Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 22:23:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xre_22294/04_2023/6xre_22294.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xre_22294/04_2023/6xre_22294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xre_22294/04_2023/6xre_22294.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xre_22294/04_2023/6xre_22294.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xre_22294/04_2023/6xre_22294.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xre_22294/04_2023/6xre_22294.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 Mg 1 5.21 5 S 217 5.16 5 C 21607 2.51 5 N 6003 2.21 5 O 6458 1.98 5 H 34248 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 859": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 875": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 903": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 924": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1058": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1432": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 785": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 814": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 887": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 949": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 956": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1020": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 68542 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 23335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1467, 23335 Classifications: {'peptide': 1467} Link IDs: {'PTRANS': 69, 'TRANS': 1397} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 18407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 18407 Classifications: {'peptide': 1150} Link IDs: {'PTRANS': 52, 'TRANS': 1097} Chain: "C" Number of atoms: 4368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 4368 Classifications: {'peptide': 275} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 257} Chain: "D" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 2105 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "E" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3425 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain: "F" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1287 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2707 Classifications: {'peptide': 171} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 2371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 2371 Classifications: {'peptide': 150} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "I" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1851 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "J" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1088 Classifications: {'peptide': 67} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1894 Classifications: {'peptide': 117} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "L" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 786 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 4909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 4909 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 30, 'TRANS': 283} Chain breaks: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 59684 SG CYS I 114 14.370 65.136 87.433 1.00 9.16 S Time building chain proxies: 21.35, per 1000 atoms: 0.31 Number of scatterers: 68542 At special positions: 0 Unit cell: (176.85, 165.06, 145.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 217 16.00 Mg 1 11.99 O 6458 8.00 N 6003 7.00 C 21607 6.00 H 34248 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 45.31 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 91 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8068 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 41 sheets defined 35.0% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.625A pdb=" N SER A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 124 through 132 removed outlier: 3.765A pdb=" N ASP A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 150 Processing helix chain 'A' and resid 220 through 225 removed outlier: 4.032A pdb=" N PHE A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.553A pdb=" N MET A 248 " --> pdb=" O PRO A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 294 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 348 through 354 removed outlier: 3.686A pdb=" N GLY A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 398 through 408 Processing helix chain 'A' and resid 465 through 469 removed outlier: 3.850A pdb=" N SER A 468 " --> pdb=" O HIS A 465 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET A 469 " --> pdb=" O LYS A 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 465 through 469' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.698A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 538 through 549 removed outlier: 3.645A pdb=" N ARG A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 587 through 593 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 661 through 682 removed outlier: 3.770A pdb=" N THR A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 695 through 721 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 868 removed outlier: 4.039A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 removed outlier: 3.506A pdb=" N ASP A 894 " --> pdb=" O TYR A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 901 removed outlier: 3.657A pdb=" N VAL A 901 " --> pdb=" O GLY A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 910 Processing helix chain 'A' and resid 912 through 920 Processing helix chain 'A' and resid 937 through 942 Processing helix chain 'A' and resid 945 through 970 Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.879A pdb=" N MET A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1019 Processing helix chain 'A' and resid 1027 through 1037 Processing helix chain 'A' and resid 1038 through 1049 removed outlier: 3.556A pdb=" N LEU A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1061 through 1079 Processing helix chain 'A' and resid 1086 through 1101 Proline residue: A1098 - end of helix removed outlier: 3.899A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 removed outlier: 3.511A pdb=" N LEU A1124 " --> pdb=" O GLY A1120 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A1129 " --> pdb=" O LYS A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.914A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 Processing helix chain 'A' and resid 1180 through 1184 removed outlier: 3.597A pdb=" N THR A1184 " --> pdb=" O PRO A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1195 removed outlier: 4.371A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1205 No H-bonds generated for 'chain 'A' and resid 1203 through 1205' Processing helix chain 'A' and resid 1217 through 1225 removed outlier: 4.102A pdb=" N MET A1221 " --> pdb=" O ASP A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.859A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1296 removed outlier: 3.752A pdb=" N PHE A1284 " --> pdb=" O ASP A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1362 through 1370 removed outlier: 3.754A pdb=" N GLY A1370 " --> pdb=" O PHE A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1407 Processing helix chain 'A' and resid 1418 through 1422 Processing helix chain 'A' and resid 1425 through 1430 removed outlier: 3.700A pdb=" N LYS A1429 " --> pdb=" O GLY A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1444 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 4.086A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1483 removed outlier: 3.595A pdb=" N CYS A1480 " --> pdb=" O ASP A1476 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 37 Processing helix chain 'B' and resid 40 through 60 removed outlier: 3.730A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 57 " --> pdb=" O MET B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 161 through 165 removed outlier: 3.786A pdb=" N ASN B 164 " --> pdb=" O CYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 268 through 275 Processing helix chain 'B' and resid 281 through 290 removed outlier: 3.672A pdb=" N LEU B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 307 removed outlier: 3.602A pdb=" N GLU B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 308 through 312 removed outlier: 4.111A pdb=" N ILE B 311 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 333 through 346 Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 360 through 378 removed outlier: 4.134A pdb=" N PHE B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 426 removed outlier: 4.585A pdb=" N LEU B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.907A pdb=" N ARG B 499 " --> pdb=" O ALA B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 549 Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.924A pdb=" N ALA B 560 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.975A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 644 removed outlier: 3.548A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 668 through 672 Processing helix chain 'B' and resid 679 through 684 removed outlier: 3.591A pdb=" N GLN B 683 " --> pdb=" O PRO B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 730 removed outlier: 3.664A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 768 removed outlier: 3.532A pdb=" N ARG B 768 " --> pdb=" O GLU B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 803 Processing helix chain 'B' and resid 971 through 976 Processing helix chain 'B' and resid 977 through 992 removed outlier: 4.356A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1015 Processing helix chain 'B' and resid 1054 through 1058 removed outlier: 4.146A pdb=" N ASP B1057 " --> pdb=" O MET B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1081 removed outlier: 3.622A pdb=" N ARG B1080 " --> pdb=" O GLY B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1095 removed outlier: 3.881A pdb=" N CYS B1093 " --> pdb=" O MET B1089 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLN B1094 " --> pdb=" O GLU B1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1106 removed outlier: 3.678A pdb=" N ARG B1106 " --> pdb=" O PHE B1102 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.552A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 269 removed outlier: 3.613A pdb=" N GLU C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER C 269 " --> pdb=" O HIS C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 23 through 28 removed outlier: 4.124A pdb=" N THR D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 52 removed outlier: 3.883A pdb=" N GLU D 52 " --> pdb=" O ASN D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 72 Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.973A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 103 Processing helix chain 'D' and resid 107 through 115 removed outlier: 4.109A pdb=" N ILE D 115 " --> pdb=" O SER D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 5 through 25 Processing helix chain 'E' and resid 29 through 35 removed outlier: 3.917A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 83 through 97 removed outlier: 4.154A pdb=" N ILE E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 122 Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.637A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 removed outlier: 3.876A pdb=" N PHE E 183 " --> pdb=" O VAL E 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 74 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.764A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 30 through 33 removed outlier: 3.556A pdb=" N ARG I 33 " --> pdb=" O LYS I 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 30 through 33' Processing helix chain 'I' and resid 69 through 73 Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 28 Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.597A pdb=" N ARG J 46 " --> pdb=" O ARG J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'J' and resid 62 through 66 removed outlier: 3.583A pdb=" N LEU J 65 " --> pdb=" O TYR J 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.645A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 Processing helix chain 'M' and resid 13 through 18 Processing helix chain 'M' and resid 21 through 25 removed outlier: 3.763A pdb=" N LYS M 24 " --> pdb=" O ASP M 21 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU M 25 " --> pdb=" O LEU M 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 21 through 25' Processing helix chain 'M' and resid 39 through 44 Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.796A pdb=" N ARG M 181 " --> pdb=" O HIS M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 281 removed outlier: 3.884A pdb=" N ARG M 280 " --> pdb=" O CYS M 277 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 291 removed outlier: 4.013A pdb=" N ASN M 288 " --> pdb=" O THR M 284 " (cutoff:3.500A) Processing helix chain 'M' and resid 337 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA2, first strand: chain 'A' and resid 458 through 459 removed outlier: 3.835A pdb=" N ASN A 502 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 364 " --> pdb=" O HIS B1060 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS B1060 " --> pdb=" O ARG A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 367 through 370 removed outlier: 6.066A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 393 Processing sheet with id=AA6, first strand: chain 'A' and resid 418 through 420 removed outlier: 3.716A pdb=" N ILE A 427 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.593A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 629 through 631 removed outlier: 7.289A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 636 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 879 through 880 removed outlier: 6.916A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB2, first strand: chain 'A' and resid 1311 through 1312 Processing sheet with id=AB3, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.316A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N TYR A1177 " --> pdb=" O PRO A1209 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1320 through 1322 Processing sheet with id=AB5, first strand: chain 'A' and resid 1472 through 1475 Processing sheet with id=AB6, first strand: chain 'B' and resid 87 through 92 removed outlier: 5.968A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP B 127 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AB8, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB9, first strand: chain 'B' and resid 198 through 200 Processing sheet with id=AC1, first strand: chain 'B' and resid 205 through 207 removed outlier: 3.521A pdb=" N VAL B 237 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 238 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 484 through 485 Processing sheet with id=AC3, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC4, first strand: chain 'B' and resid 573 through 577 removed outlier: 6.676A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 662 through 663 Processing sheet with id=AC6, first strand: chain 'B' and resid 747 through 751 removed outlier: 3.622A pdb=" N ALA B 748 " --> pdb=" O TYR B 811 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AC8, first strand: chain 'B' and resid 775 through 776 Processing sheet with id=AC9, first strand: chain 'B' and resid 795 through 796 removed outlier: 6.599A pdb=" N ILE B 779 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ILE B 967 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 781 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 780 " --> pdb=" O GLY B1044 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY B1044 " --> pdb=" O VAL B 780 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.808A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE C 21 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 23 " --> pdb=" O PHE C 229 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 121 through 122 removed outlier: 3.680A pdb=" N GLN C 157 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLU C 158 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA C 54 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ARG C 160 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE C 52 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG C 162 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL C 50 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR C 164 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 46 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL L 53 " --> pdb=" O ILE C 52 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 113 through 116 removed outlier: 3.560A pdb=" N VAL C 151 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.120A pdb=" N HIS G 9 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL G 70 " --> pdb=" O HIS G 9 " (cutoff:3.500A) removed outlier: 18.052A pdb=" N GLY G 43 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 15.295A pdb=" N LYS G 73 " --> pdb=" O GLY G 43 " (cutoff:3.500A) removed outlier: 10.377A pdb=" N VAL G 45 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE G 75 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N PHE G 77 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 15.226A pdb=" N THR G 49 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.737A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 101 through 104 removed outlier: 4.306A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE E 104 " --> pdb=" O GLU E 128 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 148 through 151 Processing sheet with id=AD8, first strand: chain 'G' and resid 141 through 143 removed outlier: 3.652A pdb=" N ASP G 141 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 4 through 14 removed outlier: 6.862A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU H 41 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 24 through 29 removed outlier: 4.228A pdb=" N ASP I 29 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE I 34 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 80 through 81 removed outlier: 4.239A pdb=" N THR I 81 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA I 94 " --> pdb=" O THR I 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU I 110 " --> pdb=" O GLU I 125 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.603A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 125 through 126 removed outlier: 4.226A pdb=" N THR M 125 " --> pdb=" O PHE M 134 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE M 134 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL M 218 " --> pdb=" O VAL M 157 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ALA M 159 " --> pdb=" O VAL M 216 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL M 216 " --> pdb=" O ALA M 159 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ALA M 161 " --> pdb=" O HIS M 214 " (cutoff:3.500A) removed outlier: 10.339A pdb=" N HIS M 214 " --> pdb=" O ALA M 161 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER M 215 " --> pdb=" O LEU M 206 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU M 206 " --> pdb=" O SER M 215 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 142 through 146 1132 hydrogen bonds defined for protein. 3114 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.33 Time building geometry restraints manager: 47.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 34157 1.13 - 1.30: 5851 1.30 - 1.47: 13318 1.47 - 1.64: 15530 1.64 - 1.81: 351 Bond restraints: 69207 Sorted by residual: bond pdb=" N PRO A 335 " pdb=" CA PRO A 335 " ideal model delta sigma weight residual 1.467 1.699 -0.232 1.17e-02 7.31e+03 3.95e+02 bond pdb=" N PRO A 623 " pdb=" CA PRO A 623 " ideal model delta sigma weight residual 1.469 1.696 -0.228 1.28e-02 6.10e+03 3.17e+02 bond pdb=" N PRO A 582 " pdb=" CA PRO A 582 " ideal model delta sigma weight residual 1.469 1.692 -0.224 1.28e-02 6.10e+03 3.05e+02 bond pdb=" N PRO A 462 " pdb=" CA PRO A 462 " ideal model delta sigma weight residual 1.469 1.686 -0.218 1.28e-02 6.10e+03 2.89e+02 bond pdb=" N PRO M 47 " pdb=" CA PRO M 47 " ideal model delta sigma weight residual 1.471 1.694 -0.223 1.32e-02 5.74e+03 2.86e+02 ... (remaining 69202 not shown) Histogram of bond angle deviations from ideal: 14.80 - 42.68: 1 42.68 - 70.56: 1 70.56 - 98.44: 107 98.44 - 126.32: 124456 126.32 - 154.20: 736 Bond angle restraints: 125301 Sorted by residual: angle pdb=" C SER M 127 " pdb=" N PRO M 128 " pdb=" CD PRO M 128 " ideal model delta sigma weight residual 125.00 14.80 110.20 4.10e+00 5.95e-02 7.22e+02 angle pdb=" C SER M 46 " pdb=" N PRO M 47 " pdb=" CA PRO M 47 " ideal model delta sigma weight residual 119.87 139.75 -19.88 1.04e+00 9.25e-01 3.65e+02 angle pdb=" C ARG A 334 " pdb=" N PRO A 335 " pdb=" CA PRO A 335 " ideal model delta sigma weight residual 119.93 139.78 -19.85 1.07e+00 8.73e-01 3.44e+02 angle pdb=" C CYS M 176 " pdb=" N PRO M 177 " pdb=" CA PRO M 177 " ideal model delta sigma weight residual 119.47 140.27 -20.80 1.16e+00 7.43e-01 3.22e+02 angle pdb=" C GLN A 461 " pdb=" N PRO A 462 " pdb=" CA PRO A 462 " ideal model delta sigma weight residual 119.84 141.90 -22.06 1.25e+00 6.40e-01 3.12e+02 ... (remaining 125296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 26627 17.94 - 35.88: 831 35.88 - 53.82: 187 53.82 - 71.76: 64 71.76 - 89.70: 30 Dihedral angle restraints: 27739 sinusoidal: 13396 harmonic: 14343 Sorted by residual: dihedral pdb=" C THR M 118 " pdb=" N THR M 118 " pdb=" CA THR M 118 " pdb=" CB THR M 118 " ideal model delta harmonic sigma weight residual -122.00 -162.95 40.95 0 2.50e+00 1.60e-01 2.68e+02 dihedral pdb=" N THR M 118 " pdb=" C THR M 118 " pdb=" CA THR M 118 " pdb=" CB THR M 118 " ideal model delta harmonic sigma weight residual 123.40 163.38 -39.98 0 2.50e+00 1.60e-01 2.56e+02 dihedral pdb=" CA HIS A 620 " pdb=" C HIS A 620 " pdb=" N ILE A 621 " pdb=" CA ILE A 621 " ideal model delta harmonic sigma weight residual -180.00 -153.97 -26.03 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 27736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.360: 5221 0.360 - 0.720: 5 0.720 - 1.081: 0 1.081 - 1.441: 0 1.441 - 1.801: 1 Chirality restraints: 5227 Sorted by residual: chirality pdb=" CA THR M 118 " pdb=" N THR M 118 " pdb=" C THR M 118 " pdb=" CB THR M 118 " both_signs ideal model delta sigma weight residual False 2.53 0.72 1.80 2.00e-01 2.50e+01 8.11e+01 chirality pdb=" CA PRO M 58 " pdb=" N PRO M 58 " pdb=" C PRO M 58 " pdb=" CB PRO M 58 " both_signs ideal model delta sigma weight residual False 2.72 3.38 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA PRO A 623 " pdb=" N PRO A 623 " pdb=" C PRO A 623 " pdb=" CB PRO A 623 " both_signs ideal model delta sigma weight residual False 2.72 3.35 -0.63 2.00e-01 2.50e+01 9.90e+00 ... (remaining 5224 not shown) Planarity restraints: 10231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR M 107 " -0.055 2.00e-02 2.50e+03 1.14e-01 1.30e+02 pdb=" C TYR M 107 " 0.197 2.00e-02 2.50e+03 pdb=" O TYR M 107 " -0.070 2.00e-02 2.50e+03 pdb=" N GLY M 108 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU M 114 " 0.046 2.00e-02 2.50e+03 9.78e-02 9.56e+01 pdb=" C LEU M 114 " -0.169 2.00e-02 2.50e+03 pdb=" O LEU M 114 " 0.067 2.00e-02 2.50e+03 pdb=" N HIS M 115 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY M 112 " 0.044 2.00e-02 2.50e+03 8.35e-02 6.97e+01 pdb=" C GLY M 112 " -0.144 2.00e-02 2.50e+03 pdb=" O GLY M 112 " 0.052 2.00e-02 2.50e+03 pdb=" N PHE M 113 " 0.048 2.00e-02 2.50e+03 ... (remaining 10228 not shown) Histogram of nonbonded interaction distances: 0.77 - 1.54: 40 1.54 - 2.30: 11998 2.30 - 3.07: 209352 3.07 - 3.83: 272981 3.83 - 4.60: 442179 Warning: very small nonbonded interaction distances. Nonbonded interactions: 936550 Sorted by model distance: nonbonded pdb=" O SER M 127 " pdb=" CD PRO M 128 " model vdw 0.771 2.480 nonbonded pdb=" HG CYS B 510 " pdb=" H ALA B 512 " model vdw 1.017 2.270 nonbonded pdb=" O SER M 127 " pdb=" CG PRO M 128 " model vdw 1.050 3.100 nonbonded pdb=" C SER M 127 " pdb=" HD3 PRO M 128 " model vdw 1.088 2.336 nonbonded pdb=" O SER M 127 " pdb=" HD2 PRO M 128 " model vdw 1.153 2.620 ... (remaining 936545 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: 1.200 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: 0.730 Extract box with map and model: 9.780 Check model and map are aligned: 0.720 Set scattering table: 0.440 Process input model: 179.770 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 196.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2983 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 : 0.011 0.232 34959 Z= 0.713 Angle : 1.162 110.201 47237 Z= 0.692 Chirality : 0.066 1.801 5227 Planarity : 0.006 0.114 6175 Dihedral : 10.732 89.695 13420 Min Nonbonded Distance : 0.771 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.89 % Favored : 91.53 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.11), residues: 4261 helix: -1.66 (0.12), residues: 1252 sheet: -2.74 (0.20), residues: 440 loop : -2.99 (0.10), residues: 2569 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 194 is missing expected H atoms. Skipping. Evaluate side-chains 397 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 388 time to evaluate : 4.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 397 average time/residue: 1.0875 time to fit residues: 663.9916 Evaluate side-chains 273 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 269 time to evaluate : 4.331 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 4 average time/residue: 0.8000 time to fit residues: 10.9785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 356 optimal weight: 6.9990 chunk 319 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 330 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 383 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 412 GLN A 671 ASN A 731 ASN A1236 ASN A1310 HIS B 525 ASN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN D 55 GLN ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 GLN I 18 GLN K 55 GLN K 84 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3084 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.271 34959 Z= 0.253 Angle : 0.682 43.504 47237 Z= 0.365 Chirality : 0.043 0.246 5227 Planarity : 0.005 0.244 6175 Dihedral : 5.555 40.935 4696 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.81 % Favored : 90.00 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.12), residues: 4261 helix: -0.83 (0.14), residues: 1268 sheet: -2.37 (0.21), residues: 423 loop : -2.87 (0.11), residues: 2570 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 194 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 284 time to evaluate : 4.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 285 average time/residue: 1.0455 time to fit residues: 457.9575 Evaluate side-chains 240 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 4.262 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.6579 time to fit residues: 7.3839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 212 optimal weight: 0.2980 chunk 118 optimal weight: 5.9990 chunk 318 optimal weight: 8.9990 chunk 260 optimal weight: 40.0000 chunk 105 optimal weight: 10.0000 chunk 383 optimal weight: 0.6980 chunk 414 optimal weight: 0.8980 chunk 341 optimal weight: 10.0000 chunk 380 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 307 optimal weight: 8.9990 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3127 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 34959 Z= 0.177 Angle : 0.590 32.276 47237 Z= 0.309 Chirality : 0.042 0.272 5227 Planarity : 0.005 0.220 6175 Dihedral : 5.325 41.564 4696 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.88 % Favored : 90.03 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.76 (0.12), residues: 4261 helix: -0.40 (0.14), residues: 1268 sheet: -2.22 (0.23), residues: 385 loop : -2.66 (0.11), residues: 2608 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 194 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 266 time to evaluate : 4.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 267 average time/residue: 1.0650 time to fit residues: 440.7849 Evaluate side-chains 236 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 4.332 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.5794 time to fit residues: 6.6693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 379 optimal weight: 10.0000 chunk 288 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 257 optimal weight: 9.9990 chunk 385 optimal weight: 9.9990 chunk 407 optimal weight: 30.0000 chunk 201 optimal weight: 6.9990 chunk 365 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 136 GLN A 210 GLN A 529 GLN A 780 ASN A1108 HIS B 906 GLN ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3485 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.099 34959 Z= 0.387 Angle : 0.795 31.407 47237 Z= 0.430 Chirality : 0.045 0.355 5227 Planarity : 0.006 0.217 6175 Dihedral : 5.847 40.422 4696 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.31 % Favored : 86.60 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.12), residues: 4261 helix: -1.27 (0.13), residues: 1259 sheet: -2.27 (0.23), residues: 386 loop : -2.98 (0.11), residues: 2616 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 194 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 253 time to evaluate : 4.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 259 average time/residue: 1.0003 time to fit residues: 403.7858 Evaluate side-chains 217 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 213 time to evaluate : 4.328 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.6291 time to fit residues: 10.1154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 339 optimal weight: 1.9990 chunk 231 optimal weight: 0.2980 chunk 5 optimal weight: 50.0000 chunk 303 optimal weight: 0.9990 chunk 168 optimal weight: 8.9990 chunk 348 optimal weight: 2.9990 chunk 281 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 208 optimal weight: 0.9990 chunk 366 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN B 716 HIS ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3333 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.090 34959 Z= 0.171 Angle : 0.585 28.677 47237 Z= 0.304 Chirality : 0.042 0.220 5227 Planarity : 0.005 0.206 6175 Dihedral : 5.431 40.326 4696 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.07 % Favored : 89.91 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.12), residues: 4261 helix: -0.46 (0.14), residues: 1271 sheet: -2.25 (0.24), residues: 360 loop : -2.68 (0.11), residues: 2630 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 194 is missing expected H atoms. Skipping. Evaluate side-chains 246 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 4.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 246 average time/residue: 1.0341 time to fit residues: 399.7310 Evaluate side-chains 217 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 5.000 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.6193 time to fit residues: 8.2340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 137 optimal weight: 9.9990 chunk 367 optimal weight: 0.0770 chunk 80 optimal weight: 20.0000 chunk 239 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 408 optimal weight: 4.9990 chunk 338 optimal weight: 0.0770 chunk 189 optimal weight: 10.0000 chunk 33 optimal weight: 40.0000 chunk 135 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 overall best weight: 2.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3342 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 34959 Z= 0.153 Angle : 0.554 28.628 47237 Z= 0.288 Chirality : 0.041 0.203 5227 Planarity : 0.005 0.204 6175 Dihedral : 5.247 39.835 4696 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.01 % Favored : 88.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.57 (0.12), residues: 4261 helix: -0.22 (0.14), residues: 1274 sheet: -2.07 (0.24), residues: 368 loop : -2.57 (0.12), residues: 2619 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 194 is missing expected H atoms. Skipping. Evaluate side-chains 234 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 4.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 1.0163 time to fit residues: 374.9226 Evaluate side-chains 209 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 4.272 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 393 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 232 optimal weight: 10.0000 chunk 298 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 343 optimal weight: 20.0000 chunk 227 optimal weight: 30.0000 chunk 406 optimal weight: 30.0000 chunk 254 optimal weight: 20.0000 chunk 247 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 757 GLN ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN A1291 ASN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 ASN ** C 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3614 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.088 34959 Z= 0.333 Angle : 0.737 24.102 47237 Z= 0.400 Chirality : 0.044 0.247 5227 Planarity : 0.006 0.189 6175 Dihedral : 5.751 39.540 4696 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 24.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 15.18 % Favored : 84.77 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: -3.25 (0.12), residues: 4261 helix: -1.02 (0.13), residues: 1256 sheet: -2.16 (0.23), residues: 415 loop : -2.90 (0.11), residues: 2590 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 194 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 4.316 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 outliers start: 1 outliers final: 1 residues processed: 225 average time/residue: 1.0077 time to fit residues: 356.1149 Evaluate side-chains 199 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 4.307 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.5648 time to fit residues: 6.6760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 251 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 258 optimal weight: 6.9990 chunk 277 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 319 optimal weight: 7.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN A 210 GLN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3567 moved from start: 0.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 34959 Z= 0.226 Angle : 0.626 29.340 47237 Z= 0.333 Chirality : 0.042 0.216 5227 Planarity : 0.005 0.206 6175 Dihedral : 5.673 39.587 4696 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.31 % Favored : 86.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.12), residues: 4261 helix: -0.72 (0.14), residues: 1265 sheet: -2.38 (0.23), residues: 418 loop : -2.84 (0.11), residues: 2578 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 194 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 4.491 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 outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 1.0559 time to fit residues: 368.7930 Evaluate side-chains 197 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 4.424 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 369 optimal weight: 5.9990 chunk 389 optimal weight: 8.9990 chunk 355 optimal weight: 8.9990 chunk 379 optimal weight: 4.9990 chunk 228 optimal weight: 40.0000 chunk 165 optimal weight: 9.9990 chunk 297 optimal weight: 40.0000 chunk 116 optimal weight: 1.9990 chunk 342 optimal weight: 6.9990 chunk 358 optimal weight: 1.9990 chunk 377 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A1270 GLN B 370 HIS ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3521 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 34959 Z= 0.176 Angle : 0.574 24.254 47237 Z= 0.302 Chirality : 0.041 0.200 5227 Planarity : 0.005 0.188 6175 Dihedral : 5.443 39.474 4696 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.60 % Favored : 87.35 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: -2.75 (0.12), residues: 4261 helix: -0.33 (0.14), residues: 1275 sheet: -2.24 (0.24), residues: 406 loop : -2.69 (0.12), residues: 2580 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 194 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 4.366 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 outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 1.0230 time to fit residues: 354.5484 Evaluate side-chains 199 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 4.287 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 248 optimal weight: 0.5980 chunk 400 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 278 optimal weight: 9.9990 chunk 420 optimal weight: 0.0030 chunk 386 optimal weight: 7.9990 chunk 334 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 258 optimal weight: 6.9990 chunk 205 optimal weight: 8.9990 overall best weight: 4.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 991 GLN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3567 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 34959 Z= 0.207 Angle : 0.585 21.085 47237 Z= 0.311 Chirality : 0.041 0.198 5227 Planarity : 0.005 0.178 6175 Dihedral : 5.441 38.799 4696 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.17 % Favored : 86.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: -2.74 (0.12), residues: 4261 helix: -0.32 (0.14), residues: 1270 sheet: -2.25 (0.24), residues: 408 loop : -2.68 (0.12), residues: 2583 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8522 Ramachandran restraints generated. 4261 Oldfield, 0 Emsley, 4261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 194 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 4.338 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 outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 1.0411 time to fit residues: 356.4827 Evaluate side-chains 195 residues out of total 3804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 4.383 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 265 optimal weight: 5.9990 chunk 356 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 308 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 335 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 344 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.078347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.061744 restraints weight = 1516599.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.062156 restraints weight = 1266692.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.062509 restraints weight = 1085443.649| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 34959 Z= 0.259 Angle : 0.640 18.680 47237 Z= 0.344 Chirality : 0.042 0.262 5227 Planarity : 0.005 0.169 6175 Dihedral : 5.630 39.380 4696 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.79 % Favored : 85.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: -2.98 (0.12), residues: 4261 helix: -0.58 (0.14), residues: 1260 sheet: -2.38 (0.24), residues: 407 loop : -2.78 (0.11), residues: 2594 =============================================================================== Job complete usr+sys time: 9870.18 seconds wall clock time: 173 minutes 44.67 seconds (10424.67 seconds total)