Starting phenix.real_space_refine on Sun Mar 3 09:46:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9z_6315/03_2024/3j9z_6315_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9z_6315/03_2024/3j9z_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_6315/03_2024/3j9z_6315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9z_6315/03_2024/3j9z_6315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9z_6315/03_2024/3j9z_6315_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9z_6315/03_2024/3j9z_6315_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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, 'rna2p_pyr': 83, 'rna3p_pur': 753, 'rna3p_pyr': 583} Link IDs: {'rna2p': 205, 'rna3p': 1336} Chain: "S6" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1639 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 13, 'rna3p': 63} 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, 'rna2p_pyr': 9, 'rna3p_pur': 35, 'rna3p_pyr': 27} Link IDs: {'rna2p': 12, 'rna3p': 61} 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, 'rna2p_pyr': 146, 'rna3p_pur': 1401, 'rna3p_pyr': 1086} Link IDs: {'rna2p': 417, 'rna3p': 2486} Chain: "LB" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2566 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 58, 'rna3p_pyr': 52} Link IDs: {'rna2p': 10, 'rna3p': 109} 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: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 226} 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: {'CIS': 1, 'PTRANS': 5, '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: 58.26, per 1000 atoms: 0.37 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: 63.34 Conformation dependent library (CDL) restraints added in 7.3 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 for structures that cannot fit in PDB format. 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: 75.84 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: 222.51 Time building geometry restraints manager: 68.50 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: 96212 35.98 - 71.97: 10898 71.97 - 107.95: 1209 107.95 - 143.93: 66 143.93 - 179.92: 130 Dihedral angle restraints: 108515 sinusoidal: 88207 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 108512 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 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: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 15.520 Check model and map are aligned: 1.650 Set scattering table: 1.040 Process input model: 525.000 Find NCS groups from input model: 3.120 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 552.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3829 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 : 24.242 179.917 95419 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 % Allowed : 8.71 % Favored : 87.46 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.196 0.026 TRPSC 200 HIS 0.018 0.002 HISLF 47 PHE 0.114 0.018 PHESO 14 TYR 0.266 0.035 TYRSD 102 ARG 0.056 0.004 ARGLP 79 *********************** 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 : 6.682 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: SD 43 ARG cc_start: 0.3069 (OUTLIER) cc_final: 0.2405 (ptm160) REVERT: SD 46 ARG cc_start: 0.1311 (OUTLIER) cc_final: -0.0150 (mmm160) REVERT: SD 187 ARG cc_start: 0.1068 (OUTLIER) cc_final: 0.0347 (tpt170) REVERT: SD 190 LEU cc_start: 0.5343 (tt) cc_final: 0.5122 (tp) REVERT: SE 55 VAL cc_start: 0.2804 (t) cc_final: 0.2368 (p) REVERT: S1 105 LEU cc_start: 0.4600 (mt) cc_final: 0.4352 (mt) REVERT: S1 368 ASN cc_start: 0.3576 (OUTLIER) cc_final: 0.3085 (p0) REVERT: S1 493 ILE cc_start: 0.4661 (OUTLIER) cc_final: 0.4448 (mt) REVERT: LM 23 ASP cc_start: 0.0152 (m-30) cc_final: -0.0248 (m-30) REVERT: LM 55 HIS cc_start: 0.3891 (m90) cc_final: 0.3547 (m-70) REVERT: LD 83 TYR cc_start: 0.2088 (p90) cc_final: 0.1739 (p90) REVERT: LD 85 MET cc_start: 0.1784 (mmm) cc_final: 0.0716 (ppp) REVERT: LD 139 MET cc_start: 0.3682 (ttt) cc_final: 0.2118 (mtt) REVERT: L7 172 PHE cc_start: 0.3683 (m-80) cc_final: 0.3177 (m-80) outliers start: 222 outliers final: 49 residues processed: 2322 average time/residue: 1.5091 time to fit residues: 5835.0356 Evaluate side-chains 1225 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1171 time to evaluate : 6.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SJ residue 59 LYS Chi-restraints excluded: chain SJ residue 71 LEU Chi-restraints excluded: chain SK residue 56 LYS Chi-restraints excluded: chain SM residue 6 ILE Chi-restraints excluded: chain SM residue 90 HIS Chi-restraints excluded: chain SM residue 108 ARG Chi-restraints excluded: chain SS residue 55 GLN Chi-restraints excluded: chain SC residue 6 PRO Chi-restraints excluded: chain SD residue 43 ARG Chi-restraints excluded: chain SD residue 46 ARG Chi-restraints excluded: chain SD residue 187 ARG Chi-restraints excluded: chain SD residue 194 ILE Chi-restraints excluded: chain SE residue 14 LEU Chi-restraints excluded: chain SE residue 104 ILE Chi-restraints excluded: chain SE residue 158 LYS Chi-restraints excluded: chain SE residue 161 GLU Chi-restraints excluded: chain SF residue 97 THR Chi-restraints excluded: chain SF residue 102 MET Chi-restraints excluded: chain SG residue 82 SER Chi-restraints excluded: chain SH residue 68 LYS Chi-restraints excluded: chain SH residue 111 THR Chi-restraints excluded: chain SH residue 128 VAL Chi-restraints excluded: chain S1 residue 120 PRO Chi-restraints excluded: chain S1 residue 341 VAL Chi-restraints excluded: chain S1 residue 368 ASN Chi-restraints excluded: chain S1 residue 377 ARG Chi-restraints excluded: chain S1 residue 493 ILE Chi-restraints excluded: chain S1 residue 514 TYR Chi-restraints excluded: chain S1 residue 553 ASP Chi-restraints excluded: chain S1 residue 582 TYR Chi-restraints excluded: chain LC residue 174 THR Chi-restraints excluded: chain LM residue 3 ILE Chi-restraints excluded: chain LM residue 91 VAL Chi-restraints excluded: chain LN residue 93 VAL Chi-restraints excluded: chain LN residue 244 VAL Chi-restraints excluded: chain LO residue 91 ARG Chi-restraints excluded: chain LP residue 48 LYS Chi-restraints excluded: chain LR residue 66 LYS Chi-restraints excluded: chain LS residue 27 VAL Chi-restraints excluded: chain LT residue 69 GLU Chi-restraints excluded: chain LX residue 2 ILE Chi-restraints excluded: chain LX residue 24 VAL Chi-restraints excluded: chain LX residue 194 PRO Chi-restraints excluded: chain L1 residue 38 LEU Chi-restraints excluded: chain LE residue 32 VAL Chi-restraints excluded: chain LE residue 34 ILE Chi-restraints excluded: chain LE residue 56 VAL Chi-restraints excluded: chain LE residue 96 LYS Chi-restraints excluded: chain L8 residue 163 TYR Chi-restraints excluded: chain LF residue 81 ILE Chi-restraints excluded: chain LH residue 64 PHE Chi-restraints excluded: chain LH residue 122 VAL Chi-restraints excluded: chain LI residue 112 LEU Chi-restraints excluded: chain LI residue 126 ILE 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: 0.9990 chunk 300 optimal weight: 5.9990 chunk 592 optimal weight: 5.9990 chunk 469 optimal weight: 7.9990 chunk 908 optimal weight: 10.0000 chunk 351 optimal weight: 6.9990 chunk 552 optimal weight: 0.9980 chunk 676 optimal weight: 0.7980 chunk 1052 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 SM 90 HIS SN 42 ASN SN 65 GLN SP 18 GLN SP 63 GLN SQ 30 HIS SQ 44 HIS SS 51 HIS SS 55 GLN SS 82 HIS SB 121 GLN 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 103 GLN ** 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** LN 45 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 12 HIS LR 70 HIS LS 26 ASN LT 80 HIS LU 2 HIS LU 45 HIS LU 49 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: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4238 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 169620 Z= 0.206 Angle : 0.845 18.304 252372 Z= 0.435 Chirality : 0.045 0.621 32049 Planarity : 0.006 0.079 14531 Dihedral : 24.062 179.750 81651 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.93 % Allowed : 6.80 % Favored : 92.28 % Rotamer: Outliers : 5.55 % Allowed : 18.59 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.01 % Twisted Proline : 0.82 % Twisted General : 0.26 % 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: -1.86 (0.09), residues: 7019 helix: -0.35 (0.10), residues: 2241 sheet: -0.68 (0.14), residues: 1152 loop : -2.03 (0.09), residues: 3626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRPSS 33 HIS 0.018 0.002 HISSO 41 PHE 0.024 0.002 PHESN 20 TYR 0.026 0.002 TYRLK 99 ARG 0.011 0.001 ARGLH 132 *********************** 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 1725 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 1404 time to evaluate : 6.969 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: SJ 83 THR cc_start: 0.3024 (m) cc_final: 0.2679 (m) REVERT: SK 55 ARG cc_start: 0.3941 (ttm170) cc_final: 0.3617 (ttm-80) REVERT: SR 2 ARG cc_start: 0.3186 (tpm-80) cc_final: 0.2890 (mmm160) REVERT: SB 22 TRP cc_start: 0.3432 (OUTLIER) cc_final: 0.3194 (p-90) REVERT: SC 229 LYS cc_start: 0.0886 (mttp) cc_final: 0.0477 (mmmt) REVERT: SD 46 ARG cc_start: 0.0674 (OUTLIER) cc_final: -0.0506 (mmm160) REVERT: SG 85 GLN cc_start: 0.6543 (mm-40) cc_final: 0.6193 (mp10) REVERT: S1 28 ARG cc_start: 0.5776 (mmm160) cc_final: 0.5151 (mmm160) REVERT: S1 548 TYR cc_start: 0.3111 (m-80) cc_final: 0.2894 (m-80) REVERT: S1 663 PHE cc_start: 0.4792 (m-80) cc_final: 0.4482 (m-80) REVERT: LC 97 MET cc_start: 0.3192 (tpp) cc_final: 0.2992 (tpp) REVERT: LC 121 MET cc_start: 0.0828 (ppp) cc_final: -0.0162 (tpt) REVERT: LN 52 HIS cc_start: 0.5963 (m170) cc_final: 0.5555 (m90) REVERT: LN 82 TYR cc_start: 0.3139 (t80) cc_final: 0.2860 (t80) REVERT: LR 66 LYS cc_start: 0.4104 (OUTLIER) cc_final: 0.3573 (pttt) REVERT: LU 69 GLU cc_start: 0.4788 (OUTLIER) cc_final: 0.4352 (tt0) REVERT: LD 85 MET cc_start: 0.2264 (mmm) cc_final: 0.1083 (ppp) REVERT: LD 139 MET cc_start: 0.2730 (ttt) cc_final: 0.1544 (mtt) REVERT: L6 141 MET cc_start: 0.6918 (mmm) cc_final: 0.6624 (mmp) REVERT: LE 133 ARG cc_start: 0.3813 (ttp-170) cc_final: 0.3357 (tmm-80) REVERT: LK 1 MET cc_start: -0.1202 (mtt) cc_final: -0.1649 (mtt) REVERT: LK 63 LYS cc_start: 0.4003 (OUTLIER) cc_final: 0.3743 (ptpp) outliers start: 321 outliers final: 150 residues processed: 1587 average time/residue: 1.4542 time to fit residues: 3941.6591 Evaluate side-chains 1287 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1132 time to evaluate : 6.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SJ residue 56 HIS Chi-restraints excluded: chain SJ residue 58 ASN Chi-restraints excluded: chain SJ residue 78 GLU Chi-restraints excluded: chain SJ residue 90 LEU Chi-restraints excluded: chain SK residue 56 LYS Chi-restraints excluded: chain SK residue 84 MET Chi-restraints excluded: chain SK residue 85 VAL Chi-restraints excluded: chain SL residue 6 LEU Chi-restraints excluded: chain SL residue 85 ARG Chi-restraints excluded: chain SL residue 118 VAL Chi-restraints excluded: chain SM residue 6 ILE Chi-restraints excluded: chain SM residue 51 GLN Chi-restraints excluded: chain SM residue 80 MET Chi-restraints excluded: chain SM residue 97 ARG Chi-restraints excluded: chain SM residue 108 ARG Chi-restraints excluded: chain SN residue 53 ASP Chi-restraints excluded: chain SN residue 61 ASN Chi-restraints excluded: chain SO residue 26 VAL Chi-restraints excluded: chain SP residue 2 VAL Chi-restraints excluded: chain SP residue 9 HIS Chi-restraints excluded: chain SP residue 50 THR Chi-restraints excluded: chain SP residue 52 LEU Chi-restraints excluded: chain SQ residue 41 THR Chi-restraints excluded: chain SQ residue 43 LEU Chi-restraints excluded: chain SQ residue 74 LEU Chi-restraints excluded: chain SQ residue 77 VAL Chi-restraints excluded: chain SR residue 41 SER Chi-restraints excluded: chain SS residue 3 SER Chi-restraints excluded: chain SS residue 12 LEU Chi-restraints excluded: chain SS residue 52 ASN Chi-restraints excluded: chain SB residue 22 TRP Chi-restraints excluded: chain SB residue 67 LEU Chi-restraints excluded: chain SB residue 113 LEU Chi-restraints excluded: chain SB residue 129 THR Chi-restraints excluded: chain SB residue 162 VAL Chi-restraints excluded: chain ST residue 33 LYS Chi-restraints excluded: chain SU residue 59 LEU Chi-restraints excluded: chain SC residue 13 ILE Chi-restraints excluded: chain SC residue 46 LEU Chi-restraints excluded: chain SC residue 192 TYR Chi-restraints excluded: chain SD residue 35 GLN Chi-restraints excluded: chain SD residue 46 ARG Chi-restraints excluded: chain SD residue 159 GLU Chi-restraints excluded: chain SD residue 187 ARG Chi-restraints excluded: chain SD residue 191 SER Chi-restraints excluded: chain SD residue 194 ILE Chi-restraints excluded: chain SE residue 14 LEU Chi-restraints excluded: chain SE residue 104 ILE Chi-restraints excluded: chain SE residue 116 VAL Chi-restraints excluded: chain SF residue 6 ILE Chi-restraints excluded: chain SF residue 9 MET Chi-restraints excluded: chain SF residue 97 THR Chi-restraints excluded: chain SG residue 82 SER Chi-restraints excluded: chain SH residue 41 GLU Chi-restraints excluded: chain SH residue 60 LEU Chi-restraints excluded: chain SI residue 8 THR Chi-restraints excluded: chain SI residue 74 GLN Chi-restraints excluded: chain S1 residue 67 THR Chi-restraints excluded: chain S1 residue 209 ASP Chi-restraints excluded: chain S1 residue 279 ASP Chi-restraints excluded: chain S1 residue 329 VAL Chi-restraints excluded: chain S1 residue 341 VAL Chi-restraints excluded: chain S1 residue 363 VAL Chi-restraints excluded: chain S1 residue 394 ASP Chi-restraints excluded: chain S1 residue 397 CYS Chi-restraints excluded: chain S1 residue 514 TYR Chi-restraints excluded: chain S1 residue 553 ASP Chi-restraints excluded: chain S1 residue 633 ASP Chi-restraints excluded: chain S1 residue 634 LEU Chi-restraints excluded: chain S1 residue 653 ILE Chi-restraints excluded: chain S1 residue 662 MET Chi-restraints excluded: chain LC residue 29 LEU Chi-restraints excluded: chain LC residue 202 THR Chi-restraints excluded: chain LM residue 3 ILE Chi-restraints excluded: chain LM residue 25 VAL Chi-restraints excluded: chain LM residue 79 VAL Chi-restraints excluded: chain LM residue 84 SER Chi-restraints excluded: chain LM residue 91 VAL Chi-restraints excluded: chain LN residue 219 VAL Chi-restraints excluded: chain LN residue 244 VAL Chi-restraints excluded: chain LN residue 249 VAL Chi-restraints excluded: chain LO residue 91 ARG Chi-restraints excluded: chain LP residue 35 PHE Chi-restraints excluded: chain LQ residue 4 ILE Chi-restraints excluded: chain LQ residue 55 ILE Chi-restraints excluded: chain LR residue 47 VAL Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 66 LYS Chi-restraints excluded: chain LR residue 85 VAL Chi-restraints excluded: chain LS residue 27 VAL Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 77 VAL Chi-restraints excluded: chain LU residue 8 SER Chi-restraints excluded: chain LU residue 69 GLU Chi-restraints excluded: chain LV residue 64 ASP Chi-restraints excluded: chain LV residue 65 THR Chi-restraints excluded: chain LD residue 46 GLU Chi-restraints excluded: chain LX residue 2 ILE Chi-restraints excluded: chain LX residue 22 ILE Chi-restraints excluded: chain LX residue 37 VAL Chi-restraints excluded: chain LX residue 60 VAL Chi-restraints excluded: chain LY residue 16 LEU Chi-restraints excluded: chain LY residue 56 VAL Chi-restraints excluded: chain L1 residue 31 LYS Chi-restraints excluded: chain L3 residue 24 THR Chi-restraints excluded: chain L3 residue 44 VAL Chi-restraints excluded: chain L5 residue 1 MET Chi-restraints excluded: chain L5 residue 25 VAL Chi-restraints excluded: chain LE residue 32 VAL Chi-restraints excluded: chain LE residue 34 ILE Chi-restraints excluded: chain LE residue 48 ILE Chi-restraints excluded: chain LE residue 56 VAL Chi-restraints excluded: chain LE residue 96 LYS Chi-restraints excluded: chain LE residue 125 THR Chi-restraints excluded: chain LE residue 131 THR Chi-restraints excluded: chain L7 residue 33 ILE Chi-restraints excluded: chain L7 residue 49 LEU Chi-restraints excluded: chain L7 residue 67 THR Chi-restraints excluded: chain L7 residue 131 VAL Chi-restraints excluded: chain L7 residue 151 LEU Chi-restraints excluded: chain L7 residue 157 THR Chi-restraints excluded: chain L7 residue 164 GLU Chi-restraints excluded: chain L8 residue 5 LYS Chi-restraints excluded: chain L8 residue 59 ASP Chi-restraints excluded: chain L8 residue 61 TRP Chi-restraints excluded: chain L8 residue 66 THR Chi-restraints excluded: chain L8 residue 104 LEU Chi-restraints excluded: chain L8 residue 128 THR Chi-restraints excluded: chain L8 residue 147 LEU Chi-restraints excluded: chain L9 residue 4 ILE Chi-restraints excluded: chain L9 residue 46 PHE Chi-restraints excluded: chain L9 residue 78 VAL Chi-restraints excluded: chain L9 residue 130 VAL Chi-restraints excluded: chain LF residue 3 THR Chi-restraints excluded: chain LF residue 10 THR Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 73 VAL Chi-restraints excluded: chain LF residue 81 ILE Chi-restraints excluded: chain LF residue 88 THR Chi-restraints excluded: chain LF residue 139 VAL Chi-restraints excluded: chain LG residue 20 MET Chi-restraints excluded: chain LG residue 88 ASN Chi-restraints excluded: chain LH residue 3 LEU Chi-restraints excluded: chain LH residue 64 PHE Chi-restraints excluded: chain LH residue 122 VAL Chi-restraints excluded: chain LI residue 17 ASN Chi-restraints excluded: chain LI residue 110 GLU Chi-restraints excluded: chain LI residue 126 ILE Chi-restraints excluded: chain LI residue 131 VAL Chi-restraints excluded: chain LJ residue 4 ARG Chi-restraints excluded: chain LJ residue 98 LEU Chi-restraints excluded: chain LK residue 63 LYS Chi-restraints excluded: chain LK residue 90 VAL Chi-restraints excluded: chain LK residue 103 VAL 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: 6.9990 chunk 875 optimal weight: 9.9990 chunk 716 optimal weight: 10.0000 chunk 290 optimal weight: 7.9990 chunk 1054 optimal weight: 20.0000 chunk 1139 optimal weight: 0.3980 chunk 939 optimal weight: 9.9990 chunk 1045 optimal weight: 0.4980 chunk 359 optimal weight: 20.0000 chunk 845 optimal weight: 5.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- 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** SM 13 HIS SO 41 HIS SO 45 HIS SO 50 HIS ** SP 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SP 59 HIS ** SS 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SB 50 ASN SB 169 HIS ST 12 GLN ST 74 HIS SC 7 ASN ** SC 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 121 ASN SF 11 HIS SG 141 HIS SH 66 GLN ** SI 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 343 ASN ** S1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 47 ASN LC 148 ASN ** LC 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 234 ASN ** LM 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 74 GLN ** LN 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 229 HIS ** LN 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LN 238 ASN LO 51 GLN ** LO 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LQ 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LQ 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LR 59 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 ** both conformations clash, **PLEASE CHECK MANUALLY** LX 134 HIS ** LX 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 8 GLN ** L1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 29 HIS L6 97 ASN ** L6 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 30 GLN L7 80 GLN L8 44 HIS L8 63 GLN ** LF 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LH 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LI 3 GLN ** LJ 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 104 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.8047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.402 169620 Z= 0.391 Angle : 1.025 29.894 252372 Z= 0.517 Chirality : 0.050 0.779 32049 Planarity : 0.010 0.186 14531 Dihedral : 24.199 179.836 81585 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 25.43 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.00 % Favored : 90.20 % Rotamer: Outliers : 7.60 % Allowed : 20.51 % Favored : 71.89 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.01 % Twisted Proline : 0.41 % Twisted General : 0.16 % 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: -0.96 (0.10), residues: 2219 sheet: -0.80 (0.14), residues: 1210 loop : -2.26 (0.09), residues: 3590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.005 TRPLN 212 HIS 0.048 0.003 HISSB 38 PHE 0.055 0.005 PHEL7 174 TYR 0.032 0.004 TYRSL 65 ARG 0.041 0.002 ARGSF 44 *********************** 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 2242 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 440 poor density : 1802 time to evaluate : 6.953 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: SL 75 GLU cc_start: 0.5237 (mt-10) cc_final: 0.4566 (mt-10) REVERT: SN 84 ARG cc_start: 0.6330 (OUTLIER) cc_final: 0.5990 (tmm-80) REVERT: SR 2 ARG cc_start: 0.3451 (tpm-80) cc_final: 0.2932 (tpp-160) REVERT: SB 24 PRO cc_start: 0.5128 (Cg_exo) cc_final: 0.4863 (Cg_endo) REVERT: ST 20 ASN cc_start: 0.5583 (m-40) cc_final: 0.5333 (m-40) REVERT: SU 38 GLU cc_start: 0.5575 (tp30) cc_final: 0.5231 (tp30) REVERT: SC 229 LYS cc_start: 0.2052 (mttp) cc_final: 0.1608 (mtpt) REVERT: SD 144 ILE cc_start: 0.5674 (OUTLIER) cc_final: 0.5361 (pt) REVERT: SD 187 ARG cc_start: 0.1826 (OUTLIER) cc_final: 0.1380 (tpt90) REVERT: SH 2 MET cc_start: 0.5381 (ppp) cc_final: 0.4613 (ptm) REVERT: SH 53 ASP cc_start: 0.4641 (OUTLIER) cc_final: 0.4374 (p0) REVERT: S1 381 ILE cc_start: 0.5335 (pt) cc_final: 0.5108 (pt) REVERT: S1 396 LEU cc_start: 0.4275 (OUTLIER) cc_final: 0.3912 (mp) REVERT: S1 547 GLU cc_start: 0.5574 (OUTLIER) cc_final: 0.5261 (tp30) REVERT: S1 548 TYR cc_start: 0.4112 (m-80) cc_final: 0.3754 (m-80) REVERT: S1 615 ILE cc_start: 0.5920 (mm) cc_final: 0.5456 (mm) REVERT: LC 121 MET cc_start: 0.1843 (ppp) cc_final: 0.0493 (tpt) REVERT: LN 12 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.6509 (tpp80) REVERT: LO 94 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6556 (mm) REVERT: LQ 86 MET cc_start: 0.6319 (tpt) cc_final: 0.5817 (tpt) REVERT: LR 60 THR cc_start: 0.7647 (p) cc_final: 0.7277 (p) REVERT: LR 61 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6837 (pp) REVERT: LR 66 LYS cc_start: 0.5533 (OUTLIER) cc_final: 0.4909 (pttm) REVERT: LV 31 ASN cc_start: 0.7689 (t0) cc_final: 0.7364 (t0) REVERT: LV 64 ASP cc_start: 0.5196 (OUTLIER) cc_final: 0.4981 (p0) REVERT: LD 139 MET cc_start: 0.1972 (ttt) cc_final: 0.1089 (mtt) REVERT: LX 183 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5776 (tt0) REVERT: L4 29 ARG cc_start: 0.6075 (OUTLIER) cc_final: 0.5688 (ptm160) REVERT: L8 105 SER cc_start: 0.4965 (m) cc_final: 0.4456 (m) REVERT: LF 68 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7070 (mtmt) REVERT: LH 55 MET cc_start: 0.7015 (tpp) cc_final: 0.6380 (tpt) REVERT: LI 41 LEU cc_start: 0.7845 (mt) cc_final: 0.7560 (mt) REVERT: LZ 44 PHE cc_start: 0.3735 (OUTLIER) cc_final: 0.3397 (t80) outliers start: 440 outliers final: 170 residues processed: 2040 average time/residue: 1.4079 time to fit residues: 4917.3847 Evaluate side-chains 1544 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1359 time to evaluate : 7.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SK residue 96 ILE Chi-restraints excluded: chain SK residue 109 ILE Chi-restraints excluded: chain SL residue 2 THR Chi-restraints excluded: chain SL residue 20 VAL Chi-restraints excluded: chain SM residue 43 LYS Chi-restraints excluded: chain SM residue 96 VAL Chi-restraints excluded: chain SN residue 29 ILE Chi-restraints excluded: chain SN residue 61 ASN Chi-restraints excluded: chain SN residue 84 ARG Chi-restraints excluded: chain SO residue 26 VAL Chi-restraints excluded: chain SP residue 26 ASN Chi-restraints excluded: chain SQ residue 41 THR Chi-restraints excluded: chain SQ residue 75 VAL Chi-restraints excluded: chain SQ residue 77 VAL Chi-restraints excluded: chain SR residue 41 SER Chi-restraints excluded: chain SS residue 12 LEU Chi-restraints excluded: chain SS residue 42 ASN Chi-restraints excluded: chain SB residue 8 MET Chi-restraints excluded: chain SB residue 79 VAL Chi-restraints excluded: chain SB residue 93 HIS Chi-restraints excluded: chain SB residue 129 THR Chi-restraints excluded: chain ST residue 34 VAL Chi-restraints excluded: chain SC residue 46 LEU Chi-restraints excluded: chain SC residue 51 VAL Chi-restraints excluded: chain SC residue 54 ILE Chi-restraints excluded: chain SC residue 148 ILE Chi-restraints excluded: chain SC residue 195 ILE Chi-restraints excluded: chain SD residue 24 VAL Chi-restraints excluded: chain SD residue 46 ARG Chi-restraints excluded: chain SD residue 52 VAL Chi-restraints excluded: chain SD residue 144 ILE Chi-restraints excluded: chain SD residue 187 ARG Chi-restraints excluded: chain SD residue 194 ILE Chi-restraints excluded: chain SD residue 199 ILE Chi-restraints excluded: chain SE residue 14 LEU Chi-restraints excluded: chain SE residue 24 VAL Chi-restraints excluded: chain SE residue 70 MET Chi-restraints excluded: chain SE residue 104 ILE Chi-restraints excluded: chain SE residue 162 GLU Chi-restraints excluded: chain SF residue 9 MET Chi-restraints excluded: chain SF residue 22 ILE Chi-restraints excluded: chain SG residue 29 LEU Chi-restraints excluded: chain SG residue 36 SER Chi-restraints excluded: chain SG residue 65 LEU Chi-restraints excluded: chain SG residue 89 GLU Chi-restraints excluded: chain SG residue 148 LYS Chi-restraints excluded: chain SG residue 161 PHE Chi-restraints excluded: chain SH residue 50 VAL Chi-restraints excluded: chain SH residue 53 ASP Chi-restraints excluded: chain SH residue 60 LEU Chi-restraints excluded: chain SH residue 74 ILE Chi-restraints excluded: chain SI residue 8 THR Chi-restraints excluded: chain SI residue 18 VAL Chi-restraints excluded: chain SI residue 92 SER Chi-restraints excluded: chain SI residue 103 VAL Chi-restraints excluded: chain S1 residue 9 TYR Chi-restraints excluded: chain S1 residue 18 ILE Chi-restraints excluded: chain S1 residue 83 ILE Chi-restraints excluded: chain S1 residue 92 VAL Chi-restraints excluded: chain S1 residue 206 ILE Chi-restraints excluded: chain S1 residue 209 ASP Chi-restraints excluded: chain S1 residue 221 LEU Chi-restraints excluded: chain S1 residue 263 VAL Chi-restraints excluded: chain S1 residue 274 VAL Chi-restraints excluded: chain S1 residue 279 ASP Chi-restraints excluded: chain S1 residue 289 VAL Chi-restraints excluded: chain S1 residue 295 ASN Chi-restraints excluded: chain S1 residue 394 ASP Chi-restraints excluded: chain S1 residue 396 LEU Chi-restraints excluded: chain S1 residue 397 CYS Chi-restraints excluded: chain S1 residue 482 VAL Chi-restraints excluded: chain S1 residue 514 TYR Chi-restraints excluded: chain S1 residue 518 VAL Chi-restraints excluded: chain S1 residue 547 GLU Chi-restraints excluded: chain S1 residue 553 ASP Chi-restraints excluded: chain S1 residue 583 HIS Chi-restraints excluded: chain S1 residue 633 ASP Chi-restraints excluded: chain S1 residue 634 LEU Chi-restraints excluded: chain LC residue 32 GLU Chi-restraints excluded: chain LC residue 225 ASP Chi-restraints excluded: chain LM residue 3 ILE Chi-restraints excluded: chain LM residue 16 VAL Chi-restraints excluded: chain LM residue 91 VAL Chi-restraints excluded: chain LN residue 9 SER Chi-restraints excluded: chain LN residue 12 ARG Chi-restraints excluded: chain LN residue 53 ILE Chi-restraints excluded: chain LN residue 191 LEU Chi-restraints excluded: chain LN residue 212 TRP Chi-restraints excluded: chain LN residue 230 PRO Chi-restraints excluded: chain LN residue 249 VAL Chi-restraints excluded: chain LO residue 50 ARG Chi-restraints excluded: chain LO residue 91 ARG Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LO residue 100 PHE Chi-restraints excluded: chain LQ residue 12 SER Chi-restraints excluded: chain LQ residue 39 THR Chi-restraints excluded: chain LQ residue 67 ASP Chi-restraints excluded: chain LQ residue 75 PHE Chi-restraints excluded: chain LQ residue 107 VAL Chi-restraints excluded: chain LR residue 61 LEU Chi-restraints excluded: chain LR residue 66 LYS Chi-restraints excluded: chain LR residue 80 TRP Chi-restraints excluded: chain LS residue 10 VAL Chi-restraints excluded: chain LS residue 27 VAL Chi-restraints excluded: chain LS residue 81 ARG Chi-restraints excluded: chain LT residue 17 SER Chi-restraints excluded: chain LT residue 30 ILE Chi-restraints excluded: chain LT residue 31 TYR Chi-restraints excluded: chain LT residue 62 THR Chi-restraints excluded: chain LT residue 77 VAL Chi-restraints excluded: chain LT residue 78 GLN Chi-restraints excluded: chain LT residue 82 TYR Chi-restraints excluded: chain LU residue 31 LEU Chi-restraints excluded: chain LU residue 56 HIS Chi-restraints excluded: chain LV residue 41 SER Chi-restraints excluded: chain LV residue 63 ILE Chi-restraints excluded: chain LV residue 64 ASP Chi-restraints excluded: chain LW residue 50 VAL Chi-restraints excluded: chain LX residue 2 ILE Chi-restraints excluded: chain LX residue 29 VAL Chi-restraints excluded: chain LX residue 60 VAL Chi-restraints excluded: chain LX residue 183 GLU Chi-restraints excluded: chain LY residue 56 VAL Chi-restraints excluded: chain L1 residue 31 LYS Chi-restraints excluded: chain L2 residue 10 LEU Chi-restraints excluded: chain L2 residue 16 THR Chi-restraints excluded: chain L3 residue 24 THR Chi-restraints excluded: chain L3 residue 44 VAL Chi-restraints excluded: chain L4 residue 29 ARG Chi-restraints excluded: chain L5 residue 17 VAL Chi-restraints excluded: chain L6 residue 7 ASP Chi-restraints excluded: chain L6 residue 13 THR Chi-restraints excluded: chain L6 residue 181 ILE Chi-restraints excluded: chain L6 residue 188 MET Chi-restraints excluded: chain LE residue 34 ILE Chi-restraints excluded: chain LE residue 48 ILE Chi-restraints excluded: chain LE residue 56 VAL Chi-restraints excluded: chain LE residue 72 THR Chi-restraints excluded: chain L7 residue 20 ASN Chi-restraints excluded: chain L7 residue 24 VAL Chi-restraints excluded: chain L7 residue 43 ILE Chi-restraints excluded: chain L7 residue 93 GLU Chi-restraints excluded: chain L7 residue 112 ASP Chi-restraints excluded: chain L8 residue 40 VAL Chi-restraints excluded: chain L8 residue 59 ASP Chi-restraints excluded: chain L8 residue 102 ILE Chi-restraints excluded: chain L8 residue 104 LEU Chi-restraints excluded: chain L8 residue 112 VAL Chi-restraints excluded: chain L8 residue 147 LEU Chi-restraints excluded: chain L8 residue 161 VAL Chi-restraints excluded: chain L9 residue 4 ILE Chi-restraints excluded: chain L9 residue 11 ASN Chi-restraints excluded: chain L9 residue 130 VAL Chi-restraints excluded: chain LF residue 3 THR Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 68 LYS Chi-restraints excluded: chain LF residue 70 THR Chi-restraints excluded: chain LF residue 78 THR Chi-restraints excluded: chain LF residue 81 ILE Chi-restraints excluded: chain LF residue 88 THR Chi-restraints excluded: chain LF residue 100 VAL Chi-restraints excluded: chain LF residue 120 ARG Chi-restraints excluded: chain LG residue 20 MET Chi-restraints excluded: chain LG residue 73 ASP Chi-restraints excluded: chain LG residue 99 ILE Chi-restraints excluded: chain LH residue 3 LEU Chi-restraints excluded: chain LH residue 64 PHE Chi-restraints excluded: chain LH residue 73 ILE Chi-restraints excluded: chain LH residue 84 LYS Chi-restraints excluded: chain LH residue 92 LEU Chi-restraints excluded: chain LH residue 118 THR Chi-restraints excluded: chain LH residue 121 THR Chi-restraints excluded: chain LH residue 122 VAL Chi-restraints excluded: chain LI residue 17 ASN Chi-restraints excluded: chain LI residue 57 VAL Chi-restraints excluded: chain LI residue 67 VAL Chi-restraints excluded: chain LI residue 78 LEU Chi-restraints excluded: chain LI residue 126 ILE Chi-restraints excluded: chain LJ residue 70 THR Chi-restraints excluded: chain LJ residue 76 VAL Chi-restraints excluded: chain LK residue 18 LEU Chi-restraints excluded: chain LK residue 63 LYS Chi-restraints excluded: chain LK residue 103 VAL Chi-restraints excluded: chain LZ residue 16 CYS Chi-restraints excluded: chain LZ residue 44 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1159 random chunks: chunk 1041 optimal weight: 9.9990 chunk 792 optimal weight: 9.9990 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: 20.0000 chunk 1120 optimal weight: 0.9990 chunk 552 optimal weight: 10.0000 chunk 1002 optimal weight: 9.9990 chunk 301 optimal weight: 2.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SJ 58 ASN ** SK 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 28 GLN SM 51 GLN SO 19 ASN ** SO 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SO 49 HIS SO 50 HIS SS 51 HIS ** SS 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ST 47 GLN ** 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 58 GLN SD 125 ASN ** 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 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SF 17 GLN ** SF 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 94 HIS SG 141 HIS S1 121 GLN S1 197 GLN S1 220 ASN ** S1 454 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** LC 47 ASN LC 67 HIS LC 129 GLN ** LC 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LM 74 GLN ** 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 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LR 92 ASN LT 49 ASN ** LT 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LU 2 HIS LV 33 HIS ** LD 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LW 20 ASN LW 45 GLN ** LX 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 148 GLN LX 150 GLN ** LY 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 18 HIS L3 26 ASN L4 42 HIS L6 29 HIS L6 41 GLN L6 90 GLN ** L6 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 93 ASN L8 37 ASN L8 63 GLN L8 127 GLN ** L9 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LG 9 ASN LG 93 GLN ** LH 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 1.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.217 169620 Z= 0.400 Angle : 0.944 19.400 252372 Z= 0.478 Chirality : 0.048 0.350 32049 Planarity : 0.009 0.118 14531 Dihedral : 24.145 179.610 81566 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.29 % Favored : 91.91 % Rotamer: Outliers : 7.76 % Allowed : 23.83 % Favored : 68.42 % Cbeta Deviations : 0.02 % 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: -2.30 (0.09), residues: 7019 helix: -0.78 (0.10), residues: 2229 sheet: -0.89 (0.14), residues: 1208 loop : -2.28 (0.09), residues: 3582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.006 TRPL8 61 HIS 0.110 0.004 HISLU 56 PHE 0.049 0.004 PHELC 180 TYR 0.054 0.004 TYRLD 83 ARG 0.045 0.002 ARGL8 54 *********************** 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 2143 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 449 poor density : 1694 time to evaluate : 6.990 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: SJ 51 VAL cc_start: 0.7589 (m) cc_final: 0.7360 (m) REVERT: SP 1 MET cc_start: 0.5197 (tmm) cc_final: 0.4857 (tmm) REVERT: SQ 36 PHE cc_start: 0.5853 (OUTLIER) cc_final: 0.5486 (t80) REVERT: SR 2 ARG cc_start: 0.3414 (tpm-80) cc_final: 0.2674 (mmm160) REVERT: SB 34 ARG cc_start: 0.5026 (OUTLIER) cc_final: 0.4423 (tpp80) REVERT: SB 153 MET cc_start: 0.4787 (mmm) cc_final: 0.4488 (mmm) REVERT: SU 38 GLU cc_start: 0.6167 (tp30) cc_final: 0.5803 (tp30) REVERT: SE 65 LYS cc_start: 0.7142 (tppt) cc_final: 0.6914 (tptt) REVERT: SF 88 MET cc_start: 0.2878 (OUTLIER) cc_final: 0.2477 (mmt) REVERT: SI 56 MET cc_start: 0.3636 (OUTLIER) cc_final: 0.2908 (mmm) REVERT: S1 28 ARG cc_start: 0.6366 (mmm160) cc_final: 0.6162 (mmt-90) REVERT: S1 49 MET cc_start: 0.6026 (tpp) cc_final: 0.5816 (tpp) REVERT: S1 53 GLU cc_start: 0.4004 (tp30) cc_final: 0.3299 (tp30) REVERT: S1 547 GLU cc_start: 0.6034 (OUTLIER) cc_final: 0.5812 (tp30) REVERT: LC 121 MET cc_start: 0.2089 (ppp) cc_final: 0.0573 (ttt) REVERT: LN 139 THR cc_start: 0.7824 (p) cc_final: 0.7573 (p) REVERT: LO 50 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7057 (mtm-85) REVERT: LR 66 LYS cc_start: 0.6098 (OUTLIER) cc_final: 0.5498 (pttt) REVERT: LU 76 ARG cc_start: 0.5033 (OUTLIER) cc_final: 0.4400 (mmm-85) REVERT: LV 31 ASN cc_start: 0.8461 (t0) cc_final: 0.8090 (t0) REVERT: LV 60 LYS cc_start: 0.5593 (OUTLIER) cc_final: 0.4909 (tttt) REVERT: LD 139 MET cc_start: 0.1969 (ttt) cc_final: 0.1419 (mtm) REVERT: LW 14 LEU cc_start: 0.5702 (tp) cc_final: 0.5270 (mt) REVERT: L3 24 THR cc_start: 0.7319 (OUTLIER) cc_final: 0.7095 (p) REVERT: L4 29 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.6419 (ptm160) REVERT: LF 85 LYS cc_start: 0.6819 (OUTLIER) cc_final: 0.6363 (mtpt) REVERT: LG 20 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.7005 (ttp) REVERT: LG 88 ASN cc_start: 0.6372 (m-40) cc_final: 0.6104 (m-40) REVERT: LH 55 MET cc_start: 0.7135 (tpp) cc_final: 0.6641 (tpt) outliers start: 449 outliers final: 223 residues processed: 1923 average time/residue: 1.3507 time to fit residues: 4495.8993 Evaluate side-chains 1600 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1364 time to evaluate : 6.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SJ residue 52 LEU Chi-restraints excluded: chain SJ residue 83 THR Chi-restraints excluded: chain SK residue 19 VAL Chi-restraints excluded: chain SK residue 83 VAL Chi-restraints excluded: chain SL residue 20 VAL Chi-restraints excluded: chain SL residue 39 THR Chi-restraints excluded: chain SL residue 40 THR Chi-restraints excluded: chain SL residue 54 VAL Chi-restraints excluded: chain SL residue 64 SER Chi-restraints excluded: chain SL residue 86 VAL Chi-restraints excluded: chain SL residue 92 VAL Chi-restraints excluded: chain SL residue 104 SER Chi-restraints excluded: chain SL residue 109 ARG Chi-restraints excluded: chain SL residue 116 TYR Chi-restraints excluded: chain SL residue 118 VAL Chi-restraints excluded: chain SM residue 32 ILE Chi-restraints excluded: chain SM residue 55 LEU Chi-restraints excluded: chain SM residue 103 THR Chi-restraints excluded: chain SN residue 29 ILE Chi-restraints excluded: chain SN residue 61 ASN Chi-restraints excluded: chain SO residue 26 VAL Chi-restraints excluded: chain SO residue 55 LEU Chi-restraints excluded: chain SO residue 86 LEU Chi-restraints excluded: chain SP residue 20 VAL Chi-restraints excluded: chain SP residue 79 ASN Chi-restraints excluded: chain SQ residue 19 SER Chi-restraints excluded: chain SQ residue 28 VAL Chi-restraints excluded: chain SQ residue 36 PHE Chi-restraints excluded: chain SQ residue 41 THR Chi-restraints excluded: chain SQ residue 59 GLU Chi-restraints excluded: chain SQ residue 77 VAL Chi-restraints excluded: chain SR residue 41 SER Chi-restraints excluded: chain SR residue 43 ILE Chi-restraints excluded: chain SR residue 54 LEU Chi-restraints excluded: chain SR residue 58 ILE Chi-restraints excluded: chain SR residue 69 TYR Chi-restraints excluded: chain SS residue 12 LEU Chi-restraints excluded: chain SS residue 38 THR Chi-restraints excluded: chain SB residue 19 THR Chi-restraints excluded: chain SB residue 22 TRP Chi-restraints excluded: chain SB residue 34 ARG Chi-restraints excluded: chain SB residue 38 HIS Chi-restraints excluded: chain SB residue 79 VAL Chi-restraints excluded: chain SB residue 109 SER Chi-restraints excluded: chain SB residue 117 GLU Chi-restraints excluded: chain SB residue 129 THR Chi-restraints excluded: chain SB residue 182 VAL Chi-restraints excluded: chain SB residue 198 VAL Chi-restraints excluded: chain SB residue 207 ARG Chi-restraints excluded: chain SB residue 210 THR Chi-restraints excluded: chain ST residue 38 ILE Chi-restraints excluded: chain SC residue 13 ILE Chi-restraints excluded: chain SC residue 31 ASN Chi-restraints excluded: chain SC residue 35 ASP Chi-restraints excluded: chain SC residue 46 LEU Chi-restraints excluded: chain SC residue 120 THR Chi-restraints excluded: chain SC residue 148 ILE Chi-restraints excluded: chain SC residue 185 THR Chi-restraints excluded: chain SD residue 52 VAL Chi-restraints excluded: chain SD residue 102 TYR Chi-restraints excluded: chain SD residue 142 VAL Chi-restraints excluded: chain SD residue 144 ILE Chi-restraints excluded: chain SD residue 170 LEU Chi-restraints excluded: chain SD residue 187 ARG Chi-restraints excluded: chain SD residue 191 SER Chi-restraints excluded: chain SD residue 194 ILE Chi-restraints excluded: chain SE residue 14 LEU Chi-restraints excluded: chain SE residue 70 MET Chi-restraints excluded: chain SE residue 73 VAL Chi-restraints excluded: chain SE residue 104 ILE Chi-restraints excluded: chain SF residue 9 MET Chi-restraints excluded: chain SF residue 10 VAL Chi-restraints excluded: chain SF residue 22 ILE Chi-restraints excluded: chain SF residue 61 LEU Chi-restraints excluded: chain SF residue 88 MET Chi-restraints excluded: chain SG residue 79 VAL Chi-restraints excluded: chain SG residue 105 GLU Chi-restraints excluded: chain SG residue 161 PHE Chi-restraints excluded: chain SH residue 60 LEU Chi-restraints excluded: chain SH residue 89 ASP Chi-restraints excluded: chain SH residue 102 VAL Chi-restraints excluded: chain SH residue 105 THR Chi-restraints excluded: chain SH residue 111 THR Chi-restraints excluded: chain SI residue 18 VAL Chi-restraints excluded: chain SI residue 56 MET Chi-restraints excluded: chain SI residue 92 SER Chi-restraints excluded: chain S1 residue 9 TYR Chi-restraints excluded: chain S1 residue 18 ILE Chi-restraints excluded: chain S1 residue 67 THR Chi-restraints excluded: chain S1 residue 92 VAL Chi-restraints excluded: chain S1 residue 137 ILE Chi-restraints excluded: chain S1 residue 181 VAL Chi-restraints excluded: chain S1 residue 263 VAL Chi-restraints excluded: chain S1 residue 342 VAL Chi-restraints excluded: chain S1 residue 348 VAL Chi-restraints excluded: chain S1 residue 351 SER Chi-restraints excluded: chain S1 residue 363 VAL Chi-restraints excluded: chain S1 residue 397 CYS Chi-restraints excluded: chain S1 residue 404 ILE Chi-restraints excluded: chain S1 residue 422 LYS Chi-restraints excluded: chain S1 residue 426 ASP Chi-restraints excluded: chain S1 residue 482 VAL Chi-restraints excluded: chain S1 residue 514 TYR Chi-restraints excluded: chain S1 residue 518 VAL Chi-restraints excluded: chain S1 residue 547 GLU Chi-restraints excluded: chain S1 residue 553 ASP Chi-restraints excluded: chain S1 residue 582 TYR Chi-restraints excluded: chain S1 residue 585 VAL Chi-restraints excluded: chain S1 residue 633 ASP Chi-restraints excluded: chain S1 residue 634 LEU Chi-restraints excluded: chain LC residue 24 ASN Chi-restraints excluded: chain LC residue 202 THR Chi-restraints excluded: chain LC residue 203 GLN Chi-restraints excluded: chain LM residue 3 ILE Chi-restraints excluded: chain LM residue 13 LYS Chi-restraints excluded: chain LM residue 16 VAL Chi-restraints excluded: chain LM residue 25 VAL Chi-restraints excluded: chain LM residue 91 VAL Chi-restraints excluded: chain LM residue 99 LEU Chi-restraints excluded: chain LN residue 9 SER Chi-restraints excluded: chain LN residue 38 LYS Chi-restraints excluded: chain LN residue 63 ILE Chi-restraints excluded: chain LN residue 93 VAL Chi-restraints excluded: chain LN residue 136 VAL Chi-restraints excluded: chain LN residue 159 THR Chi-restraints excluded: chain LN residue 225 ASN Chi-restraints excluded: chain LN residue 249 VAL Chi-restraints excluded: chain LO residue 50 ARG Chi-restraints excluded: chain LO residue 91 ARG Chi-restraints excluded: chain LP residue 4 VAL Chi-restraints excluded: chain LP residue 22 LEU Chi-restraints excluded: chain LP residue 33 VAL Chi-restraints excluded: chain LP residue 63 VAL Chi-restraints excluded: chain LP residue 99 THR Chi-restraints excluded: chain LQ residue 101 SER Chi-restraints excluded: chain LR residue 66 LYS Chi-restraints excluded: chain LR residue 80 TRP Chi-restraints excluded: chain LS residue 12 VAL Chi-restraints excluded: chain LS residue 27 VAL Chi-restraints excluded: chain LT residue 45 ASP Chi-restraints excluded: chain LT residue 47 VAL Chi-restraints excluded: chain LT residue 49 ASN Chi-restraints excluded: chain LT residue 56 PHE Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 77 VAL Chi-restraints excluded: chain LT residue 90 ASP Chi-restraints excluded: chain LT residue 92 VAL Chi-restraints excluded: chain LU residue 56 HIS Chi-restraints excluded: chain LU residue 76 ARG Chi-restraints excluded: chain LV residue 7 THR Chi-restraints excluded: chain LV residue 39 VAL Chi-restraints excluded: chain LV residue 60 LYS Chi-restraints excluded: chain LV residue 63 ILE Chi-restraints excluded: chain LV residue 64 ASP Chi-restraints excluded: chain LW residue 55 THR Chi-restraints excluded: chain LX residue 2 ILE Chi-restraints excluded: chain LX residue 43 ASP Chi-restraints excluded: chain LX residue 177 VAL Chi-restraints excluded: chain LX residue 178 VAL Chi-restraints excluded: chain LX residue 201 LEU Chi-restraints excluded: chain LY residue 54 VAL Chi-restraints excluded: chain L1 residue 8 THR Chi-restraints excluded: chain L1 residue 43 THR Chi-restraints excluded: chain L1 residue 48 TYR Chi-restraints excluded: chain L1 residue 54 ILE Chi-restraints excluded: chain L2 residue 10 LEU Chi-restraints excluded: chain L2 residue 21 THR Chi-restraints excluded: chain L3 residue 24 THR Chi-restraints excluded: chain L3 residue 43 THR Chi-restraints excluded: chain L4 residue 29 ARG Chi-restraints excluded: chain L6 residue 7 ASP Chi-restraints excluded: chain L6 residue 16 GLU Chi-restraints excluded: chain L6 residue 33 VAL Chi-restraints excluded: chain L6 residue 48 THR Chi-restraints excluded: chain L6 residue 83 VAL Chi-restraints excluded: chain L6 residue 84 THR Chi-restraints excluded: chain L6 residue 173 THR Chi-restraints excluded: chain L6 residue 180 LEU Chi-restraints excluded: chain LE residue 34 ILE Chi-restraints excluded: chain LE residue 48 ILE Chi-restraints excluded: chain LE residue 56 VAL Chi-restraints excluded: chain LE residue 57 VAL Chi-restraints excluded: chain LE residue 72 THR Chi-restraints excluded: chain LE residue 94 LYS Chi-restraints excluded: chain L7 residue 17 THR Chi-restraints excluded: chain L7 residue 20 ASN Chi-restraints excluded: chain L7 residue 24 VAL Chi-restraints excluded: chain L7 residue 33 ILE Chi-restraints excluded: chain L7 residue 60 SER Chi-restraints excluded: chain L7 residue 67 THR Chi-restraints excluded: chain L7 residue 88 VAL Chi-restraints excluded: chain L7 residue 131 VAL Chi-restraints excluded: chain L7 residue 136 ILE Chi-restraints excluded: chain L7 residue 153 ILE Chi-restraints excluded: chain L8 residue 59 ASP Chi-restraints excluded: chain L8 residue 73 SER Chi-restraints excluded: chain L8 residue 75 VAL Chi-restraints excluded: chain L8 residue 128 THR Chi-restraints excluded: chain L8 residue 147 LEU Chi-restraints excluded: chain L8 residue 150 TYR Chi-restraints excluded: chain L8 residue 161 VAL Chi-restraints excluded: chain L9 residue 4 ILE Chi-restraints excluded: chain L9 residue 125 THR Chi-restraints excluded: chain LF residue 3 THR Chi-restraints excluded: chain LF residue 10 THR Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 52 ASP Chi-restraints excluded: chain LF residue 78 THR Chi-restraints excluded: chain LF residue 81 ILE Chi-restraints excluded: chain LF residue 84 ILE Chi-restraints excluded: chain LF residue 85 LYS Chi-restraints excluded: chain LG residue 1 MET Chi-restraints excluded: chain LG residue 8 LEU Chi-restraints excluded: chain LG residue 20 MET Chi-restraints excluded: chain LG residue 61 VAL Chi-restraints excluded: chain LG residue 76 VAL Chi-restraints excluded: chain LG residue 84 CYS Chi-restraints excluded: chain LG residue 92 GLU Chi-restraints excluded: chain LH residue 23 ILE Chi-restraints excluded: chain LH residue 64 PHE Chi-restraints excluded: chain LH residue 92 LEU Chi-restraints excluded: chain LH residue 121 THR Chi-restraints excluded: chain LH residue 122 VAL Chi-restraints excluded: chain LH residue 142 ILE Chi-restraints excluded: chain LI residue 7 THR Chi-restraints excluded: chain LI residue 17 ASN Chi-restraints excluded: chain LI residue 67 VAL Chi-restraints excluded: chain LI residue 88 ASN Chi-restraints excluded: chain LI residue 126 ILE Chi-restraints excluded: chain LI residue 128 THR Chi-restraints excluded: chain LJ residue 8 ARG Chi-restraints excluded: chain LJ residue 27 SER Chi-restraints excluded: chain LJ residue 76 VAL Chi-restraints excluded: chain LJ residue 94 TYR Chi-restraints excluded: chain LK residue 17 LYS Chi-restraints excluded: chain LK residue 63 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1159 random chunks: chunk 933 optimal weight: 30.0000 chunk 635 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 834 optimal weight: 0.2980 chunk 462 optimal weight: 9.9990 chunk 955 optimal weight: 8.9990 chunk 774 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 572 optimal weight: 20.0000 chunk 1005 optimal weight: 0.7980 chunk 282 optimal weight: 0.0970 overall best weight: 4.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SK 100 ASN SL 5 GLN SM 51 GLN SO 41 HIS ** SP 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ST 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ST 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 40 GLN ** SC 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 121 ASN ** SF 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SG 129 ASN SG 141 HIS SI 125 GLN ** S1 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 121 GLN ** LC 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 51 ASN LM 74 GLN ** LM 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LN 44 ASN ** LN 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 238 ASN LP 6 GLN ** LP 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 51 GLN ** LT 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LV 33 HIS ** LV 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L6 97 ASN ** L6 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 195 GLN LE 104 GLN L7 80 GLN L8 63 GLN LF 40 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 1.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 169620 Z= 0.222 Angle : 0.699 14.648 252372 Z= 0.357 Chirality : 0.038 0.313 32049 Planarity : 0.006 0.072 14531 Dihedral : 23.882 179.831 81562 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.85 % Favored : 91.52 % Rotamer: Outliers : 5.37 % Allowed : 28.11 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.09), residues: 7019 helix: -0.21 (0.10), residues: 2241 sheet: -0.80 (0.14), residues: 1254 loop : -2.11 (0.10), residues: 3524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRPLM 30 HIS 0.033 0.002 HISLU 56 PHE 0.040 0.002 PHELN 66 TYR 0.024 0.002 TYRSD 134 ARG 0.015 0.001 ARGS1 436 *********************** 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 1830 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 1519 time to evaluate : 6.994 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: SJ 51 VAL cc_start: 0.7805 (m) cc_final: 0.7589 (m) REVERT: SK 84 MET cc_start: 0.6590 (mmm) cc_final: 0.6057 (mmt) REVERT: SL 64 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.8256 (t) REVERT: SR 2 ARG cc_start: 0.3794 (tpm-80) cc_final: 0.3370 (mmm160) REVERT: SU 38 GLU cc_start: 0.6311 (tp30) cc_final: 0.6048 (mm-30) REVERT: SF 79 ARG cc_start: 0.5578 (tpt-90) cc_final: 0.5289 (tpp80) REVERT: SI 56 MET cc_start: 0.3320 (OUTLIER) cc_final: 0.2847 (mmm) REVERT: S1 28 ARG cc_start: 0.6527 (mmm160) cc_final: 0.6326 (mmt-90) REVERT: S1 105 LEU cc_start: 0.6487 (mt) cc_final: 0.6100 (mt) REVERT: S1 460 MET cc_start: 0.4996 (mmt) cc_final: 0.4685 (mmp) REVERT: S1 531 LYS cc_start: 0.6348 (OUTLIER) cc_final: 0.5896 (tptp) REVERT: S1 659 LEU cc_start: 0.7337 (tt) cc_final: 0.6897 (tt) REVERT: LC 121 MET cc_start: 0.2214 (ppp) cc_final: 0.0769 (ttt) REVERT: LC 193 LEU cc_start: 0.5394 (OUTLIER) cc_final: 0.5118 (pp) REVERT: LC 229 LEU cc_start: 0.3799 (OUTLIER) cc_final: 0.2623 (mp) REVERT: LO 51 GLN cc_start: 0.6556 (tp40) cc_final: 0.6296 (tp40) REVERT: LQ 12 SER cc_start: 0.7610 (OUTLIER) cc_final: 0.7391 (p) REVERT: LQ 92 ARG cc_start: 0.7171 (ptp90) cc_final: 0.6909 (ptt180) REVERT: LR 66 LYS cc_start: 0.6317 (OUTLIER) cc_final: 0.5981 (pttt) REVERT: LU 76 ARG cc_start: 0.5113 (OUTLIER) cc_final: 0.4401 (mmm-85) REVERT: LD 139 MET cc_start: 0.2081 (ttt) cc_final: 0.1419 (mtt) REVERT: LX 46 ARG cc_start: 0.7058 (ttm-80) cc_final: 0.6762 (ttm-80) REVERT: L2 5 ARG cc_start: 0.7851 (mtm180) cc_final: 0.7576 (mtp180) REVERT: L4 28 LEU cc_start: 0.7377 (tt) cc_final: 0.7169 (tp) REVERT: LG 20 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6857 (ttp) REVERT: LH 58 TYR cc_start: 0.8135 (p90) cc_final: 0.7917 (p90) REVERT: LZ 39 LYS cc_start: 0.4819 (tptp) cc_final: 0.4511 (mmtt) REVERT: LZ 44 PHE cc_start: 0.4235 (OUTLIER) cc_final: 0.3840 (t80) outliers start: 311 outliers final: 182 residues processed: 1685 average time/residue: 1.3299 time to fit residues: 3929.5704 Evaluate side-chains 1540 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1348 time to evaluate : 6.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SJ residue 17 LEU Chi-restraints excluded: chain SJ residue 85 ASP Chi-restraints excluded: chain SK residue 19 VAL Chi-restraints excluded: chain SK residue 32 THR Chi-restraints excluded: chain SL residue 20 VAL Chi-restraints excluded: chain SL residue 54 VAL Chi-restraints excluded: chain SL residue 64 SER Chi-restraints excluded: chain SL residue 86 VAL Chi-restraints excluded: chain SL residue 104 SER Chi-restraints excluded: chain SM residue 96 VAL Chi-restraints excluded: chain SN residue 4 SER Chi-restraints excluded: chain SN residue 29 ILE Chi-restraints excluded: chain SN residue 61 ASN Chi-restraints excluded: chain SQ residue 19 SER Chi-restraints excluded: chain SQ residue 43 LEU Chi-restraints excluded: chain SQ residue 44 HIS Chi-restraints excluded: chain SQ residue 77 VAL Chi-restraints excluded: chain SR residue 38 ILE Chi-restraints excluded: chain SR residue 41 SER Chi-restraints excluded: chain SB residue 22 TRP Chi-restraints excluded: chain SB residue 79 VAL Chi-restraints excluded: chain SB residue 129 THR Chi-restraints excluded: chain SB residue 198 VAL Chi-restraints excluded: chain SB residue 207 ARG Chi-restraints excluded: chain ST residue 34 VAL Chi-restraints excluded: chain SC residue 31 ASN Chi-restraints excluded: chain SC residue 51 VAL Chi-restraints excluded: chain SC residue 148 ILE Chi-restraints excluded: chain SC residue 185 THR Chi-restraints excluded: chain SC residue 191 THR Chi-restraints excluded: chain SD residue 24 VAL Chi-restraints excluded: chain SD residue 52 VAL Chi-restraints excluded: chain SD residue 187 ARG Chi-restraints excluded: chain SD residue 194 ILE Chi-restraints excluded: chain SE residue 14 LEU Chi-restraints excluded: chain SE residue 38 VAL Chi-restraints excluded: chain SE residue 79 THR Chi-restraints excluded: chain SE residue 104 ILE Chi-restraints excluded: chain SE residue 143 LEU Chi-restraints excluded: chain SF residue 22 ILE Chi-restraints excluded: chain SF residue 97 THR Chi-restraints excluded: chain SG residue 29 LEU Chi-restraints excluded: chain SG residue 44 SER Chi-restraints excluded: chain SG residue 46 LEU Chi-restraints excluded: chain SG residue 85 GLN Chi-restraints excluded: chain SG residue 86 VAL Chi-restraints excluded: chain SG residue 129 ASN Chi-restraints excluded: chain SH residue 60 LEU Chi-restraints excluded: chain SH residue 74 ILE Chi-restraints excluded: chain SH residue 105 THR Chi-restraints excluded: chain SH residue 111 THR Chi-restraints excluded: chain SI residue 34 LEU Chi-restraints excluded: chain SI residue 56 MET Chi-restraints excluded: chain SI residue 74 GLN Chi-restraints excluded: chain S1 residue 9 TYR Chi-restraints excluded: chain S1 residue 67 THR Chi-restraints excluded: chain S1 residue 83 ILE Chi-restraints excluded: chain S1 residue 85 ILE Chi-restraints excluded: chain S1 residue 206 ILE Chi-restraints excluded: chain S1 residue 263 VAL Chi-restraints excluded: chain S1 residue 333 THR Chi-restraints excluded: chain S1 residue 348 VAL Chi-restraints excluded: chain S1 residue 394 ASP Chi-restraints excluded: chain S1 residue 397 CYS Chi-restraints excluded: chain S1 residue 404 ILE Chi-restraints excluded: chain S1 residue 514 TYR Chi-restraints excluded: chain S1 residue 518 VAL Chi-restraints excluded: chain S1 residue 531 LYS Chi-restraints excluded: chain S1 residue 553 ASP Chi-restraints excluded: chain S1 residue 633 ASP Chi-restraints excluded: chain S1 residue 634 LEU Chi-restraints excluded: chain S1 residue 657 VAL Chi-restraints excluded: chain S1 residue 660 SER Chi-restraints excluded: chain S1 residue 688 GLU Chi-restraints excluded: chain LC residue 24 ASN Chi-restraints excluded: chain LC residue 32 GLU Chi-restraints excluded: chain LC residue 33 LEU Chi-restraints excluded: chain LC residue 193 LEU Chi-restraints excluded: chain LC residue 203 GLN Chi-restraints excluded: chain LC residue 229 LEU Chi-restraints excluded: chain LM residue 3 ILE Chi-restraints excluded: chain LM residue 25 VAL Chi-restraints excluded: chain LM residue 27 VAL Chi-restraints excluded: chain LM residue 46 VAL Chi-restraints excluded: chain LM residue 83 ILE Chi-restraints excluded: chain LM residue 91 VAL Chi-restraints excluded: chain LM residue 99 LEU Chi-restraints excluded: chain LN residue 2 VAL Chi-restraints excluded: chain LN residue 53 ILE Chi-restraints excluded: chain LN residue 63 ILE Chi-restraints excluded: chain LN residue 134 ILE Chi-restraints excluded: chain LN residue 224 MET Chi-restraints excluded: chain LN residue 225 ASN Chi-restraints excluded: chain LN residue 238 ASN Chi-restraints excluded: chain LN residue 249 VAL Chi-restraints excluded: chain LO residue 91 ARG Chi-restraints excluded: chain LP residue 63 VAL Chi-restraints excluded: chain LQ residue 4 ILE Chi-restraints excluded: chain LQ residue 12 SER Chi-restraints excluded: chain LQ residue 61 ASN Chi-restraints excluded: chain LQ residue 85 ILE Chi-restraints excluded: chain LQ residue 101 SER Chi-restraints excluded: chain LQ residue 106 VAL Chi-restraints excluded: chain LR residue 61 LEU Chi-restraints excluded: chain LR residue 62 VAL Chi-restraints excluded: chain LR residue 66 LYS Chi-restraints excluded: chain LR residue 80 TRP Chi-restraints excluded: chain LS residue 14 THR Chi-restraints excluded: chain LS residue 27 VAL Chi-restraints excluded: chain LS residue 51 LEU Chi-restraints excluded: chain LT residue 51 GLN Chi-restraints excluded: chain LT residue 62 THR Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 77 VAL Chi-restraints excluded: chain LT residue 87 GLN Chi-restraints excluded: chain LU residue 15 SER Chi-restraints excluded: chain LU residue 63 ASP Chi-restraints excluded: chain LU residue 76 ARG Chi-restraints excluded: chain LV residue 21 LEU Chi-restraints excluded: chain LV residue 39 VAL Chi-restraints excluded: chain LV residue 64 ASP Chi-restraints excluded: chain LW residue 22 LEU Chi-restraints excluded: chain LW residue 50 VAL Chi-restraints excluded: chain LX residue 2 ILE Chi-restraints excluded: chain LX residue 25 THR Chi-restraints excluded: chain LX residue 175 LEU Chi-restraints excluded: chain LX residue 177 VAL Chi-restraints excluded: chain LX residue 178 VAL Chi-restraints excluded: chain LX residue 203 VAL Chi-restraints excluded: chain LY residue 47 ILE Chi-restraints excluded: chain L1 residue 14 MET Chi-restraints excluded: chain L1 residue 48 TYR Chi-restraints excluded: chain L3 residue 24 THR Chi-restraints excluded: chain L3 residue 43 THR Chi-restraints excluded: chain L4 residue 54 LEU Chi-restraints excluded: chain L5 residue 17 VAL Chi-restraints excluded: chain L6 residue 7 ASP Chi-restraints excluded: chain L6 residue 22 ASP Chi-restraints excluded: chain L6 residue 75 SER Chi-restraints excluded: chain L6 residue 84 THR Chi-restraints excluded: chain L6 residue 180 LEU Chi-restraints excluded: chain LE residue 34 ILE Chi-restraints excluded: chain LE residue 48 ILE Chi-restraints excluded: chain LE residue 56 VAL Chi-restraints excluded: chain LE residue 72 THR Chi-restraints excluded: chain L7 residue 5 ASP Chi-restraints excluded: chain L7 residue 20 ASN Chi-restraints excluded: chain L7 residue 22 ASN Chi-restraints excluded: chain L7 residue 24 VAL Chi-restraints excluded: chain L7 residue 39 VAL Chi-restraints excluded: chain L7 residue 88 VAL Chi-restraints excluded: chain L8 residue 40 VAL Chi-restraints excluded: chain L8 residue 59 ASP Chi-restraints excluded: chain L8 residue 113 ASP Chi-restraints excluded: chain L8 residue 128 THR Chi-restraints excluded: chain L8 residue 147 LEU Chi-restraints excluded: chain L8 residue 161 VAL Chi-restraints excluded: chain L9 residue 46 PHE Chi-restraints excluded: chain L9 residue 78 VAL Chi-restraints excluded: chain L9 residue 143 ILE Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 70 THR Chi-restraints excluded: chain LF residue 78 THR Chi-restraints excluded: chain LF residue 81 ILE Chi-restraints excluded: chain LF residue 101 ILE Chi-restraints excluded: chain LG residue 10 VAL Chi-restraints excluded: chain LG residue 20 MET Chi-restraints excluded: chain LG residue 21 CYS Chi-restraints excluded: chain LG residue 61 VAL Chi-restraints excluded: chain LG residue 77 ILE Chi-restraints excluded: chain LG residue 99 ILE Chi-restraints excluded: chain LH residue 64 PHE Chi-restraints excluded: chain LH residue 84 LYS Chi-restraints excluded: chain LH residue 92 LEU Chi-restraints excluded: chain LH residue 100 ILE Chi-restraints excluded: chain LH residue 118 THR Chi-restraints excluded: chain LH residue 120 VAL Chi-restraints excluded: chain LH residue 121 THR Chi-restraints excluded: chain LI residue 17 ASN Chi-restraints excluded: chain LI residue 67 VAL Chi-restraints excluded: chain LI residue 95 LEU Chi-restraints excluded: chain LI residue 96 ILE Chi-restraints excluded: chain LI residue 105 MET Chi-restraints excluded: chain LI residue 126 ILE Chi-restraints excluded: chain LJ residue 13 ASN Chi-restraints excluded: chain LJ residue 18 GLN Chi-restraints excluded: chain LJ residue 27 SER Chi-restraints excluded: chain LJ residue 79 LEU Chi-restraints excluded: chain LZ residue 16 CYS Chi-restraints excluded: chain LZ residue 24 ILE Chi-restraints excluded: chain LZ residue 35 ASP Chi-restraints excluded: chain LZ residue 44 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1159 random chunks: chunk 376 optimal weight: 3.9990 chunk 1008 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 657 optimal weight: 30.0000 chunk 276 optimal weight: 0.0010 chunk 1121 optimal weight: 8.9990 chunk 930 optimal weight: 6.9990 chunk 519 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 370 optimal weight: 9.9990 chunk 588 optimal weight: 10.0000 overall best weight: 3.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SK 100 ASN SN 34 ASN SN 59 GLN SO 39 GLN ** SP 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 44 HIS ** SS 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 145 ASN ST 20 ASN ST 60 GLN ** SC 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SC 31 ASN SD 35 GLN ** SE 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 14 GLN ** SF 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 55 HIS SG 141 HIS ** SG 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 178 ASN SH 75 GLN SI 109 GLN SI 125 GLN S1 77 GLN ** S1 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 168 ASN LM 51 ASN LM 76 HIS ** LN 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 36 GLN ** LP 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LV 33 HIS LD 87 HIS LX 148 GLN LX 164 GLN L6 163 ASN L7 80 GLN L9 18 GLN LG 9 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 1.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 169620 Z= 0.209 Angle : 0.666 13.777 252372 Z= 0.341 Chirality : 0.037 0.269 32049 Planarity : 0.006 0.095 14531 Dihedral : 23.782 179.848 81561 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.72 % Favored : 91.68 % Rotamer: Outliers : 5.63 % Allowed : 28.65 % Favored : 65.72 % Cbeta Deviations : 0.02 % 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: -1.70 (0.10), residues: 7019 helix: 0.03 (0.11), residues: 2239 sheet: -0.81 (0.14), residues: 1218 loop : -2.05 (0.10), residues: 3562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRPLM 30 HIS 0.015 0.001 HISSF 55 PHE 0.031 0.002 PHELN 66 TYR 0.024 0.002 TYRLZ 9 ARG 0.016 0.001 ARGSM 106 *********************** 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 1799 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 1473 time to evaluate : 7.016 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: SJ 1 MET cc_start: 0.1982 (mmp) cc_final: 0.0314 (mmm) REVERT: SJ 71 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5940 (tt) REVERT: SK 84 MET cc_start: 0.6514 (mmm) cc_final: 0.6048 (mmt) REVERT: SP 1 MET cc_start: 0.5049 (tmm) cc_final: 0.4455 (tmm) REVERT: SR 2 ARG cc_start: 0.3552 (OUTLIER) cc_final: 0.2391 (tpt170) REVERT: SB 5 MET cc_start: 0.3718 (ppp) cc_final: 0.3504 (ppp) REVERT: SB 34 ARG cc_start: 0.4860 (OUTLIER) cc_final: 0.3909 (tpp80) REVERT: ST 30 PHE cc_start: 0.4100 (t80) cc_final: 0.3856 (t80) REVERT: SU 38 GLU cc_start: 0.6295 (tp30) cc_final: 0.6032 (mm-30) REVERT: SD 123 MET cc_start: 0.6486 (ttp) cc_final: 0.6270 (ttp) REVERT: SD 144 ILE cc_start: 0.5798 (OUTLIER) cc_final: 0.5491 (pt) REVERT: SE 13 LYS cc_start: 0.6108 (mttp) cc_final: 0.5206 (mptt) REVERT: SF 79 ARG cc_start: 0.5580 (tpt-90) cc_final: 0.5291 (tpp80) REVERT: SI 56 MET cc_start: 0.3594 (mmm) cc_final: 0.3205 (mmm) REVERT: S1 54 GLN cc_start: 0.5645 (mm-40) cc_final: 0.5183 (mm110) REVERT: S1 396 LEU cc_start: 0.4935 (OUTLIER) cc_final: 0.4358 (mp) REVERT: S1 422 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6942 (ptpp) REVERT: S1 460 MET cc_start: 0.5188 (mmt) cc_final: 0.4962 (mmp) REVERT: S1 531 LYS cc_start: 0.6290 (OUTLIER) cc_final: 0.5929 (tptp) REVERT: LC 121 MET cc_start: 0.2079 (ppp) cc_final: 0.0952 (ttt) REVERT: LC 229 LEU cc_start: 0.4260 (OUTLIER) cc_final: 0.2876 (mp) REVERT: LN 81 GLU cc_start: 0.6647 (mt-10) cc_final: 0.6415 (mt-10) REVERT: LO 51 GLN cc_start: 0.6762 (tp40) cc_final: 0.6537 (tp40) REVERT: LP 86 GLN cc_start: 0.7813 (pm20) cc_final: 0.7399 (pm20) REVERT: LQ 77 ASP cc_start: 0.7837 (p0) cc_final: 0.7600 (p0) REVERT: LR 66 LYS cc_start: 0.6662 (OUTLIER) cc_final: 0.6436 (pttm) REVERT: LT 41 GLU cc_start: 0.5564 (pt0) cc_final: 0.4976 (pt0) REVERT: LT 47 VAL cc_start: 0.6138 (OUTLIER) cc_final: 0.5903 (m) REVERT: LV 60 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.5773 (ptmt) REVERT: LD 85 MET cc_start: 0.4468 (ppp) cc_final: 0.0727 (mmp) REVERT: LD 139 MET cc_start: 0.2330 (ttt) cc_final: 0.1544 (mtm) REVERT: LX 46 ARG cc_start: 0.6975 (ttm-80) cc_final: 0.6692 (ttm-80) REVERT: LJ 44 LEU cc_start: 0.8214 (tp) cc_final: 0.7925 (tp) REVERT: LZ 1 MET cc_start: 0.5565 (tpt) cc_final: 0.5186 (mmm) REVERT: LZ 44 PHE cc_start: 0.4756 (OUTLIER) cc_final: 0.4404 (t80) outliers start: 326 outliers final: 215 residues processed: 1662 average time/residue: 1.3239 time to fit residues: 3850.5439 Evaluate side-chains 1580 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1353 time to evaluate : 6.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SJ residue 17 LEU Chi-restraints excluded: chain SJ residue 69 THR Chi-restraints excluded: chain SJ residue 71 LEU Chi-restraints excluded: chain SJ residue 90 LEU Chi-restraints excluded: chain SK residue 19 VAL Chi-restraints excluded: chain SK residue 32 THR Chi-restraints excluded: chain SK residue 57 SER Chi-restraints excluded: chain SL residue 20 VAL Chi-restraints excluded: chain SL residue 64 SER Chi-restraints excluded: chain SL residue 86 VAL Chi-restraints excluded: chain SL residue 104 SER Chi-restraints excluded: chain SM residue 19 THR Chi-restraints excluded: chain SM residue 27 THR Chi-restraints excluded: chain SM residue 72 ILE Chi-restraints excluded: chain SM residue 96 VAL Chi-restraints excluded: chain SN residue 4 SER Chi-restraints excluded: chain SN residue 29 ILE Chi-restraints excluded: chain SN residue 61 ASN Chi-restraints excluded: chain SN residue 92 ILE Chi-restraints excluded: chain SP residue 50 THR Chi-restraints excluded: chain SQ residue 19 SER Chi-restraints excluded: chain SQ residue 25 GLU Chi-restraints excluded: chain SQ residue 28 VAL Chi-restraints excluded: chain SQ residue 41 THR Chi-restraints excluded: chain SQ residue 44 HIS Chi-restraints excluded: chain SQ residue 45 VAL Chi-restraints excluded: chain SQ residue 71 SER Chi-restraints excluded: chain SQ residue 77 VAL Chi-restraints excluded: chain SR residue 2 ARG Chi-restraints excluded: chain SR residue 38 ILE Chi-restraints excluded: chain SR residue 41 SER Chi-restraints excluded: chain SS residue 27 LYS Chi-restraints excluded: chain SS residue 62 THR Chi-restraints excluded: chain SB residue 19 THR Chi-restraints excluded: chain SB residue 34 ARG Chi-restraints excluded: chain SB residue 79 VAL Chi-restraints excluded: chain SB residue 117 GLU Chi-restraints excluded: chain SB residue 129 THR Chi-restraints excluded: chain SB residue 198 VAL Chi-restraints excluded: chain SB residue 226 GLN Chi-restraints excluded: chain ST residue 34 VAL Chi-restraints excluded: chain ST residue 66 ILE Chi-restraints excluded: chain SC residue 13 ILE Chi-restraints excluded: chain SC residue 31 ASN Chi-restraints excluded: chain SC residue 35 ASP Chi-restraints excluded: chain SC residue 51 VAL Chi-restraints excluded: chain SC residue 102 ILE Chi-restraints excluded: chain SC residue 148 ILE Chi-restraints excluded: chain SC residue 185 THR Chi-restraints excluded: chain SC residue 190 THR Chi-restraints excluded: chain SC residue 191 THR Chi-restraints excluded: chain SD residue 24 VAL Chi-restraints excluded: chain SD residue 144 ILE Chi-restraints excluded: chain SD residue 194 ILE Chi-restraints excluded: chain SE residue 11 GLN Chi-restraints excluded: chain SE residue 14 LEU Chi-restraints excluded: chain SE residue 31 SER Chi-restraints excluded: chain SE residue 38 VAL Chi-restraints excluded: chain SE residue 87 VAL Chi-restraints excluded: chain SE residue 104 ILE Chi-restraints excluded: chain SF residue 22 ILE Chi-restraints excluded: chain SF residue 71 ILE Chi-restraints excluded: chain SF residue 97 THR Chi-restraints excluded: chain SG residue 46 LEU Chi-restraints excluded: chain SG residue 105 GLU Chi-restraints excluded: chain SG residue 161 PHE Chi-restraints excluded: chain SH residue 60 LEU Chi-restraints excluded: chain SH residue 74 ILE Chi-restraints excluded: chain SH residue 105 THR Chi-restraints excluded: chain SH residue 111 THR Chi-restraints excluded: chain SI residue 34 LEU Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 74 GLN Chi-restraints excluded: chain S1 residue 9 TYR Chi-restraints excluded: chain S1 residue 83 ILE Chi-restraints excluded: chain S1 residue 85 ILE Chi-restraints excluded: chain S1 residue 92 VAL Chi-restraints excluded: chain S1 residue 211 VAL Chi-restraints excluded: chain S1 residue 263 VAL Chi-restraints excluded: chain S1 residue 279 ASP Chi-restraints excluded: chain S1 residue 289 VAL Chi-restraints excluded: chain S1 residue 348 VAL Chi-restraints excluded: chain S1 residue 351 SER Chi-restraints excluded: chain S1 residue 394 ASP Chi-restraints excluded: chain S1 residue 396 LEU Chi-restraints excluded: chain S1 residue 397 CYS Chi-restraints excluded: chain S1 residue 404 ILE Chi-restraints excluded: chain S1 residue 422 LYS Chi-restraints excluded: chain S1 residue 482 VAL Chi-restraints excluded: chain S1 residue 499 ASP Chi-restraints excluded: chain S1 residue 514 TYR Chi-restraints excluded: chain S1 residue 518 VAL Chi-restraints excluded: chain S1 residue 531 LYS Chi-restraints excluded: chain S1 residue 553 ASP Chi-restraints excluded: chain S1 residue 633 ASP Chi-restraints excluded: chain S1 residue 634 LEU Chi-restraints excluded: chain S1 residue 667 THR Chi-restraints excluded: chain S1 residue 688 GLU Chi-restraints excluded: chain LC residue 24 ASN Chi-restraints excluded: chain LC residue 32 GLU Chi-restraints excluded: chain LC residue 41 SER Chi-restraints excluded: chain LC residue 72 SER Chi-restraints excluded: chain LC residue 203 GLN Chi-restraints excluded: chain LC residue 229 LEU Chi-restraints excluded: chain LM residue 3 ILE Chi-restraints excluded: chain LM residue 18 SER Chi-restraints excluded: chain LM residue 25 VAL Chi-restraints excluded: chain LM residue 46 VAL Chi-restraints excluded: chain LM residue 51 ASN Chi-restraints excluded: chain LM residue 83 ILE Chi-restraints excluded: chain LM residue 91 VAL Chi-restraints excluded: chain LM residue 99 LEU Chi-restraints excluded: chain LN residue 2 VAL Chi-restraints excluded: chain LN residue 9 SER Chi-restraints excluded: chain LN residue 53 ILE Chi-restraints excluded: chain LN residue 59 GLN Chi-restraints excluded: chain LN residue 224 MET Chi-restraints excluded: chain LN residue 225 ASN Chi-restraints excluded: chain LN residue 249 VAL Chi-restraints excluded: chain LO residue 17 LEU Chi-restraints excluded: chain LO residue 76 SER Chi-restraints excluded: chain LO residue 91 ARG Chi-restraints excluded: chain LO residue 96 ASP Chi-restraints excluded: chain LP residue 63 VAL Chi-restraints excluded: chain LP residue 99 THR Chi-restraints excluded: chain LQ residue 36 LEU Chi-restraints excluded: chain LQ residue 85 ILE Chi-restraints excluded: chain LQ residue 101 SER Chi-restraints excluded: chain LQ residue 106 VAL Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LR residue 62 VAL Chi-restraints excluded: chain LR residue 66 LYS Chi-restraints excluded: chain LR residue 74 ILE Chi-restraints excluded: chain LR residue 80 TRP Chi-restraints excluded: chain LS residue 27 VAL Chi-restraints excluded: chain LS residue 51 LEU Chi-restraints excluded: chain LT residue 30 ILE Chi-restraints excluded: chain LT residue 47 VAL Chi-restraints excluded: chain LT residue 60 VAL Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 77 VAL Chi-restraints excluded: chain LU residue 52 CYS Chi-restraints excluded: chain LU residue 63 ASP Chi-restraints excluded: chain LV residue 33 HIS Chi-restraints excluded: chain LV residue 39 VAL Chi-restraints excluded: chain LV residue 50 VAL Chi-restraints excluded: chain LV residue 60 LYS Chi-restraints excluded: chain LV residue 65 THR Chi-restraints excluded: chain LD residue 22 LEU Chi-restraints excluded: chain LX residue 2 ILE Chi-restraints excluded: chain LX residue 25 THR Chi-restraints excluded: chain LX residue 34 VAL Chi-restraints excluded: chain LX residue 73 VAL Chi-restraints excluded: chain LX residue 137 SER Chi-restraints excluded: chain LX residue 161 MET Chi-restraints excluded: chain LX residue 165 MET Chi-restraints excluded: chain LX residue 175 LEU Chi-restraints excluded: chain LX residue 177 VAL Chi-restraints excluded: chain LX residue 178 VAL Chi-restraints excluded: chain LY residue 47 ILE Chi-restraints excluded: chain L1 residue 14 MET Chi-restraints excluded: chain L1 residue 38 LEU Chi-restraints excluded: chain L1 residue 48 TYR Chi-restraints excluded: chain L3 residue 24 THR Chi-restraints excluded: chain L3 residue 43 THR Chi-restraints excluded: chain L6 residue 7 ASP Chi-restraints excluded: chain L6 residue 75 SER Chi-restraints excluded: chain L6 residue 180 LEU Chi-restraints excluded: chain L6 residue 195 GLN Chi-restraints excluded: chain LE residue 32 VAL Chi-restraints excluded: chain LE residue 34 ILE Chi-restraints excluded: chain LE residue 48 ILE Chi-restraints excluded: chain LE residue 56 VAL Chi-restraints excluded: chain LE residue 57 VAL Chi-restraints excluded: chain LE residue 72 THR Chi-restraints excluded: chain L7 residue 12 VAL Chi-restraints excluded: chain L7 residue 17 THR Chi-restraints excluded: chain L7 residue 20 ASN Chi-restraints excluded: chain L7 residue 24 VAL Chi-restraints excluded: chain L7 residue 39 VAL Chi-restraints excluded: chain L7 residue 88 VAL Chi-restraints excluded: chain L7 residue 135 ILE Chi-restraints excluded: chain L7 residue 136 ILE Chi-restraints excluded: chain L7 residue 153 ILE Chi-restraints excluded: chain L7 residue 157 THR Chi-restraints excluded: chain L8 residue 40 VAL Chi-restraints excluded: chain L8 residue 59 ASP Chi-restraints excluded: chain L8 residue 128 THR Chi-restraints excluded: chain L8 residue 147 LEU Chi-restraints excluded: chain L8 residue 161 VAL Chi-restraints excluded: chain L9 residue 4 ILE Chi-restraints excluded: chain L9 residue 19 VAL Chi-restraints excluded: chain L9 residue 78 VAL Chi-restraints excluded: chain L9 residue 89 LYS Chi-restraints excluded: chain L9 residue 143 ILE Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 60 ASP Chi-restraints excluded: chain LF residue 70 THR Chi-restraints excluded: chain LF residue 78 THR Chi-restraints excluded: chain LF residue 81 ILE Chi-restraints excluded: chain LF residue 84 ILE Chi-restraints excluded: chain LF residue 101 ILE Chi-restraints excluded: chain LG residue 10 VAL Chi-restraints excluded: chain LG residue 21 CYS Chi-restraints excluded: chain LG residue 76 VAL Chi-restraints excluded: chain LH residue 55 MET Chi-restraints excluded: chain LH residue 57 LEU Chi-restraints excluded: chain LH residue 64 PHE Chi-restraints excluded: chain LH residue 92 LEU Chi-restraints excluded: chain LH residue 118 THR Chi-restraints excluded: chain LH residue 121 THR Chi-restraints excluded: chain LI residue 7 THR Chi-restraints excluded: chain LI residue 17 ASN Chi-restraints excluded: chain LI residue 67 VAL Chi-restraints excluded: chain LI residue 88 ASN Chi-restraints excluded: chain LI residue 126 ILE Chi-restraints excluded: chain LI residue 135 VAL Chi-restraints excluded: chain LJ residue 13 ASN Chi-restraints excluded: chain LJ residue 27 SER Chi-restraints excluded: chain LJ residue 29 VAL Chi-restraints excluded: chain LJ residue 53 THR Chi-restraints excluded: chain LK residue 17 LYS Chi-restraints excluded: chain LK residue 18 LEU Chi-restraints excluded: chain LZ residue 16 CYS Chi-restraints excluded: chain LZ residue 24 ILE Chi-restraints excluded: chain LZ residue 35 ASP Chi-restraints excluded: chain LZ residue 44 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1159 random chunks: chunk 1081 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 638 optimal weight: 30.0000 chunk 818 optimal weight: 0.6980 chunk 634 optimal weight: 20.0000 chunk 943 optimal weight: 8.9990 chunk 626 optimal weight: 40.0000 chunk 1117 optimal weight: 9.9990 chunk 699 optimal weight: 50.0000 chunk 681 optimal weight: 10.0000 chunk 515 optimal weight: 20.0000 overall best weight: 7.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SK 39 ASN SK 100 ASN SL 45 ASN SL 76 HIS SO 39 GLN ** SP 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 44 HIS SR 51 GLN ** SS 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 177 ASN ST 20 ASN ST 60 GLN SC 31 ASN ** SD 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 40 HIS SD 163 GLN ** SE 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 145 ASN SF 14 GLN ** SF 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 141 HIS SG 164 GLN SH 75 GLN SI 125 GLN ** S1 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 258 ASN S1 504 HIS LM 51 ASN LM 74 GLN LM 76 HIS ** LN 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LP 82 HIS ** LR 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LV 35 HIS LX 148 GLN L3 16 HIS L7 80 GLN ** L8 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 5 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 1.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.155 169620 Z= 0.349 Angle : 0.796 13.563 252372 Z= 0.407 Chirality : 0.043 0.567 32049 Planarity : 0.007 0.068 14531 Dihedral : 23.838 179.892 81557 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.82 % Favored : 89.56 % Rotamer: Outliers : 6.57 % Allowed : 28.71 % Favored : 64.72 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.09), residues: 7019 helix: -0.27 (0.10), residues: 2259 sheet: -0.93 (0.14), residues: 1219 loop : -2.28 (0.10), residues: 3541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.004 TRPLN 212 HIS 0.069 0.003 HISSQ 44 PHE 0.038 0.003 PHEL7 174 TYR 0.035 0.003 TYRSP 17 ARG 0.023 0.001 ARGLM 52 *********************** 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 1817 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 380 poor density : 1437 time to evaluate : 7.044 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: SK 84 MET cc_start: 0.6652 (mmm) cc_final: 0.6197 (mmt) REVERT: SL 64 SER cc_start: 0.8795 (OUTLIER) cc_final: 0.8428 (t) REVERT: SP 1 MET cc_start: 0.5809 (tmm) cc_final: 0.5253 (ttp) REVERT: SP 40 ASN cc_start: 0.6230 (p0) cc_final: 0.5953 (p0) REVERT: SR 2 ARG cc_start: 0.4051 (OUTLIER) cc_final: 0.3298 (mmm160) REVERT: SR 6 ARG cc_start: 0.2169 (ptm160) cc_final: 0.1967 (ptm160) REVERT: SS 32 THR cc_start: 0.4745 (m) cc_final: 0.4532 (m) REVERT: ST 77 ASN cc_start: 0.6852 (m-40) cc_final: 0.6620 (m-40) REVERT: SU 38 GLU cc_start: 0.6478 (tp30) cc_final: 0.6010 (mm-30) REVERT: SC 31 ASN cc_start: 0.6510 (OUTLIER) cc_final: 0.6249 (p0) REVERT: SD 159 GLU cc_start: 0.5000 (OUTLIER) cc_final: 0.4761 (mm-30) REVERT: SF 61 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6730 (tt) REVERT: SF 79 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.5997 (tpp80) REVERT: SG 161 PHE cc_start: 0.3808 (OUTLIER) cc_final: 0.3212 (m-10) REVERT: SI 56 MET cc_start: 0.3577 (OUTLIER) cc_final: 0.3135 (mmm) REVERT: SI 87 MET cc_start: 0.7234 (tmm) cc_final: 0.6771 (tmm) REVERT: S1 396 LEU cc_start: 0.5001 (OUTLIER) cc_final: 0.4507 (mp) REVERT: S1 531 LYS cc_start: 0.6449 (OUTLIER) cc_final: 0.6073 (tptp) REVERT: LC 1 MET cc_start: 0.4527 (mmt) cc_final: 0.3540 (ptm) REVERT: LC 121 MET cc_start: 0.2832 (ppp) cc_final: 0.1578 (ttt) REVERT: LC 229 LEU cc_start: 0.4419 (OUTLIER) cc_final: 0.2981 (mp) REVERT: LM 12 MET cc_start: 0.7244 (ttp) cc_final: 0.6933 (ttp) REVERT: LN 73 ILE cc_start: 0.6672 (mm) cc_final: 0.6452 (mt) REVERT: LN 180 MET cc_start: 0.7236 (mmm) cc_final: 0.6952 (mmm) REVERT: LO 50 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7124 (mtm-85) REVERT: LO 51 GLN cc_start: 0.6912 (tp40) cc_final: 0.6620 (tp40) REVERT: LQ 1 MET cc_start: 0.6371 (tmm) cc_final: 0.5181 (ttt) REVERT: LR 66 LYS cc_start: 0.6711 (OUTLIER) cc_final: 0.6300 (pttm) REVERT: LS 59 GLU cc_start: 0.7136 (tp30) cc_final: 0.6628 (tp30) REVERT: LU 40 ARG cc_start: 0.5853 (tmt170) cc_final: 0.5534 (tmt170) REVERT: LV 60 LYS cc_start: 0.6943 (ptmt) cc_final: 0.6230 (ptmt) REVERT: LD 85 MET cc_start: 0.4205 (ppp) cc_final: 0.0944 (mmp) REVERT: LD 139 MET cc_start: 0.2445 (ttt) cc_final: 0.1705 (mtm) REVERT: LW 43 LEU cc_start: 0.6699 (mm) cc_final: 0.6396 (mm) REVERT: L8 154 GLU cc_start: 0.7355 (pp20) cc_final: 0.7081 (pm20) REVERT: LG 75 SER cc_start: 0.7406 (m) cc_final: 0.7186 (p) REVERT: LI 82 MET cc_start: 0.7949 (tpp) cc_final: 0.7692 (tpp) REVERT: LK 48 LEU cc_start: 0.6379 (mm) cc_final: 0.6154 (mm) REVERT: LZ 44 PHE cc_start: 0.4689 (OUTLIER) cc_final: 0.4296 (t80) outliers start: 380 outliers final: 267 residues processed: 1667 average time/residue: 1.3212 time to fit residues: 3858.5946 Evaluate side-chains 1593 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1312 time to evaluate : 6.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SJ residue 17 LEU Chi-restraints excluded: chain SJ residue 42 LEU Chi-restraints excluded: chain SJ residue 69 THR Chi-restraints excluded: chain SJ residue 85 ASP Chi-restraints excluded: chain SK residue 19 VAL Chi-restraints excluded: chain SK residue 39 ASN Chi-restraints excluded: chain SK residue 86 LYS Chi-restraints excluded: chain SL residue 2 THR Chi-restraints excluded: chain SL residue 20 VAL Chi-restraints excluded: chain SL residue 64 SER Chi-restraints excluded: chain SL residue 78 VAL Chi-restraints excluded: chain SL residue 86 VAL Chi-restraints excluded: chain SL residue 116 TYR Chi-restraints excluded: chain SL residue 118 VAL Chi-restraints excluded: chain SM residue 27 THR Chi-restraints excluded: chain SM residue 67 ASP Chi-restraints excluded: chain SM residue 72 ILE Chi-restraints excluded: chain SM residue 79 LEU Chi-restraints excluded: chain SM residue 96 VAL Chi-restraints excluded: chain SM residue 103 THR Chi-restraints excluded: chain SN residue 29 ILE Chi-restraints excluded: chain SN residue 61 ASN Chi-restraints excluded: chain SN residue 92 ILE Chi-restraints excluded: chain SP residue 50 THR Chi-restraints excluded: chain SQ residue 19 SER Chi-restraints excluded: chain SQ residue 28 VAL Chi-restraints excluded: chain SQ residue 36 PHE Chi-restraints excluded: chain SQ residue 71 SER Chi-restraints excluded: chain SQ residue 77 VAL Chi-restraints excluded: chain SR residue 2 ARG Chi-restraints excluded: chain SR residue 38 ILE Chi-restraints excluded: chain SR residue 41 SER Chi-restraints excluded: chain SR residue 71 ASP Chi-restraints excluded: chain SS residue 27 LYS Chi-restraints excluded: chain SB residue 19 THR Chi-restraints excluded: chain SB residue 22 TRP Chi-restraints excluded: chain SB residue 79 VAL Chi-restraints excluded: chain SB residue 226 GLN Chi-restraints excluded: chain ST residue 34 VAL Chi-restraints excluded: chain ST residue 66 ILE Chi-restraints excluded: chain SC residue 4 VAL Chi-restraints excluded: chain SC residue 13 ILE Chi-restraints excluded: chain SC residue 31 ASN Chi-restraints excluded: chain SC residue 51 VAL Chi-restraints excluded: chain SC residue 54 ILE Chi-restraints excluded: chain SC residue 102 ILE Chi-restraints excluded: chain SC residue 148 ILE Chi-restraints excluded: chain SC residue 185 THR Chi-restraints excluded: chain SC residue 190 THR Chi-restraints excluded: chain SC residue 191 THR Chi-restraints excluded: chain SD residue 24 VAL Chi-restraints excluded: chain SD residue 52 VAL Chi-restraints excluded: chain SD residue 84 ASN Chi-restraints excluded: chain SD residue 118 SER Chi-restraints excluded: chain SD residue 142 VAL Chi-restraints excluded: chain SD residue 144 ILE Chi-restraints excluded: chain SD residue 159 GLU Chi-restraints excluded: chain SD residue 173 ASP Chi-restraints excluded: chain SD residue 194 ILE Chi-restraints excluded: chain SE residue 11 GLN Chi-restraints excluded: chain SE residue 14 LEU Chi-restraints excluded: chain SE residue 15 ILE Chi-restraints excluded: chain SE residue 17 VAL Chi-restraints excluded: chain SE residue 79 THR Chi-restraints excluded: chain SE residue 87 VAL Chi-restraints excluded: chain SE residue 91 SER Chi-restraints excluded: chain SE residue 104 ILE Chi-restraints excluded: chain SE residue 151 MET Chi-restraints excluded: chain SF residue 22 ILE Chi-restraints excluded: chain SF residue 54 LEU Chi-restraints excluded: chain SF residue 61 LEU Chi-restraints excluded: chain SF residue 71 ILE Chi-restraints excluded: chain SF residue 79 ARG Chi-restraints excluded: chain SF residue 81 ASN Chi-restraints excluded: chain SF residue 94 HIS Chi-restraints excluded: chain SF residue 97 THR Chi-restraints excluded: chain SG residue 46 LEU Chi-restraints excluded: chain SG residue 85 GLN Chi-restraints excluded: chain SG residue 90 VAL Chi-restraints excluded: chain SG residue 105 GLU Chi-restraints excluded: chain SG residue 161 PHE Chi-restraints excluded: chain SH residue 25 THR Chi-restraints excluded: chain SH residue 60 LEU Chi-restraints excluded: chain SH residue 74 ILE Chi-restraints excluded: chain SH residue 77 VAL Chi-restraints excluded: chain SH residue 84 ILE Chi-restraints excluded: chain SH residue 102 VAL Chi-restraints excluded: chain SH residue 105 THR Chi-restraints excluded: chain SH residue 111 THR Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 56 MET Chi-restraints excluded: chain SI residue 74 GLN Chi-restraints excluded: chain SI residue 89 TYR Chi-restraints excluded: chain S1 residue 9 TYR Chi-restraints excluded: chain S1 residue 85 ILE Chi-restraints excluded: chain S1 residue 92 VAL Chi-restraints excluded: chain S1 residue 137 ILE Chi-restraints excluded: chain S1 residue 140 VAL Chi-restraints excluded: chain S1 residue 181 VAL Chi-restraints excluded: chain S1 residue 206 ILE Chi-restraints excluded: chain S1 residue 211 VAL Chi-restraints excluded: chain S1 residue 263 VAL Chi-restraints excluded: chain S1 residue 342 VAL Chi-restraints excluded: chain S1 residue 348 VAL Chi-restraints excluded: chain S1 residue 351 SER Chi-restraints excluded: chain S1 residue 394 ASP Chi-restraints excluded: chain S1 residue 396 LEU Chi-restraints excluded: chain S1 residue 397 CYS Chi-restraints excluded: chain S1 residue 426 ASP Chi-restraints excluded: chain S1 residue 482 VAL Chi-restraints excluded: chain S1 residue 499 ASP Chi-restraints excluded: chain S1 residue 504 HIS Chi-restraints excluded: chain S1 residue 514 TYR Chi-restraints excluded: chain S1 residue 518 VAL Chi-restraints excluded: chain S1 residue 531 LYS Chi-restraints excluded: chain S1 residue 553 ASP Chi-restraints excluded: chain S1 residue 582 TYR Chi-restraints excluded: chain S1 residue 633 ASP Chi-restraints excluded: chain S1 residue 634 LEU Chi-restraints excluded: chain S1 residue 657 VAL Chi-restraints excluded: chain S1 residue 667 THR Chi-restraints excluded: chain LC residue 11 ILE Chi-restraints excluded: chain LC residue 23 ILE Chi-restraints excluded: chain LC residue 24 ASN Chi-restraints excluded: chain LC residue 32 GLU Chi-restraints excluded: chain LC residue 33 LEU Chi-restraints excluded: chain LC residue 41 SER Chi-restraints excluded: chain LC residue 72 SER Chi-restraints excluded: chain LC residue 203 GLN Chi-restraints excluded: chain LC residue 207 VAL Chi-restraints excluded: chain LC residue 214 ILE Chi-restraints excluded: chain LC residue 229 LEU Chi-restraints excluded: chain LM residue 3 ILE Chi-restraints excluded: chain LM residue 18 SER Chi-restraints excluded: chain LM residue 25 VAL Chi-restraints excluded: chain LM residue 46 VAL Chi-restraints excluded: chain LM residue 83 ILE Chi-restraints excluded: chain LM residue 91 VAL Chi-restraints excluded: chain LM residue 99 LEU Chi-restraints excluded: chain LN residue 2 VAL Chi-restraints excluded: chain LN residue 9 SER Chi-restraints excluded: chain LN residue 53 ILE Chi-restraints excluded: chain LN residue 63 ILE Chi-restraints excluded: chain LN residue 224 MET Chi-restraints excluded: chain LN residue 225 ASN Chi-restraints excluded: chain LN residue 249 VAL Chi-restraints excluded: chain LO residue 50 ARG Chi-restraints excluded: chain LO residue 76 SER Chi-restraints excluded: chain LO residue 91 ARG Chi-restraints excluded: chain LO residue 102 LYS Chi-restraints excluded: chain LP residue 1 MET Chi-restraints excluded: chain LP residue 22 LEU Chi-restraints excluded: chain LP residue 63 VAL Chi-restraints excluded: chain LP residue 99 THR Chi-restraints excluded: chain LQ residue 36 LEU Chi-restraints excluded: chain LQ residue 61 ASN Chi-restraints excluded: chain LQ residue 101 SER Chi-restraints excluded: chain LQ residue 106 VAL Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LR residue 62 VAL Chi-restraints excluded: chain LR residue 66 LYS Chi-restraints excluded: chain LR residue 74 ILE Chi-restraints excluded: chain LR residue 80 TRP Chi-restraints excluded: chain LS residue 10 VAL Chi-restraints excluded: chain LS residue 27 VAL Chi-restraints excluded: chain LT residue 8 VAL Chi-restraints excluded: chain LT residue 49 ASN Chi-restraints excluded: chain LT residue 60 VAL Chi-restraints excluded: chain LT residue 62 THR Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 77 VAL Chi-restraints excluded: chain LT residue 90 ASP Chi-restraints excluded: chain LU residue 15 SER Chi-restraints excluded: chain LU residue 39 GLN Chi-restraints excluded: chain LU residue 52 CYS Chi-restraints excluded: chain LU residue 63 ASP Chi-restraints excluded: chain LV residue 39 VAL Chi-restraints excluded: chain LV residue 63 ILE Chi-restraints excluded: chain LW residue 17 GLU Chi-restraints excluded: chain LW residue 22 LEU Chi-restraints excluded: chain LW residue 50 VAL Chi-restraints excluded: chain LX residue 2 ILE Chi-restraints excluded: chain LX residue 34 VAL Chi-restraints excluded: chain LX residue 73 VAL Chi-restraints excluded: chain LX residue 90 PHE Chi-restraints excluded: chain LX residue 137 SER Chi-restraints excluded: chain LX residue 177 VAL Chi-restraints excluded: chain LX residue 178 VAL Chi-restraints excluded: chain LX residue 200 ASP Chi-restraints excluded: chain LX residue 203 VAL Chi-restraints excluded: chain LY residue 22 THR Chi-restraints excluded: chain LY residue 47 ILE Chi-restraints excluded: chain LY residue 54 VAL Chi-restraints excluded: chain L1 residue 14 MET Chi-restraints excluded: chain L1 residue 38 LEU Chi-restraints excluded: chain L1 residue 43 THR Chi-restraints excluded: chain L1 residue 48 TYR Chi-restraints excluded: chain L3 residue 24 THR Chi-restraints excluded: chain L3 residue 43 THR Chi-restraints excluded: chain L4 residue 31 ILE Chi-restraints excluded: chain L4 residue 41 ARG Chi-restraints excluded: chain L4 residue 54 LEU Chi-restraints excluded: chain L5 residue 17 VAL Chi-restraints excluded: chain L5 residue 30 GLU Chi-restraints excluded: chain L6 residue 7 ASP Chi-restraints excluded: chain L6 residue 22 ASP Chi-restraints excluded: chain L6 residue 48 THR Chi-restraints excluded: chain L6 residue 75 SER Chi-restraints excluded: chain L6 residue 77 ILE Chi-restraints excluded: chain L6 residue 83 VAL Chi-restraints excluded: chain L6 residue 180 LEU Chi-restraints excluded: chain LE residue 32 VAL Chi-restraints excluded: chain LE residue 34 ILE Chi-restraints excluded: chain LE residue 48 ILE Chi-restraints excluded: chain LE residue 56 VAL Chi-restraints excluded: chain LE residue 57 VAL Chi-restraints excluded: chain LE residue 72 THR Chi-restraints excluded: chain LE residue 94 LYS Chi-restraints excluded: chain LE residue 100 ILE Chi-restraints excluded: chain L7 residue 12 VAL Chi-restraints excluded: chain L7 residue 17 THR Chi-restraints excluded: chain L7 residue 20 ASN Chi-restraints excluded: chain L7 residue 24 VAL Chi-restraints excluded: chain L7 residue 136 ILE Chi-restraints excluded: chain L7 residue 153 ILE Chi-restraints excluded: chain L7 residue 154 THR Chi-restraints excluded: chain L7 residue 157 THR Chi-restraints excluded: chain L7 residue 164 GLU Chi-restraints excluded: chain L8 residue 40 VAL Chi-restraints excluded: chain L8 residue 59 ASP Chi-restraints excluded: chain L8 residue 75 VAL Chi-restraints excluded: chain L8 residue 147 LEU Chi-restraints excluded: chain L8 residue 161 VAL Chi-restraints excluded: chain L9 residue 4 ILE Chi-restraints excluded: chain L9 residue 19 VAL Chi-restraints excluded: chain L9 residue 89 LYS Chi-restraints excluded: chain L9 residue 143 ILE Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 60 ASP Chi-restraints excluded: chain LF residue 70 THR Chi-restraints excluded: chain LF residue 78 THR Chi-restraints excluded: chain LF residue 81 ILE Chi-restraints excluded: chain LF residue 84 ILE Chi-restraints excluded: chain LF residue 101 ILE Chi-restraints excluded: chain LF residue 106 LYS Chi-restraints excluded: chain LG residue 1 MET Chi-restraints excluded: chain LG residue 10 VAL Chi-restraints excluded: chain LG residue 21 CYS Chi-restraints excluded: chain LG residue 43 ILE Chi-restraints excluded: chain LG residue 77 ILE Chi-restraints excluded: chain LG residue 97 THR Chi-restraints excluded: chain LG residue 103 VAL Chi-restraints excluded: chain LH residue 18 ARG Chi-restraints excluded: chain LH residue 57 LEU Chi-restraints excluded: chain LH residue 64 PHE Chi-restraints excluded: chain LH residue 92 LEU Chi-restraints excluded: chain LH residue 110 VAL Chi-restraints excluded: chain LH residue 118 THR Chi-restraints excluded: chain LH residue 121 THR Chi-restraints excluded: chain LI residue 7 THR Chi-restraints excluded: chain LI residue 17 ASN Chi-restraints excluded: chain LI residue 67 VAL Chi-restraints excluded: chain LI residue 80 VAL Chi-restraints excluded: chain LI residue 88 ASN Chi-restraints excluded: chain LI residue 95 LEU Chi-restraints excluded: chain LI residue 126 ILE Chi-restraints excluded: chain LI residue 136 MET Chi-restraints excluded: chain LJ residue 13 ASN Chi-restraints excluded: chain LJ residue 27 SER Chi-restraints excluded: chain LJ residue 37 THR Chi-restraints excluded: chain LJ residue 53 THR Chi-restraints excluded: chain LK residue 5 SER Chi-restraints excluded: chain LK residue 17 LYS Chi-restraints excluded: chain LK residue 49 VAL Chi-restraints excluded: chain LK residue 90 VAL Chi-restraints excluded: chain LZ residue 1 MET Chi-restraints excluded: chain LZ residue 16 CYS Chi-restraints excluded: chain LZ residue 21 VAL Chi-restraints excluded: chain LZ residue 24 ILE Chi-restraints excluded: chain LZ residue 35 ASP Chi-restraints excluded: chain LZ residue 44 PHE 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: 20.0000 chunk 667 optimal weight: 10.0000 chunk 336 optimal weight: 10.0000 chunk 219 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 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: 10.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SK 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 100 ASN SN 34 ASN ** SP 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 51 GLN ** SS 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 18 ASN SC 31 ASN SD 40 HIS SD 163 GLN SE 145 ASN SF 14 GLN SF 17 GLN ** SF 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 141 HIS ** S1 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 275 GLN ** S1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 238 ASN ** LP 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LP 82 HIS LQ 9 HIS LR 48 GLN ** LR 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 51 GLN ** LT 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LW 20 ASN L3 16 HIS LE 106 GLN L7 126 ASN ** L8 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 1.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 169620 Z= 0.339 Angle : 0.767 17.957 252372 Z= 0.392 Chirality : 0.042 0.353 32049 Planarity : 0.006 0.068 14531 Dihedral : 23.844 179.832 81557 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.73 % Favored : 90.70 % Rotamer: Outliers : 6.05 % Allowed : 30.41 % Favored : 63.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.01 % Twisted Proline : 0.41 % Twisted General : 0.09 % 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: -2.16 (0.09), residues: 7019 helix: -0.38 (0.10), residues: 2253 sheet: -0.96 (0.14), residues: 1231 loop : -2.37 (0.10), residues: 3535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRPLN 212 HIS 0.080 0.002 HISS1 504 PHE 0.049 0.003 PHEL7 174 TYR 0.030 0.002 TYRSL 116 ARG 0.024 0.001 ARGSO 76 *********************** 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 1792 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 1442 time to evaluate : 6.988 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: SK 39 ASN cc_start: 0.5675 (m-40) cc_final: 0.5235 (t0) REVERT: SK 84 MET cc_start: 0.6680 (mmm) cc_final: 0.6116 (mmt) REVERT: SL 64 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8380 (t) REVERT: SL 108 ASP cc_start: 0.6045 (m-30) cc_final: 0.5815 (m-30) REVERT: SL 109 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6234 (ttm-80) REVERT: SR 2 ARG cc_start: 0.3995 (OUTLIER) cc_final: 0.3089 (mmm160) REVERT: ST 77 ASN cc_start: 0.6956 (m-40) cc_final: 0.6697 (m-40) REVERT: SU 20 ARG cc_start: 0.4705 (ptt180) cc_final: 0.4091 (ptt180) REVERT: SU 38 GLU cc_start: 0.6275 (tp30) cc_final: 0.5708 (mm-30) REVERT: SC 31 ASN cc_start: 0.6395 (OUTLIER) cc_final: 0.6006 (p0) REVERT: SF 61 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6734 (tt) REVERT: SF 79 ARG cc_start: 0.6381 (OUTLIER) cc_final: 0.6090 (tpp80) REVERT: SG 161 PHE cc_start: 0.3699 (OUTLIER) cc_final: 0.3009 (m-10) REVERT: SI 56 MET cc_start: 0.3455 (mmm) cc_final: 0.3055 (mmm) REVERT: SI 87 MET cc_start: 0.7194 (tmm) cc_final: 0.6792 (tmm) REVERT: S1 70 PHE cc_start: 0.4583 (OUTLIER) cc_final: 0.3850 (m-80) REVERT: S1 391 THR cc_start: 0.7492 (t) cc_final: 0.6862 (t) REVERT: S1 396 LEU cc_start: 0.4763 (OUTLIER) cc_final: 0.4548 (mp) REVERT: S1 531 LYS cc_start: 0.6416 (OUTLIER) cc_final: 0.5978 (tptp) REVERT: S1 679 TYR cc_start: 0.6467 (OUTLIER) cc_final: 0.6035 (p90) REVERT: LC 121 MET cc_start: 0.2479 (OUTLIER) cc_final: 0.1796 (ttt) REVERT: LM 9 GLN cc_start: 0.6625 (mt0) cc_final: 0.6385 (mt0) REVERT: LN 212 TRP cc_start: 0.8424 (OUTLIER) cc_final: 0.8151 (p-90) REVERT: LO 50 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7243 (mtm-85) REVERT: LO 51 GLN cc_start: 0.6898 (tp40) cc_final: 0.6608 (tp40) REVERT: LQ 1 MET cc_start: 0.6175 (tmm) cc_final: 0.5266 (ttt) REVERT: LR 66 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6827 (pttm) REVERT: LS 59 GLU cc_start: 0.6914 (tp30) cc_final: 0.6487 (tp30) REVERT: LV 60 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.5924 (tttt) REVERT: LD 85 MET cc_start: 0.4139 (ppp) cc_final: 0.0910 (mmp) REVERT: LD 139 MET cc_start: 0.2800 (ttt) cc_final: 0.1890 (mtm) REVERT: L8 154 GLU cc_start: 0.7626 (pp20) cc_final: 0.7320 (pp20) REVERT: L8 175 LYS cc_start: 0.4748 (mmtt) cc_final: 0.3695 (tttt) REVERT: LF 102 GLU cc_start: 0.4176 (mt-10) cc_final: 0.3584 (mt-10) REVERT: LG 75 SER cc_start: 0.7442 (m) cc_final: 0.7127 (p) REVERT: LG 89 ASN cc_start: 0.7509 (t0) cc_final: 0.7271 (t0) REVERT: LH 59 ARG cc_start: 0.7958 (mtm180) cc_final: 0.7518 (mtp180) REVERT: LH 101 ILE cc_start: 0.7385 (tt) cc_final: 0.7054 (tt) REVERT: LI 82 MET cc_start: 0.8038 (tpp) cc_final: 0.7701 (tpp) REVERT: LI 104 GLU cc_start: 0.5744 (mt-10) cc_final: 0.5540 (mt-10) outliers start: 350 outliers final: 242 residues processed: 1653 average time/residue: 1.3008 time to fit residues: 3771.7343 Evaluate side-chains 1602 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1344 time to evaluate : 7.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SJ residue 17 LEU Chi-restraints excluded: chain SJ residue 69 THR Chi-restraints excluded: chain SJ residue 85 ASP Chi-restraints excluded: chain SK residue 19 VAL Chi-restraints excluded: chain SK residue 41 LEU Chi-restraints excluded: chain SK residue 86 LYS Chi-restraints excluded: chain SL residue 2 THR Chi-restraints excluded: chain SL residue 20 VAL Chi-restraints excluded: chain SL residue 64 SER Chi-restraints excluded: chain SL residue 78 VAL Chi-restraints excluded: chain SL residue 86 VAL Chi-restraints excluded: chain SL residue 109 ARG Chi-restraints excluded: chain SL residue 116 TYR Chi-restraints excluded: chain SM residue 27 THR Chi-restraints excluded: chain SM residue 65 GLU Chi-restraints excluded: chain SM residue 72 ILE Chi-restraints excluded: chain SM residue 79 LEU Chi-restraints excluded: chain SM residue 96 VAL Chi-restraints excluded: chain SN residue 29 ILE Chi-restraints excluded: chain SN residue 61 ASN Chi-restraints excluded: chain SO residue 58 MET Chi-restraints excluded: chain SQ residue 28 VAL Chi-restraints excluded: chain SQ residue 36 PHE Chi-restraints excluded: chain SQ residue 43 LEU Chi-restraints excluded: chain SQ residue 58 VAL Chi-restraints excluded: chain SQ residue 71 SER Chi-restraints excluded: chain SQ residue 77 VAL Chi-restraints excluded: chain SR residue 2 ARG Chi-restraints excluded: chain SR residue 38 ILE Chi-restraints excluded: chain SR residue 41 SER Chi-restraints excluded: chain SS residue 27 LYS Chi-restraints excluded: chain SS residue 38 THR Chi-restraints excluded: chain SB residue 19 THR Chi-restraints excluded: chain SB residue 22 TRP Chi-restraints excluded: chain SB residue 46 VAL Chi-restraints excluded: chain SB residue 79 VAL Chi-restraints excluded: chain SB residue 109 SER Chi-restraints excluded: chain SB residue 116 LEU Chi-restraints excluded: chain SB residue 226 GLN Chi-restraints excluded: chain ST residue 66 ILE Chi-restraints excluded: chain SC residue 13 ILE Chi-restraints excluded: chain SC residue 31 ASN Chi-restraints excluded: chain SC residue 34 SER Chi-restraints excluded: chain SC residue 51 VAL Chi-restraints excluded: chain SC residue 82 ASP Chi-restraints excluded: chain SC residue 83 VAL Chi-restraints excluded: chain SC residue 165 GLU Chi-restraints excluded: chain SC residue 185 THR Chi-restraints excluded: chain SC residue 190 THR Chi-restraints excluded: chain SC residue 191 THR Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SD residue 24 VAL Chi-restraints excluded: chain SD residue 52 VAL Chi-restraints excluded: chain SD residue 74 TYR Chi-restraints excluded: chain SD residue 84 ASN Chi-restraints excluded: chain SD residue 90 LEU Chi-restraints excluded: chain SD residue 118 SER Chi-restraints excluded: chain SD residue 144 ILE Chi-restraints excluded: chain SD residue 173 ASP Chi-restraints excluded: chain SD residue 194 ILE Chi-restraints excluded: chain SE residue 11 GLN Chi-restraints excluded: chain SE residue 14 LEU Chi-restraints excluded: chain SE residue 22 LYS Chi-restraints excluded: chain SE residue 33 THR Chi-restraints excluded: chain SE residue 91 SER Chi-restraints excluded: chain SE residue 104 ILE Chi-restraints excluded: chain SE residue 151 MET Chi-restraints excluded: chain SF residue 9 MET Chi-restraints excluded: chain SF residue 22 ILE Chi-restraints excluded: chain SF residue 30 THR Chi-restraints excluded: chain SF residue 54 LEU Chi-restraints excluded: chain SF residue 61 LEU Chi-restraints excluded: chain SF residue 79 ARG Chi-restraints excluded: chain SF residue 81 ASN Chi-restraints excluded: chain SF residue 82 ASP Chi-restraints excluded: chain SF residue 94 HIS Chi-restraints excluded: chain SG residue 48 THR Chi-restraints excluded: chain SG residue 85 GLN Chi-restraints excluded: chain SG residue 105 GLU Chi-restraints excluded: chain SG residue 161 PHE Chi-restraints excluded: chain SH residue 60 LEU Chi-restraints excluded: chain SH residue 74 ILE Chi-restraints excluded: chain SH residue 77 VAL Chi-restraints excluded: chain SH residue 89 ASP Chi-restraints excluded: chain SH residue 105 THR Chi-restraints excluded: chain SH residue 111 THR Chi-restraints excluded: chain SH residue 123 GLU Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 47 VAL Chi-restraints excluded: chain SI residue 74 GLN Chi-restraints excluded: chain SI residue 92 SER Chi-restraints excluded: chain S1 residue 9 TYR Chi-restraints excluded: chain S1 residue 18 ILE Chi-restraints excluded: chain S1 residue 70 PHE Chi-restraints excluded: chain S1 residue 85 ILE Chi-restraints excluded: chain S1 residue 92 VAL Chi-restraints excluded: chain S1 residue 140 VAL Chi-restraints excluded: chain S1 residue 181 VAL Chi-restraints excluded: chain S1 residue 211 VAL Chi-restraints excluded: chain S1 residue 263 VAL Chi-restraints excluded: chain S1 residue 348 VAL Chi-restraints excluded: chain S1 residue 351 SER Chi-restraints excluded: chain S1 residue 396 LEU Chi-restraints excluded: chain S1 residue 397 CYS Chi-restraints excluded: chain S1 residue 426 ASP Chi-restraints excluded: chain S1 residue 465 LEU Chi-restraints excluded: chain S1 residue 482 VAL Chi-restraints excluded: chain S1 residue 499 ASP Chi-restraints excluded: chain S1 residue 514 TYR Chi-restraints excluded: chain S1 residue 518 VAL Chi-restraints excluded: chain S1 residue 531 LYS Chi-restraints excluded: chain S1 residue 553 ASP Chi-restraints excluded: chain S1 residue 582 TYR Chi-restraints excluded: chain S1 residue 633 ASP Chi-restraints excluded: chain S1 residue 634 LEU Chi-restraints excluded: chain S1 residue 657 VAL Chi-restraints excluded: chain S1 residue 667 THR Chi-restraints excluded: chain S1 residue 679 TYR Chi-restraints excluded: chain LC residue 24 ASN Chi-restraints excluded: chain LC residue 32 GLU Chi-restraints excluded: chain LC residue 41 SER Chi-restraints excluded: chain LC residue 72 SER Chi-restraints excluded: chain LC residue 121 MET Chi-restraints excluded: chain LC residue 202 THR Chi-restraints excluded: chain LM residue 3 ILE Chi-restraints excluded: chain LM residue 7 LEU Chi-restraints excluded: chain LM residue 19 PHE Chi-restraints excluded: chain LM residue 25 VAL Chi-restraints excluded: chain LM residue 46 VAL Chi-restraints excluded: chain LM residue 83 ILE Chi-restraints excluded: chain LM residue 91 VAL Chi-restraints excluded: chain LM residue 99 LEU Chi-restraints excluded: chain LN residue 2 VAL Chi-restraints excluded: chain LN residue 9 SER Chi-restraints excluded: chain LN residue 53 ILE Chi-restraints excluded: chain LN residue 63 ILE Chi-restraints excluded: chain LN residue 212 TRP Chi-restraints excluded: chain LN residue 224 MET Chi-restraints excluded: chain LN residue 225 ASN Chi-restraints excluded: chain LN residue 249 VAL Chi-restraints excluded: chain LO residue 50 ARG Chi-restraints excluded: chain LO residue 91 ARG Chi-restraints excluded: chain LP residue 63 VAL Chi-restraints excluded: chain LP residue 99 THR Chi-restraints excluded: chain LQ residue 36 LEU Chi-restraints excluded: chain LQ residue 101 SER Chi-restraints excluded: chain LQ residue 106 VAL Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LR residue 66 LYS Chi-restraints excluded: chain LR residue 74 ILE Chi-restraints excluded: chain LR residue 80 TRP Chi-restraints excluded: chain LS residue 10 VAL Chi-restraints excluded: chain LS residue 27 VAL Chi-restraints excluded: chain LT residue 45 ASP Chi-restraints excluded: chain LT residue 49 ASN Chi-restraints excluded: chain LT residue 60 VAL Chi-restraints excluded: chain LT residue 62 THR Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 77 VAL Chi-restraints excluded: chain LU residue 15 SER Chi-restraints excluded: chain LU residue 39 GLN Chi-restraints excluded: chain LU residue 52 CYS Chi-restraints excluded: chain LU residue 63 ASP Chi-restraints excluded: chain LV residue 33 HIS Chi-restraints excluded: chain LV residue 39 VAL Chi-restraints excluded: chain LV residue 60 LYS Chi-restraints excluded: chain LV residue 63 ILE Chi-restraints excluded: chain LD residue 54 VAL Chi-restraints excluded: chain LW residue 17 GLU Chi-restraints excluded: chain LW residue 50 VAL Chi-restraints excluded: chain LX residue 2 ILE Chi-restraints excluded: chain LX residue 34 VAL Chi-restraints excluded: chain LX residue 73 VAL Chi-restraints excluded: chain LX residue 96 ILE Chi-restraints excluded: chain LX residue 161 MET Chi-restraints excluded: chain LX residue 177 VAL Chi-restraints excluded: chain LX residue 200 ASP Chi-restraints excluded: chain L1 residue 8 THR Chi-restraints excluded: chain L1 residue 38 LEU Chi-restraints excluded: chain L1 residue 43 THR Chi-restraints excluded: chain L1 residue 45 ASP Chi-restraints excluded: chain L1 residue 48 TYR Chi-restraints excluded: chain L2 residue 6 GLU Chi-restraints excluded: chain L3 residue 24 THR Chi-restraints excluded: chain L3 residue 43 THR Chi-restraints excluded: chain L5 residue 17 VAL Chi-restraints excluded: chain L6 residue 7 ASP Chi-restraints excluded: chain L6 residue 75 SER Chi-restraints excluded: chain L6 residue 77 ILE Chi-restraints excluded: chain L6 residue 83 VAL Chi-restraints excluded: chain L6 residue 180 LEU Chi-restraints excluded: chain LE residue 32 VAL Chi-restraints excluded: chain LE residue 34 ILE Chi-restraints excluded: chain LE residue 48 ILE Chi-restraints excluded: chain LE residue 56 VAL Chi-restraints excluded: chain LE residue 57 VAL Chi-restraints excluded: chain LE residue 72 THR Chi-restraints excluded: chain L7 residue 12 VAL Chi-restraints excluded: chain L7 residue 17 THR Chi-restraints excluded: chain L7 residue 20 ASN Chi-restraints excluded: chain L7 residue 24 VAL Chi-restraints excluded: chain L7 residue 86 CYS Chi-restraints excluded: chain L7 residue 136 ILE Chi-restraints excluded: chain L7 residue 153 ILE Chi-restraints excluded: chain L7 residue 154 THR Chi-restraints excluded: chain L7 residue 164 GLU Chi-restraints excluded: chain L8 residue 40 VAL Chi-restraints excluded: chain L8 residue 59 ASP Chi-restraints excluded: chain L8 residue 147 LEU Chi-restraints excluded: chain L8 residue 161 VAL Chi-restraints excluded: chain L9 residue 4 ILE Chi-restraints excluded: chain L9 residue 19 VAL Chi-restraints excluded: chain L9 residue 46 PHE Chi-restraints excluded: chain L9 residue 78 VAL Chi-restraints excluded: chain L9 residue 89 LYS Chi-restraints excluded: chain L9 residue 143 ILE Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 60 ASP Chi-restraints excluded: chain LF residue 78 THR Chi-restraints excluded: chain LF residue 81 ILE Chi-restraints excluded: chain LF residue 84 ILE Chi-restraints excluded: chain LF residue 101 ILE Chi-restraints excluded: chain LF residue 106 LYS Chi-restraints excluded: chain LF residue 142 ILE Chi-restraints excluded: chain LG residue 10 VAL Chi-restraints excluded: chain LG residue 21 CYS Chi-restraints excluded: chain LG residue 43 ILE Chi-restraints excluded: chain LG residue 61 VAL Chi-restraints excluded: chain LG residue 65 THR Chi-restraints excluded: chain LG residue 76 VAL Chi-restraints excluded: chain LG residue 77 ILE Chi-restraints excluded: chain LG residue 97 THR Chi-restraints excluded: chain LG residue 103 VAL Chi-restraints excluded: chain LH residue 18 ARG Chi-restraints excluded: chain LH residue 57 LEU Chi-restraints excluded: chain LH residue 64 PHE Chi-restraints excluded: chain LH residue 92 LEU Chi-restraints excluded: chain LH residue 110 VAL Chi-restraints excluded: chain LH residue 118 THR Chi-restraints excluded: chain LH residue 121 THR Chi-restraints excluded: chain LI residue 7 THR Chi-restraints excluded: chain LI residue 17 ASN Chi-restraints excluded: chain LI residue 67 VAL Chi-restraints excluded: chain LI residue 88 ASN Chi-restraints excluded: chain LI residue 95 LEU Chi-restraints excluded: chain LI residue 126 ILE Chi-restraints excluded: chain LJ residue 13 ASN Chi-restraints excluded: chain LJ residue 37 THR Chi-restraints excluded: chain LJ residue 53 THR Chi-restraints excluded: chain LJ residue 76 VAL Chi-restraints excluded: chain LK residue 5 SER Chi-restraints excluded: chain LK residue 17 LYS Chi-restraints excluded: chain LK residue 65 THR Chi-restraints excluded: chain LK residue 90 VAL Chi-restraints excluded: chain LZ residue 16 CYS Chi-restraints excluded: chain LZ residue 21 VAL Chi-restraints excluded: chain LZ residue 24 ILE Chi-restraints excluded: chain LZ residue 35 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1159 random chunks: chunk 1016 optimal weight: 4.9990 chunk 1070 optimal weight: 2.9990 chunk 976 optimal weight: 0.4980 chunk 1040 optimal weight: 9.9990 chunk 1069 optimal weight: 4.9990 chunk 626 optimal weight: 40.0000 chunk 453 optimal weight: 8.9990 chunk 817 optimal weight: 0.7980 chunk 319 optimal weight: 10.0000 chunk 940 optimal weight: 20.0000 chunk 984 optimal weight: 2.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SK 100 ASN SN 34 ASN ** SP 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 18 ASN SC 31 ASN SD 40 HIS SD 163 GLN SE 145 ASN SF 14 GLN ** SF 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 504 HIS ** S1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 76 HIS ** LN 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LP 82 HIS ** LR 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LV 33 HIS LW 20 ASN LX 164 GLN ** L8 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 142 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 1.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 169620 Z= 0.178 Angle : 0.663 16.380 252372 Z= 0.339 Chirality : 0.036 0.282 32049 Planarity : 0.005 0.084 14531 Dihedral : 23.767 179.721 81557 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.56 % Favored : 90.90 % Rotamer: Outliers : 4.08 % Allowed : 32.86 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.01 % Twisted Proline : 0.41 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.10), residues: 7019 helix: -0.11 (0.11), residues: 2246 sheet: -0.89 (0.14), residues: 1231 loop : -2.23 (0.10), residues: 3542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRPLN 212 HIS 0.013 0.001 HISS1 504 PHE 0.052 0.002 PHEL7 174 TYR 0.027 0.002 TYRLN 61 ARG 0.012 0.001 ARGSS 36 *********************** 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 1693 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1457 time to evaluate : 6.926 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: SJ 1 MET cc_start: 0.1957 (mmp) cc_final: 0.0027 (mmm) REVERT: SK 39 ASN cc_start: 0.6509 (m-40) cc_final: 0.6309 (t0) REVERT: SK 84 MET cc_start: 0.6452 (mmm) cc_final: 0.6064 (mmt) REVERT: SL 64 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8291 (t) REVERT: SN 72 PHE cc_start: 0.7754 (t80) cc_final: 0.7543 (t80) REVERT: SQ 19 SER cc_start: 0.6084 (m) cc_final: 0.5352 (m) REVERT: SR 2 ARG cc_start: 0.3787 (OUTLIER) cc_final: 0.2150 (tpt170) REVERT: SB 5 MET cc_start: 0.3109 (ppp) cc_final: 0.1831 (tpp) REVERT: ST 77 ASN cc_start: 0.6904 (m-40) cc_final: 0.6662 (m-40) REVERT: SU 6 ARG cc_start: 0.4583 (ptt180) cc_final: 0.4312 (ptt180) REVERT: SU 38 GLU cc_start: 0.6155 (tp30) cc_final: 0.5806 (mm-30) REVERT: SD 14 GLU cc_start: 0.6326 (tm-30) cc_final: 0.6026 (tm-30) REVERT: SD 140 ASP cc_start: 0.6315 (m-30) cc_final: 0.6027 (m-30) REVERT: SF 79 ARG cc_start: 0.6223 (OUTLIER) cc_final: 0.5916 (tpp80) REVERT: SG 161 PHE cc_start: 0.3858 (OUTLIER) cc_final: 0.2816 (m-80) REVERT: SI 56 MET cc_start: 0.3362 (mmm) cc_final: 0.2788 (mmp) REVERT: SI 87 MET cc_start: 0.7131 (tmm) cc_final: 0.6824 (tmm) REVERT: LC 1 MET cc_start: 0.4158 (mmt) cc_final: 0.3287 (ptm) REVERT: LC 121 MET cc_start: 0.2308 (ppp) cc_final: 0.1782 (ttt) REVERT: LN 180 MET cc_start: 0.7048 (mmm) cc_final: 0.6612 (mmm) REVERT: LO 51 GLN cc_start: 0.6774 (tp40) cc_final: 0.6516 (tp40) REVERT: LQ 1 MET cc_start: 0.6056 (tmm) cc_final: 0.5608 (ttt) REVERT: LR 66 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6896 (pttm) REVERT: LS 59 GLU cc_start: 0.6870 (tp30) cc_final: 0.6587 (tp30) REVERT: LU 61 LYS cc_start: 0.7707 (mmmm) cc_final: 0.7304 (mttm) REVERT: LV 60 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6130 (tttt) REVERT: LD 85 MET cc_start: 0.3827 (ppp) cc_final: 0.1359 (mmm) REVERT: LD 139 MET cc_start: 0.2620 (ttt) cc_final: 0.1743 (mtm) REVERT: LE 106 GLN cc_start: 0.5428 (pp30) cc_final: 0.5208 (pp30) REVERT: L8 175 LYS cc_start: 0.4667 (mmtt) cc_final: 0.3751 (tttt) REVERT: LG 7 MET cc_start: 0.6760 (tpp) cc_final: 0.6035 (mmt) REVERT: LH 18 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7935 (mtp180) REVERT: LH 59 ARG cc_start: 0.7883 (mtm180) cc_final: 0.7453 (mtp180) REVERT: LH 101 ILE cc_start: 0.7368 (tt) cc_final: 0.6984 (tt) REVERT: LI 82 MET cc_start: 0.7925 (tpp) cc_final: 0.7697 (tpp) REVERT: LI 128 THR cc_start: 0.7100 (t) cc_final: 0.6629 (p) outliers start: 236 outliers final: 180 residues processed: 1585 average time/residue: 1.3077 time to fit residues: 3656.8625 Evaluate side-chains 1533 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1346 time to evaluate : 7.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SJ residue 10 LEU Chi-restraints excluded: chain SJ residue 44 THR Chi-restraints excluded: chain SJ residue 69 THR Chi-restraints excluded: chain SK residue 19 VAL Chi-restraints excluded: chain SL residue 2 THR Chi-restraints excluded: chain SL residue 20 VAL Chi-restraints excluded: chain SL residue 64 SER Chi-restraints excluded: chain SL residue 86 VAL Chi-restraints excluded: chain SM residue 27 THR Chi-restraints excluded: chain SM residue 65 GLU Chi-restraints excluded: chain SM residue 72 ILE Chi-restraints excluded: chain SM residue 96 VAL Chi-restraints excluded: chain SN residue 29 ILE Chi-restraints excluded: chain SN residue 61 ASN Chi-restraints excluded: chain SN residue 92 ILE Chi-restraints excluded: chain SO residue 58 MET Chi-restraints excluded: chain SQ residue 28 VAL Chi-restraints excluded: chain SQ residue 36 PHE Chi-restraints excluded: chain SQ residue 77 VAL Chi-restraints excluded: chain SR residue 2 ARG Chi-restraints excluded: chain SR residue 38 ILE Chi-restraints excluded: chain SR residue 41 SER Chi-restraints excluded: chain SS residue 27 LYS Chi-restraints excluded: chain SS residue 38 THR Chi-restraints excluded: chain SB residue 19 THR Chi-restraints excluded: chain SB residue 22 TRP Chi-restraints excluded: chain SB residue 226 GLN Chi-restraints excluded: chain ST residue 66 ILE Chi-restraints excluded: chain SC residue 51 VAL Chi-restraints excluded: chain SC residue 82 ASP Chi-restraints excluded: chain SC residue 83 VAL Chi-restraints excluded: chain SC residue 148 ILE Chi-restraints excluded: chain SC residue 165 GLU Chi-restraints excluded: chain SC residue 185 THR Chi-restraints excluded: chain SC residue 191 THR Chi-restraints excluded: chain SD residue 74 TYR Chi-restraints excluded: chain SD residue 118 SER Chi-restraints excluded: chain SD residue 144 ILE Chi-restraints excluded: chain SD residue 173 ASP Chi-restraints excluded: chain SD residue 194 ILE Chi-restraints excluded: chain SE residue 11 GLN Chi-restraints excluded: chain SE residue 14 LEU Chi-restraints excluded: chain SE residue 91 SER Chi-restraints excluded: chain SE residue 104 ILE Chi-restraints excluded: chain SE residue 151 MET Chi-restraints excluded: chain SF residue 9 MET Chi-restraints excluded: chain SF residue 22 ILE Chi-restraints excluded: chain SF residue 30 THR Chi-restraints excluded: chain SF residue 79 ARG Chi-restraints excluded: chain SF residue 81 ASN Chi-restraints excluded: chain SF residue 94 HIS Chi-restraints excluded: chain SF residue 97 THR Chi-restraints excluded: chain SG residue 85 GLN Chi-restraints excluded: chain SG residue 105 GLU Chi-restraints excluded: chain SG residue 161 PHE Chi-restraints excluded: chain SH residue 60 LEU Chi-restraints excluded: chain SH residue 74 ILE Chi-restraints excluded: chain SH residue 103 VAL Chi-restraints excluded: chain SH residue 105 THR Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 47 VAL Chi-restraints excluded: chain SI residue 74 GLN Chi-restraints excluded: chain SI residue 92 SER Chi-restraints excluded: chain S1 residue 9 TYR Chi-restraints excluded: chain S1 residue 85 ILE Chi-restraints excluded: chain S1 residue 140 VAL Chi-restraints excluded: chain S1 residue 211 VAL Chi-restraints excluded: chain S1 residue 342 VAL Chi-restraints excluded: chain S1 residue 397 CYS Chi-restraints excluded: chain S1 residue 482 VAL Chi-restraints excluded: chain S1 residue 514 TYR Chi-restraints excluded: chain S1 residue 553 ASP Chi-restraints excluded: chain S1 residue 582 TYR Chi-restraints excluded: chain S1 residue 633 ASP Chi-restraints excluded: chain S1 residue 634 LEU Chi-restraints excluded: chain S1 residue 657 VAL Chi-restraints excluded: chain LC residue 24 ASN Chi-restraints excluded: chain LC residue 32 GLU Chi-restraints excluded: chain LC residue 41 SER Chi-restraints excluded: chain LC residue 202 THR Chi-restraints excluded: chain LM residue 3 ILE Chi-restraints excluded: chain LM residue 25 VAL Chi-restraints excluded: chain LM residue 46 VAL Chi-restraints excluded: chain LM residue 83 ILE Chi-restraints excluded: chain LM residue 91 VAL Chi-restraints excluded: chain LM residue 99 LEU Chi-restraints excluded: chain LN residue 2 VAL Chi-restraints excluded: chain LN residue 9 SER Chi-restraints excluded: chain LN residue 224 MET Chi-restraints excluded: chain LN residue 225 ASN Chi-restraints excluded: chain LN residue 249 VAL Chi-restraints excluded: chain LO residue 91 ARG Chi-restraints excluded: chain LP residue 63 VAL Chi-restraints excluded: chain LP residue 99 THR Chi-restraints excluded: chain LQ residue 36 LEU Chi-restraints excluded: chain LQ residue 74 ILE Chi-restraints excluded: chain LQ residue 85 ILE Chi-restraints excluded: chain LQ residue 97 LEU Chi-restraints excluded: chain LQ residue 101 SER Chi-restraints excluded: chain LQ residue 106 VAL Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LR residue 60 THR Chi-restraints excluded: chain LR residue 66 LYS Chi-restraints excluded: chain LR residue 80 TRP Chi-restraints excluded: chain LS residue 27 VAL Chi-restraints excluded: chain LT residue 60 VAL Chi-restraints excluded: chain LT residue 62 THR Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 77 VAL Chi-restraints excluded: chain LU residue 15 SER Chi-restraints excluded: chain LU residue 52 CYS Chi-restraints excluded: chain LU residue 63 ASP Chi-restraints excluded: chain LV residue 39 VAL Chi-restraints excluded: chain LV residue 60 LYS Chi-restraints excluded: chain LW residue 17 GLU Chi-restraints excluded: chain LW residue 50 VAL Chi-restraints excluded: chain LX residue 2 ILE Chi-restraints excluded: chain LX residue 34 VAL Chi-restraints excluded: chain LX residue 73 VAL Chi-restraints excluded: chain LX residue 161 MET Chi-restraints excluded: chain LX residue 177 VAL Chi-restraints excluded: chain LX residue 203 VAL Chi-restraints excluded: chain LY residue 40 THR Chi-restraints excluded: chain L1 residue 43 THR Chi-restraints excluded: chain L1 residue 45 ASP Chi-restraints excluded: chain L1 residue 48 TYR Chi-restraints excluded: chain L2 residue 33 LEU Chi-restraints excluded: chain L3 residue 24 THR Chi-restraints excluded: chain L4 residue 43 LEU Chi-restraints excluded: chain L4 residue 48 MET Chi-restraints excluded: chain L6 residue 62 GLN Chi-restraints excluded: chain L6 residue 75 SER Chi-restraints excluded: chain L6 residue 77 ILE Chi-restraints excluded: chain L6 residue 180 LEU Chi-restraints excluded: chain LE residue 34 ILE Chi-restraints excluded: chain LE residue 48 ILE Chi-restraints excluded: chain LE residue 56 VAL Chi-restraints excluded: chain LE residue 57 VAL Chi-restraints excluded: chain LE residue 72 THR Chi-restraints excluded: chain L7 residue 12 VAL Chi-restraints excluded: chain L7 residue 20 ASN Chi-restraints excluded: chain L7 residue 135 ILE Chi-restraints excluded: chain L7 residue 136 ILE Chi-restraints excluded: chain L7 residue 164 GLU Chi-restraints excluded: chain L8 residue 40 VAL Chi-restraints excluded: chain L8 residue 59 ASP Chi-restraints excluded: chain L8 residue 71 LEU Chi-restraints excluded: chain L8 residue 75 VAL Chi-restraints excluded: chain L8 residue 147 LEU Chi-restraints excluded: chain L8 residue 161 VAL Chi-restraints excluded: chain L9 residue 4 ILE Chi-restraints excluded: chain L9 residue 19 VAL Chi-restraints excluded: chain L9 residue 78 VAL Chi-restraints excluded: chain L9 residue 89 LYS Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 60 ASP Chi-restraints excluded: chain LF residue 78 THR Chi-restraints excluded: chain LF residue 81 ILE Chi-restraints excluded: chain LF residue 84 ILE Chi-restraints excluded: chain LF residue 101 ILE Chi-restraints excluded: chain LG residue 1 MET Chi-restraints excluded: chain LG residue 10 VAL Chi-restraints excluded: chain LG residue 21 CYS Chi-restraints excluded: chain LG residue 43 ILE Chi-restraints excluded: chain LG residue 61 VAL Chi-restraints excluded: chain LG residue 65 THR Chi-restraints excluded: chain LG residue 76 VAL Chi-restraints excluded: chain LG residue 77 ILE Chi-restraints excluded: chain LG residue 97 THR Chi-restraints excluded: chain LH residue 18 ARG Chi-restraints excluded: chain LH residue 57 LEU Chi-restraints excluded: chain LH residue 64 PHE Chi-restraints excluded: chain LH residue 110 VAL Chi-restraints excluded: chain LH residue 118 THR Chi-restraints excluded: chain LH residue 121 THR Chi-restraints excluded: chain LI residue 7 THR Chi-restraints excluded: chain LI residue 17 ASN Chi-restraints excluded: chain LI residue 67 VAL Chi-restraints excluded: chain LI residue 117 PHE Chi-restraints excluded: chain LI residue 126 ILE Chi-restraints excluded: chain LJ residue 13 ASN Chi-restraints excluded: chain LJ residue 53 THR Chi-restraints excluded: chain LJ residue 76 VAL Chi-restraints excluded: chain LK residue 65 THR Chi-restraints excluded: chain LK residue 90 VAL Chi-restraints excluded: chain LZ residue 16 CYS Chi-restraints excluded: chain LZ residue 24 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1159 random chunks: chunk 1037 optimal weight: 6.9990 chunk 683 optimal weight: 10.0000 chunk 1100 optimal weight: 7.9990 chunk 671 optimal weight: 20.0000 chunk 522 optimal weight: 10.0000 chunk 765 optimal weight: 30.0000 chunk 1154 optimal weight: 5.9990 chunk 1062 optimal weight: 7.9990 chunk 919 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 710 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SN 34 ASN SN 59 GLN ** SP 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SS 42 ASN ** SS 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 12 GLN SC 31 ASN SC 40 GLN SD 40 HIS SD 53 GLN ** SD 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 163 GLN SF 14 GLN ** SF 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 128 GLN S1 464 HIS ** S1 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 74 GLN LM 76 HIS ** LN 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LP 82 HIS ** LQ 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 44 HIS LT 12 GLN ** LT 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LU 75 ASN LV 33 HIS ** LX 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3 16 HIS ** LE 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L8 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 1.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 169620 Z= 0.358 Angle : 0.787 14.520 252372 Z= 0.399 Chirality : 0.042 0.446 32049 Planarity : 0.006 0.067 14531 Dihedral : 23.788 179.665 81557 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.94 % Favored : 89.50 % Rotamer: Outliers : 4.44 % Allowed : 32.72 % Favored : 62.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.01 % Twisted Proline : 0.41 % 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: -2.15 (0.09), residues: 7019 helix: -0.33 (0.10), residues: 2250 sheet: -0.94 (0.15), residues: 1187 loop : -2.38 (0.09), residues: 3582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.122 0.003 TRPLN 212 HIS 0.015 0.002 HISL6 92 PHE 0.057 0.003 PHEL7 174 TYR 0.026 0.003 TYRSD 50 ARG 0.031 0.001 ARGL7 132 ********************** 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 1611 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1354 time to evaluate : 6.966 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: SK 84 MET cc_start: 0.6619 (mmm) cc_final: 0.6217 (mmt) REVERT: SL 64 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8379 (t) REVERT: SR 2 ARG cc_start: 0.3867 (OUTLIER) cc_final: 0.2678 (mmm160) REVERT: SB 5 MET cc_start: 0.2951 (ppp) cc_final: 0.1872 (tpp) REVERT: ST 77 ASN cc_start: 0.6958 (m-40) cc_final: 0.6697 (m-40) REVERT: SD 14 GLU cc_start: 0.6401 (tm-30) cc_final: 0.6167 (tm-30) REVERT: SG 161 PHE cc_start: 0.3747 (OUTLIER) cc_final: 0.2798 (m-10) REVERT: SI 87 MET cc_start: 0.7238 (tmm) cc_final: 0.6831 (tmm) REVERT: S1 284 TYR cc_start: 0.4272 (m-80) cc_final: 0.4014 (m-80) REVERT: LC 1 MET cc_start: 0.4814 (mmt) cc_final: 0.3519 (ptm) REVERT: LC 121 MET cc_start: 0.2547 (OUTLIER) cc_final: 0.2006 (ttt) REVERT: LM 3 ILE cc_start: 0.6550 (OUTLIER) cc_final: 0.6242 (pt) REVERT: LM 12 MET cc_start: 0.7261 (ttp) cc_final: 0.6976 (ttp) REVERT: LN 180 MET cc_start: 0.7324 (mmm) cc_final: 0.7118 (mmm) REVERT: LO 50 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7269 (mtm-85) REVERT: LO 51 GLN cc_start: 0.6909 (tp40) cc_final: 0.6705 (tp40) REVERT: LQ 1 MET cc_start: 0.6244 (tmm) cc_final: 0.5857 (ttt) REVERT: LS 59 GLU cc_start: 0.7191 (tp30) cc_final: 0.6657 (tp30) REVERT: LT 41 GLU cc_start: 0.5618 (pt0) cc_final: 0.5395 (pt0) REVERT: LV 60 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.5713 (tttt) REVERT: LD 85 MET cc_start: 0.3827 (ppp) cc_final: 0.1559 (mmm) REVERT: LD 139 MET cc_start: 0.2763 (ttt) cc_final: 0.1889 (mtm) REVERT: L8 175 LYS cc_start: 0.4813 (mmtt) cc_final: 0.3851 (tttt) REVERT: LG 7 MET cc_start: 0.6878 (tpp) cc_final: 0.6445 (tpt) REVERT: LH 59 ARG cc_start: 0.8014 (mtm180) cc_final: 0.7607 (mtp180) REVERT: LH 101 ILE cc_start: 0.7475 (tt) cc_final: 0.7159 (tt) REVERT: LI 82 MET cc_start: 0.8066 (tpp) cc_final: 0.7801 (tpp) outliers start: 257 outliers final: 213 residues processed: 1503 average time/residue: 1.3585 time to fit residues: 3609.6592 Evaluate side-chains 1536 residues out of total 5788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1316 time to evaluate : 6.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SJ residue 10 LEU Chi-restraints excluded: chain SJ residue 44 THR Chi-restraints excluded: chain SJ residue 50 THR Chi-restraints excluded: chain SJ residue 69 THR Chi-restraints excluded: chain SK residue 19 VAL Chi-restraints excluded: chain SL residue 2 THR Chi-restraints excluded: chain SL residue 20 VAL Chi-restraints excluded: chain SL residue 39 THR Chi-restraints excluded: chain SL residue 57 THR Chi-restraints excluded: chain SL residue 64 SER Chi-restraints excluded: chain SL residue 86 VAL Chi-restraints excluded: chain SL residue 116 TYR Chi-restraints excluded: chain SM residue 27 THR Chi-restraints excluded: chain SM residue 65 GLU Chi-restraints excluded: chain SM residue 67 ASP Chi-restraints excluded: chain SM residue 72 ILE Chi-restraints excluded: chain SM residue 96 VAL Chi-restraints excluded: chain SN residue 29 ILE Chi-restraints excluded: chain SN residue 61 ASN Chi-restraints excluded: chain SN residue 92 ILE Chi-restraints excluded: chain SO residue 58 MET Chi-restraints excluded: chain SQ residue 4 ILE Chi-restraints excluded: chain SQ residue 25 GLU Chi-restraints excluded: chain SQ residue 28 VAL Chi-restraints excluded: chain SQ residue 36 PHE Chi-restraints excluded: chain SQ residue 43 LEU Chi-restraints excluded: chain SQ residue 77 VAL Chi-restraints excluded: chain SR residue 2 ARG Chi-restraints excluded: chain SR residue 38 ILE Chi-restraints excluded: chain SR residue 41 SER Chi-restraints excluded: chain SR residue 71 ASP Chi-restraints excluded: chain SS residue 27 LYS Chi-restraints excluded: chain SS residue 38 THR Chi-restraints excluded: chain SB residue 19 THR Chi-restraints excluded: chain SB residue 22 TRP Chi-restraints excluded: chain SB residue 79 VAL Chi-restraints excluded: chain SB residue 226 GLN Chi-restraints excluded: chain ST residue 66 ILE Chi-restraints excluded: chain SC residue 13 ILE Chi-restraints excluded: chain SC residue 51 VAL Chi-restraints excluded: chain SC residue 82 ASP Chi-restraints excluded: chain SC residue 83 VAL Chi-restraints excluded: chain SC residue 148 ILE Chi-restraints excluded: chain SC residue 165 GLU Chi-restraints excluded: chain SC residue 185 THR Chi-restraints excluded: chain SC residue 191 THR Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SD residue 74 TYR Chi-restraints excluded: chain SD residue 84 ASN Chi-restraints excluded: chain SD residue 118 SER Chi-restraints excluded: chain SD residue 144 ILE Chi-restraints excluded: chain SD residue 173 ASP Chi-restraints excluded: chain SD residue 194 ILE Chi-restraints excluded: chain SE residue 11 GLN Chi-restraints excluded: chain SE residue 14 LEU Chi-restraints excluded: chain SE residue 91 SER Chi-restraints excluded: chain SE residue 104 ILE Chi-restraints excluded: chain SE residue 151 MET Chi-restraints excluded: chain SF residue 9 MET Chi-restraints excluded: chain SF residue 22 ILE Chi-restraints excluded: chain SF residue 30 THR Chi-restraints excluded: chain SF residue 54 LEU Chi-restraints excluded: chain SF residue 81 ASN Chi-restraints excluded: chain SF residue 94 HIS Chi-restraints excluded: chain SG residue 63 VAL Chi-restraints excluded: chain SG residue 85 GLN Chi-restraints excluded: chain SG residue 105 GLU Chi-restraints excluded: chain SG residue 161 PHE Chi-restraints excluded: chain SH residue 8 ASP Chi-restraints excluded: chain SH residue 53 ASP Chi-restraints excluded: chain SH residue 60 LEU Chi-restraints excluded: chain SH residue 74 ILE Chi-restraints excluded: chain SH residue 105 THR Chi-restraints excluded: chain SH residue 111 THR Chi-restraints excluded: chain SH residue 123 GLU Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 47 VAL Chi-restraints excluded: chain SI residue 74 GLN Chi-restraints excluded: chain SI residue 92 SER Chi-restraints excluded: chain S1 residue 9 TYR Chi-restraints excluded: chain S1 residue 85 ILE Chi-restraints excluded: chain S1 residue 137 ILE Chi-restraints excluded: chain S1 residue 140 VAL Chi-restraints excluded: chain S1 residue 211 VAL Chi-restraints excluded: chain S1 residue 263 VAL Chi-restraints excluded: chain S1 residue 342 VAL Chi-restraints excluded: chain S1 residue 397 CYS Chi-restraints excluded: chain S1 residue 453 ASN Chi-restraints excluded: chain S1 residue 482 VAL Chi-restraints excluded: chain S1 residue 499 ASP Chi-restraints excluded: chain S1 residue 514 TYR Chi-restraints excluded: chain S1 residue 553 ASP Chi-restraints excluded: chain S1 residue 558 GLU Chi-restraints excluded: chain S1 residue 582 TYR Chi-restraints excluded: chain S1 residue 633 ASP Chi-restraints excluded: chain S1 residue 634 LEU Chi-restraints excluded: chain S1 residue 657 VAL Chi-restraints excluded: chain LC residue 24 ASN Chi-restraints excluded: chain LC residue 32 GLU Chi-restraints excluded: chain LC residue 41 SER Chi-restraints excluded: chain LC residue 121 MET Chi-restraints excluded: chain LC residue 202 THR Chi-restraints excluded: chain LC residue 203 GLN Chi-restraints excluded: chain LM residue 3 ILE Chi-restraints excluded: chain LM residue 7 LEU Chi-restraints excluded: chain LM residue 25 VAL Chi-restraints excluded: chain LM residue 46 VAL Chi-restraints excluded: chain LM residue 83 ILE Chi-restraints excluded: chain LM residue 91 VAL Chi-restraints excluded: chain LM residue 99 LEU Chi-restraints excluded: chain LN residue 2 VAL Chi-restraints excluded: chain LN residue 53 ILE Chi-restraints excluded: chain LN residue 224 MET Chi-restraints excluded: chain LN residue 225 ASN Chi-restraints excluded: chain LN residue 249 VAL Chi-restraints excluded: chain LO residue 50 ARG Chi-restraints excluded: chain LO residue 91 ARG Chi-restraints excluded: chain LP residue 63 VAL Chi-restraints excluded: chain LP residue 99 THR Chi-restraints excluded: chain LQ residue 36 LEU Chi-restraints excluded: chain LQ residue 74 ILE Chi-restraints excluded: chain LQ residue 101 SER Chi-restraints excluded: chain LQ residue 106 VAL Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LR residue 66 LYS Chi-restraints excluded: chain LR residue 80 TRP Chi-restraints excluded: chain LS residue 14 THR Chi-restraints excluded: chain LS residue 27 VAL Chi-restraints excluded: chain LS residue 44 HIS Chi-restraints excluded: chain LT residue 60 VAL Chi-restraints excluded: chain LT residue 62 THR Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 77 VAL Chi-restraints excluded: chain LU residue 15 SER Chi-restraints excluded: chain LU residue 39 GLN Chi-restraints excluded: chain LU residue 63 ASP Chi-restraints excluded: chain LV residue 33 HIS Chi-restraints excluded: chain LV residue 39 VAL Chi-restraints excluded: chain LV residue 60 LYS Chi-restraints excluded: chain LV residue 64 ASP Chi-restraints excluded: chain LW residue 17 GLU Chi-restraints excluded: chain LX residue 2 ILE Chi-restraints excluded: chain LX residue 34 VAL Chi-restraints excluded: chain LX residue 161 MET Chi-restraints excluded: chain LX residue 177 VAL Chi-restraints excluded: chain LX residue 200 ASP Chi-restraints excluded: chain LX residue 203 VAL Chi-restraints excluded: chain LY residue 40 THR Chi-restraints excluded: chain LY residue 54 VAL Chi-restraints excluded: chain L1 residue 36 LYS Chi-restraints excluded: chain L1 residue 43 THR Chi-restraints excluded: chain L1 residue 45 ASP Chi-restraints excluded: chain L2 residue 33 LEU Chi-restraints excluded: chain L3 residue 24 THR Chi-restraints excluded: chain L4 residue 43 LEU Chi-restraints excluded: chain L4 residue 48 MET Chi-restraints excluded: chain L6 residue 62 GLN Chi-restraints excluded: chain L6 residue 75 SER Chi-restraints excluded: chain L6 residue 77 ILE Chi-restraints excluded: chain L6 residue 173 THR Chi-restraints excluded: chain L6 residue 180 LEU Chi-restraints excluded: chain LE residue 34 ILE Chi-restraints excluded: chain LE residue 48 ILE Chi-restraints excluded: chain LE residue 56 VAL Chi-restraints excluded: chain LE residue 57 VAL Chi-restraints excluded: chain LE residue 72 THR Chi-restraints excluded: chain L7 residue 12 VAL Chi-restraints excluded: chain L7 residue 20 ASN Chi-restraints excluded: chain L7 residue 24 VAL Chi-restraints excluded: chain L7 residue 135 ILE Chi-restraints excluded: chain L7 residue 136 ILE Chi-restraints excluded: chain L7 residue 164 GLU Chi-restraints excluded: chain L8 residue 40 VAL Chi-restraints excluded: chain L8 residue 59 ASP Chi-restraints excluded: chain L8 residue 131 VAL Chi-restraints excluded: chain L8 residue 147 LEU Chi-restraints excluded: chain L8 residue 161 VAL Chi-restraints excluded: chain L9 residue 4 ILE Chi-restraints excluded: chain L9 residue 19 VAL Chi-restraints excluded: chain L9 residue 78 VAL Chi-restraints excluded: chain L9 residue 89 LYS Chi-restraints excluded: chain L9 residue 143 ILE Chi-restraints excluded: chain LF residue 18 VAL Chi-restraints excluded: chain LF residue 60 ASP Chi-restraints excluded: chain LF residue 71 ASP Chi-restraints excluded: chain LF residue 78 THR Chi-restraints excluded: chain LF residue 81 ILE Chi-restraints excluded: chain LF residue 84 ILE Chi-restraints excluded: chain LF residue 101 ILE Chi-restraints excluded: chain LF residue 106 LYS Chi-restraints excluded: chain LF residue 142 ILE Chi-restraints excluded: chain LG residue 1 MET Chi-restraints excluded: chain LG residue 10 VAL Chi-restraints excluded: chain LG residue 21 CYS Chi-restraints excluded: chain LG residue 43 ILE Chi-restraints excluded: chain LG residue 61 VAL Chi-restraints excluded: chain LG residue 65 THR Chi-restraints excluded: chain LG residue 77 ILE Chi-restraints excluded: chain LH residue 18 ARG Chi-restraints excluded: chain LH residue 57 LEU Chi-restraints excluded: chain LH residue 64 PHE Chi-restraints excluded: chain LH residue 118 THR Chi-restraints excluded: chain LH residue 121 THR Chi-restraints excluded: chain LI residue 7 THR Chi-restraints excluded: chain LI residue 17 ASN Chi-restraints excluded: chain LI residue 26 VAL Chi-restraints excluded: chain LI residue 67 VAL Chi-restraints excluded: chain LI residue 126 ILE Chi-restraints excluded: chain LJ residue 13 ASN Chi-restraints excluded: chain LJ residue 53 THR Chi-restraints excluded: chain LJ residue 75 ILE Chi-restraints excluded: chain LJ residue 76 VAL Chi-restraints excluded: chain LJ residue 97 ILE Chi-restraints excluded: chain LK residue 5 SER Chi-restraints excluded: chain LK residue 46 GLU Chi-restraints excluded: chain LK residue 65 THR Chi-restraints excluded: chain LK residue 90 VAL Chi-restraints excluded: chain LZ residue 16 CYS Chi-restraints excluded: chain LZ residue 24 ILE Chi-restraints excluded: chain LZ residue 35 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1159 random chunks: chunk 563 optimal weight: 7.9990 chunk 730 optimal weight: 10.0000 chunk 979 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 847 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 chunk 255 optimal weight: 0.9990 chunk 920 optimal weight: 5.9990 chunk 385 optimal weight: 2.9990 chunk 945 optimal weight: 1.9990 chunk 116 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SN 34 ASN ** SP 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 12 GLN SC 40 GLN SD 40 HIS ** SD 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 163 GLN SE 145 ASN ** SF 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 30 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LP 82 HIS ** LQ 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 28 ASN ** LR 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 44 HIS ** LT 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LV 33 HIS ** LX 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3 16 HIS ** LE 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L8 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L9 2 GLN ** LG 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.094996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.077360 restraints weight = 549590.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.079064 restraints weight = 193846.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.080030 restraints weight = 108456.179| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 1.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.147 169620 Z= 0.213 Angle : 0.696 14.835 252372 Z= 0.358 Chirality : 0.038 0.296 32049 Planarity : 0.005 0.079 14531 Dihedral : 23.787 179.780 81557 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.05 % Favored : 90.43 % Rotamer: Outliers : 3.65 % Allowed : 33.36 % Favored : 62.99 % Cbeta Deviations : 0.02 % 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: -2.04 (0.09), residues: 7019 helix: -0.23 (0.11), residues: 2246 sheet: -0.91 (0.15), residues: 1194 loop : -2.31 (0.10), residues: 3579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.102 0.002 TRPLN 212 HIS 0.074 0.002 HISLV 33 PHE 0.053 0.002 PHEL7 174 TYR 0.028 0.002 TYRLN 61 ARG 0.011 0.001 ARGSF 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 52188.31 seconds wall clock time: 906 minutes 17.47 seconds (54377.47 seconds total)