.376 Angle : 0.799 16.683 252372 Z= 0.409 Chirality : 0.043 0.362 32049 Planarity : 0.007 0.120 14531 Dihedral : 15.949 179.767 64492 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.05 % Favored : 90.31 % Rotamer Outliers : 3.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.29 (0.09), residues: 7019 helix: -0.58 (0.10), residues: 2247 sheet: -1.04 (0.15), residues: 1200 loop : -2.36 (0.09), residues: 3572 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1686 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1456 time to evaluate : 6.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 230 outliers final: 134 residues processed: 1579 average time/residue: 1.2663 time to fit residues: 3515.5279 Evaluate side-chains 1458 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1324 time to evaluate : 6.404 Switching outliers to nearest non-outliers outliers start: 134 outliers final: 0 residues processed: 134 average time/residue: 1.0638 time to fit residues: 276.9533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1159 random chunks: chunk 1081 optimal weight: 7.9990 chunk 126 optimal weight: 20.0000 chunk 638 optimal weight: 30.0000 chunk 818 optimal weight: 6.9990 chunk 634 optimal weight: 20.0000 chunk 943 optimal weight: 2.9990 chunk 626 optimal weight: 40.0000 chunk 1117 optimal weight: 0.9990 chunk 699 optimal weight: 50.0000 chunk 681 optimal weight: 10.0000 chunk 515 optimal weight: 20.0000 overall best weight: 5.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SK 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 27 ASN SK 39 ASN SO 27 GLN SB 93 HIS SB 102 ASN SC 40 GLN SD 40 HIS ** SD 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 163 GLN SF 11 HIS SF 14 GLN ** SF 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 141 HIS ** S1 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LM 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 51 ASN ** LN 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LP 82 HIS LQ 57 ASN LR 48 GLN ** LS 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 44 HIS LT 51 GLN ** LT 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LT 87 GLN LU 75 ASN LW 20 ASN ** LX 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L6 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 106 GLN L7 126 ASN L9 18 GLN LJ 3 HIS ** LK 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 1.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.119 169620 Z= 0.280 Angle : 0.724 17.363 252372 Z= 0.372 Chirality : 0.040 0.304 32049 Planarity : 0.006 0.101 14531 Dihedral : 15.746 179.695 64492 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.52 % Favored : 89.87 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.13 (0.09), residues: 7019 helix: -0.35 (0.10), residues: 2254 sheet: -0.93 (0.15), residues: 1200 loop : -2.35 (0.10), residues: 3565 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1602 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1450 time to evaluate : 6.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 152 outliers final: 90 residues processed: 1520 average time/residue: 1.2729 time to fit residues: 3418.5349 Evaluate side-chains 1429 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1339 time to evaluate : 6.448 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 0 residues processed: 90 average time/residue: 1.0801 time to fit residues: 191.6849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1159 random chunks: chunk 691 optimal weight: 9.9990 chunk 446 optimal weight: 7.9990 chunk 667 optimal weight: 10.0000 chunk 336 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 chunk 216 optimal weight: 30.0000 chunk 710 optimal weight: 10.0000 chunk 761 optimal weight: 10.0000 chunk 552 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 878 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SK 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SN 34 ASN SC 31 ASN SC 40 GLN SD 40 HIS SD 99 ASN SD 163 GLN ** SE 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 14 GLN ** SF 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 141 HIS SH 17 GLN ** S1 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LM 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 238 ASN ** LP 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LP 82 HIS ** LQ 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LQ 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 57 ASN LR 48 GLN ** LS 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LU 75 ASN ** LD 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 163 ASN L7 20 ASN ** LK 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 1.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.140 169620 Z= 0.325 Angle : 0.757 16.418 252372 Z= 0.388 Chirality : 0.041 0.297 32049 Planarity : 0.006 0.104 14531 Dihedral : 15.813 179.960 64492 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.70 % Favored : 89.70 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.01 % Twisted Proline : 0.41 % 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: -2.19 (0.09), residues: 7019 helix: -0.41 (0.10), residues: 2261 sheet: -0.92 (0.15), residues: 1217 loop : -2.40 (0.10), residues: 3541 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1553 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1406 time to evaluate : 6.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 147 outliers final: 89 residues processed: 1469 average time/residue: 1.2717 time to fit residues: 3300.1573 Evaluate side-chains 1405 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1316 time to evaluate : 6.417 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 0 residues processed: 89 average time/residue: 1.1567 time to fit residues: 205.5421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1159 random chunks: chunk 1016 optimal weight: 5.9990 chunk 1070 optimal weight: 40.0000 chunk 976 optimal weight: 8.9990 chunk 1040 optimal weight: 20.0000 chunk 1069 optimal weight: 0.0980 chunk 626 optimal weight: 40.0000 chunk 453 optimal weight: 30.0000 chunk 817 optimal weight: 6.9990 chunk 319 optimal weight: 5.9990 chunk 940 optimal weight: 7.9990 chunk 984 optimal weight: 10.0000 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SK 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SN 34 ASN ** SP 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 93 HIS ST 12 GLN SC 40 GLN SD 40 HIS SD 163 GLN ** SE 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 14 GLN ** SF 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 141 HIS ** SI 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LM 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 51 ASN ** LN 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LP 82 HIS ** LQ 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LR 48 GLN ** LS 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 75 ASN ** LD 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LW 20 ASN ** LX 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 148 GLN ** LE 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L9 2 GLN ** LK 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 1.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.188 169620 Z= 0.269 Angle : 0.712 18.460 252372 Z= 0.366 Chirality : 0.039 0.358 32049 Planarity : 0.006 0.169 14531 Dihedral : 15.662 179.812 64492 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.57 % Allowed : 9.69 % Favored : 89.74 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.01 % Twisted Proline : 0.00 % 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: -2.10 (0.10), residues: 7019 helix: -0.31 (0.11), residues: 2260 sheet: -0.94 (0.15), residues: 1211 loop : -2.33 (0.10), residues: 3548 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1490 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1411 time to evaluate : 6.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 53 residues processed: 1437 average time/residue: 1.2464 time to fit residues: 3174.3738 Evaluate side-chains 1381 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1328 time to evaluate : 6.269 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 1.0524 time to fit residues: 113.6615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1159 random chunks: chunk 1037 optimal weight: 5.9990 chunk 683 optimal weight: 10.0000 chunk 1100 optimal weight: 3.9990 chunk 671 optimal weight: 20.0000 chunk 522 optimal weight: 10.0000 chunk 765 optimal weight: 30.0000 chunk 1154 optimal weight: 20.0000 chunk 1062 optimal weight: 6.9990 chunk 919 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 710 optimal weight: 10.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SK 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 39 ASN SN 34 ASN SB 119 GLN ST 12 GLN SC 31 ASN SD 163 GLN SE 6 GLN ** SE 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 14 GLN SF 17 GLN ** SF 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 141 HIS ** SI 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LM 11 GLN LM 51 ASN ** LO 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LP 82 HIS ** LQ 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 57 ASN LT 12 GLN LT 80 HIS LU 75 ASN ** LD 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LW 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 148 GLN L3 16 HIS ** LE 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 1.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.212 169620 Z= 0.326 Angle : 0.760 16.513 252372 Z= 0.390 Chirality : 0.041 0.327 32049 Planarity : 0.007 0.135 14531 Dihedral : 15.793 179.533 64492 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.56 % Allowed : 10.30 % Favored : 89.14 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.23 (0.09), residues: 7019 helix: -0.42 (0.10), residues: 2252 sheet: -1.00 (0.15), residues: 1222 loop : -2.43 (0.10), residues: 3545 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1417 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1357 time to evaluate : 6.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 40 residues processed: 1385 average time/residue: 1.2520 time to fit residues: 3082.1668 Evaluate side-chains 1362 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1322 time to evaluate : 6.419 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 1.1339 time to fit residues: 91.7887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1159 random chunks: chunk 563 optimal weight: 10.0000 chunk 730 optimal weight: 10.0000 chunk 979 optimal weight: 2.9990 chunk 281 optimal weight: 9.9990 chunk 847 optimal weight: 5.9990 chunk 135 optimal weight: 20.0000 chunk 255 optimal weight: 1.9990 chunk 920 optimal weight: 7.9990 chunk 385 optimal weight: 1.9990 chunk 945 optimal weight: 1.9990 chunk 116 optimal weight: 30.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SK 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SN 34 ASN SB 93 HIS ST 12 GLN SC 40 GLN SD 163 GLN ** SE 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 121 ASN SG 141 HIS SH 20 ASN ** SI 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 51 ASN ** LM 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LP 82 HIS LQ 7 HIS ** LQ 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LU 75 ASN ** LX 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 136 ASN LX 140 HIS LX 148 GLN ** LE 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L9 2 GLN ** LG 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.095514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.077982 restraints weight = 549146.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.079685 restraints weight = 193209.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.080650 restraints weight = 108027.109| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 1.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.189 169620 Z= 0.202 Angle : 0.674 19.113 252372 Z= 0.346 Chirality : 0.036 0.290 32049 Planarity : 0.006 0.128 14531 Dihedral : 15.505 179.890 64492 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.08 % Favored : 90.37 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.01 % Twisted Proline : 0.00 % 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: -2.02 (0.10), residues: 7019 helix: -0.20 (0.11), residues: 2257 sheet: -0.93 (0.15), residues: 1205 loop : -2.30 (0.10), residues: 3557 =============================================================================== Job complete usr+sys time: 52094.58 seconds wall clock time: 892 minutes 17.26 seconds (53537.26 seconds total)