Starting phenix.real_space_refine (version: dev) on Mon Feb 27 02:54:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oca_12802/02_2023/7oca_12802_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oca_12802/02_2023/7oca_12802.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oca_12802/02_2023/7oca_12802_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oca_12802/02_2023/7oca_12802_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oca_12802/02_2023/7oca_12802_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oca_12802/02_2023/7oca_12802.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oca_12802/02_2023/7oca_12802.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oca_12802/02_2023/7oca_12802_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oca_12802/02_2023/7oca_12802_updated.pdb" } resolution = 3.4 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 42": "OD1" <-> "OD2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 55": "NH1" <-> "NH2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 515": "OD1" <-> "OD2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 541": "NH1" <-> "NH2" Residue "A PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 624": "NH1" <-> "NH2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 656": "NH1" <-> "NH2" Residue "A TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 809": "OE1" <-> "OE2" Residue "A PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 17": "OD1" <-> "OD2" Residue "B TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 134": "OD1" <-> "OD2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B ASP 189": "OD1" <-> "OD2" Residue "B ASP 193": "OD1" <-> "OD2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 225": "OD1" <-> "OD2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 281": "OD1" <-> "OD2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ASP 308": "OD1" <-> "OD2" Residue "B ASP 342": "OD1" <-> "OD2" Residue "B TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 519": "OD1" <-> "OD2" Residue "B TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "B ASP 728": "OD1" <-> "OD2" Residue "B GLU 772": "OE1" <-> "OE2" Residue "B PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 59": "NH1" <-> "NH2" Residue "G PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "G PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 216": "OE1" <-> "OE2" Residue "D PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 17": "OD1" <-> "OD2" Residue "D TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "D TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D ASP 189": "OD1" <-> "OD2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "D ASP 197": "OD1" <-> "OD2" Residue "D ASP 200": "OD1" <-> "OD2" Residue "D TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "D PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 281": "OD1" <-> "OD2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ASP 308": "OD1" <-> "OD2" Residue "D ASP 342": "OD1" <-> "OD2" Residue "D TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "D PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 519": "OD1" <-> "OD2" Residue "D TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 705": "OE1" <-> "OE2" Residue "D ASP 728": "OD1" <-> "OD2" Residue "D GLU 772": "OE1" <-> "OE2" Residue "D PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 216": "OE1" <-> "OE2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 55": "NH1" <-> "NH2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 149": "OE1" <-> "OE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 256": "OD1" <-> "OD2" Residue "C PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 389": "NH1" <-> "NH2" Residue "C TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 515": "OD1" <-> "OD2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 541": "NH1" <-> "NH2" Residue "C PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 624": "NH1" <-> "NH2" Residue "C GLU 633": "OE1" <-> "OE2" Residue "C TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 656": "NH1" <-> "NH2" Residue "C TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 809": "OE1" <-> "OE2" Residue "C PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 87": "OE1" <-> "OE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 126": "OD1" <-> "OD2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 29294 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 5637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 5637 Classifications: {'peptide': 775} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PCIS': 4, 'PTRANS': 23, 'TRANS': 747} Chain breaks: 4 Unresolved non-hydrogen bonds: 551 Unresolved non-hydrogen angles: 659 Unresolved non-hydrogen dihedrals: 452 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 12, 'ASP:plan': 19, 'PHE:plan': 2, 'GLU:plan': 22, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 333 Chain: "B" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 5815 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 759} Chain breaks: 3 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 22, 'ASN:plan1': 6, 'ASP:plan': 12, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 201 Chain: "G" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1248 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "I" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1284 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 84 Chain: "D" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 5815 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 759} Chain breaks: 3 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 22, 'ASN:plan1': 6, 'ASP:plan': 12, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 201 Chain: "J" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1284 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 5637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 5637 Classifications: {'peptide': 775} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PCIS': 4, 'PTRANS': 23, 'TRANS': 747} Chain breaks: 4 Unresolved non-hydrogen bonds: 551 Unresolved non-hydrogen angles: 659 Unresolved non-hydrogen dihedrals: 452 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 12, 'ASP:plan': 19, 'PHE:plan': 2, 'GLU:plan': 22, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 333 Chain: "E" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1248 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 170 Unusual residues: {'E2Q': 1, 'NAG': 2, 'PC1': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PC1:plan-2': 5, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 216 Unusual residues: {'E2Q': 1, 'NAG': 1, 'PC1': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PC1:plan-2': 8, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {'CLR': 1, 'PC1': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 96 Unusual residues: {'PC1': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PC1:plan-2': 5} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 216 Unusual residues: {'E2Q': 1, 'NAG': 1, 'PC1': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PC1:plan-2': 8, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 35 Chain: "J" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 96 Unusual residues: {'PC1': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PC1:plan-2': 5} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 170 Unusual residues: {'E2Q': 1, 'NAG': 2, 'PC1': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PC1:plan-2': 5, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {'CLR': 1, 'PC1': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 16.23, per 1000 atoms: 0.55 Number of scatterers: 29294 At special positions: 0 Unit cell: (133.75, 126.26, 224.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 5216 8.00 N 4660 7.00 C 19268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.05 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 90 " - pdb=" SG CYS I 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.05 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 902 " - " ASN A 231 " " NAG A 903 " - " ASN A 239 " " NAG B2903 " - " ASN B 349 " " NAG C2703 " - " ASN C 231 " " NAG C2704 " - " ASN C 239 " " NAG D 902 " - " ASN D 349 " " NAG F 1 " - " ASN A 45 " " NAG H 1 " - " ASN A 345 " " NAG K 1 " - " ASN B 235 " " NAG L 1 " - " ASN D 235 " " NAG M 1 " - " ASN C 45 " " NAG N 1 " - " ASN C 345 " Time building additional restraints: 13.30 Conformation dependent library (CDL) restraints added in 4.7 seconds 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7032 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 122 helices and 24 sheets defined 47.5% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 removed outlier: 3.676A pdb=" N LEU A 28 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 62 Processing helix chain 'A' and resid 73 through 85 removed outlier: 4.779A pdb=" N ASN A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N MET A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 136 through 150 removed outlier: 3.874A pdb=" N GLN A 141 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG A 142 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 147 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 148 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 150 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 175 Processing helix chain 'A' and resid 188 through 200 removed outlier: 4.002A pdb=" N ASN A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 243 through 258 Processing helix chain 'A' and resid 270 through 292 removed outlier: 3.554A pdb=" N VAL A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 325 removed outlier: 3.714A pdb=" N ILE A 319 " --> pdb=" O GLY A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 413 through 416 removed outlier: 3.834A pdb=" N ARG A 416 " --> pdb=" O GLY A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 413 through 416' Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 479 through 484 removed outlier: 4.080A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 540 Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 592 through 625 Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 661 through 669 Processing helix chain 'A' and resid 682 through 691 Processing helix chain 'A' and resid 702 through 709 Processing helix chain 'A' and resid 740 through 752 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 789 through 819 Processing helix chain 'B' and resid 17 through 30 Processing helix chain 'B' and resid 49 through 61 Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 112 through 121 removed outlier: 3.535A pdb=" N GLU B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 167 through 181 removed outlier: 3.609A pdb=" N ARG B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 202 removed outlier: 4.106A pdb=" N GLN B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 257 Processing helix chain 'B' and resid 274 through 296 Processing helix chain 'B' and resid 320 through 328 Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 523 through 546 Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 596 through 625 Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 665 through 676 Processing helix chain 'B' and resid 686 through 695 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.627A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 756 Processing helix chain 'B' and resid 758 through 766 Processing helix chain 'B' and resid 789 through 821 removed outlier: 5.586A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 39 removed outlier: 3.846A pdb=" N ALA G 18 " --> pdb=" O LEU G 14 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU G 20 " --> pdb=" O LEU G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 84 removed outlier: 4.499A pdb=" N VAL G 69 " --> pdb=" O ARG G 65 " (cutoff:3.500A) Proline residue: G 70 - end of helix Processing helix chain 'G' and resid 88 through 107 Proline residue: G 96 - end of helix Processing helix chain 'G' and resid 125 through 158 Processing helix chain 'I' and resid 17 through 40 Processing helix chain 'I' and resid 116 through 127 Processing helix chain 'I' and resid 129 through 148 Processing helix chain 'I' and resid 158 through 183 removed outlier: 3.596A pdb=" N GLY I 162 " --> pdb=" O ILE I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 239 Processing helix chain 'D' and resid 17 through 30 Processing helix chain 'D' and resid 49 through 61 Processing helix chain 'D' and resid 76 through 86 Processing helix chain 'D' and resid 112 through 121 removed outlier: 3.535A pdb=" N GLU D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 167 through 181 removed outlier: 3.609A pdb=" N ARG D 172 " --> pdb=" O ASP D 168 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 180 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS D 181 " --> pdb=" O ASP D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 202 removed outlier: 4.107A pdb=" N GLN D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 257 Processing helix chain 'D' and resid 274 through 296 Processing helix chain 'D' and resid 320 through 328 Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 523 through 546 Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 596 through 625 Processing helix chain 'D' and resid 637 through 641 Processing helix chain 'D' and resid 654 through 660 Processing helix chain 'D' and resid 665 through 676 Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.627A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 756 Processing helix chain 'D' and resid 758 through 766 Processing helix chain 'D' and resid 789 through 821 removed outlier: 5.586A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 40 Processing helix chain 'J' and resid 116 through 127 Processing helix chain 'J' and resid 129 through 148 Processing helix chain 'J' and resid 158 through 183 removed outlier: 3.597A pdb=" N GLY J 162 " --> pdb=" O ILE J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 239 Processing helix chain 'C' and resid 19 through 29 removed outlier: 3.676A pdb=" N LEU C 28 " --> pdb=" O PHE C 24 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 62 Processing helix chain 'C' and resid 73 through 85 removed outlier: 4.779A pdb=" N ASN C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N MET C 78 " --> pdb=" O ARG C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 121 Processing helix chain 'C' and resid 136 through 150 removed outlier: 3.874A pdb=" N GLN C 141 " --> pdb=" O SER C 138 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG C 142 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA C 147 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 148 " --> pdb=" O ASP C 145 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C 150 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 175 Processing helix chain 'C' and resid 188 through 200 removed outlier: 4.002A pdb=" N ASN C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 243 through 258 Processing helix chain 'C' and resid 270 through 292 removed outlier: 3.554A pdb=" N VAL C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS C 280 " --> pdb=" O TYR C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 325 removed outlier: 3.713A pdb=" N ILE C 319 " --> pdb=" O GLY C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 413 through 416 removed outlier: 3.834A pdb=" N ARG C 416 " --> pdb=" O GLY C 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 416' Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 459 through 464 Processing helix chain 'C' and resid 479 through 484 removed outlier: 4.079A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 540 Processing helix chain 'C' and resid 569 through 580 Processing helix chain 'C' and resid 592 through 625 Processing helix chain 'C' and resid 632 through 637 Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 661 through 669 Processing helix chain 'C' and resid 682 through 691 Processing helix chain 'C' and resid 702 through 709 Processing helix chain 'C' and resid 740 through 752 Processing helix chain 'C' and resid 754 through 763 Processing helix chain 'C' and resid 789 through 819 Processing helix chain 'E' and resid 5 through 39 removed outlier: 3.846A pdb=" N ALA E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 84 removed outlier: 4.499A pdb=" N VAL E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 88 through 107 Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 125 through 158 Processing sheet with id= A, first strand: chain 'A' and resid 6 through 8 removed outlier: 6.062A pdb=" N LYS A 36 " --> pdb=" O ILE A 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.908A pdb=" N ASP A 42 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLY A 11 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA A 66 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU A 12 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE A 68 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N CYS A 89 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLY A 69 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ILE A 91 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 153 through 158 removed outlier: 4.959A pdb=" N LEU A 181 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN A 231 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU A 212 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A 233 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 232 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY A 362 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLU A 352 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS A 360 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LYS A 354 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE A 358 " --> pdb=" O LYS A 354 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 391 through 393 Processing sheet with id= E, first strand: chain 'A' and resid 492 through 494 removed outlier: 3.788A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 475 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA A 731 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ALA A 473 " --> pdb=" O ALA A 731 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 716 through 719 removed outlier: 3.865A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 36 through 44 removed outlier: 3.896A pdb=" N ILE B 6 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA B 66 " --> pdb=" O GLY B 9 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LEU B 11 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE B 68 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER B 89 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 153 through 158 removed outlier: 5.195A pdb=" N ARG B 185 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N HIS B 213 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU B 188 " --> pdb=" O HIS B 213 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE B 215 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASN B 235 " --> pdb=" O TYR B 214 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE B 216 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER B 237 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VAL B 236 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY B 366 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU B 356 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS B 364 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LYS B 358 " --> pdb=" O PRO B 362 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= J, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.844A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 720 through 723 removed outlier: 4.003A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.643A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 45 through 49 removed outlier: 3.632A pdb=" N LEU I 45 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 36 through 44 removed outlier: 3.897A pdb=" N ILE D 6 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA D 66 " --> pdb=" O GLY D 9 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LEU D 11 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE D 68 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER D 89 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 153 through 158 removed outlier: 5.194A pdb=" N ARG D 185 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS D 213 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU D 188 " --> pdb=" O HIS D 213 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 215 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASN D 235 " --> pdb=" O TYR D 214 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE D 216 " --> pdb=" O ASN D 235 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER D 237 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VAL D 236 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY D 366 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLU D 356 " --> pdb=" O LYS D 364 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LYS D 364 " --> pdb=" O GLU D 356 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS D 358 " --> pdb=" O PRO D 362 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= P, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.844A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.004A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'J' and resid 45 through 49 removed outlier: 3.633A pdb=" N LEU J 45 " --> pdb=" O SER J 84 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 6 through 8 removed outlier: 6.063A pdb=" N LYS C 36 " --> pdb=" O ILE C 7 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'C' and resid 41 through 43 removed outlier: 7.910A pdb=" N ASP C 42 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY C 11 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ALA C 66 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU C 12 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE C 68 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N CYS C 89 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLY C 69 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE C 91 " --> pdb=" O GLY C 69 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 153 through 158 removed outlier: 4.959A pdb=" N LEU C 181 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN C 231 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU C 212 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR C 233 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL C 232 " --> pdb=" O MET C 353 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY C 362 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLU C 352 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS C 360 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LYS C 354 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE C 358 " --> pdb=" O LYS C 354 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 391 through 393 Processing sheet with id= W, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.787A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU C 475 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA C 731 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ALA C 473 " --> pdb=" O ALA C 731 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 716 through 719 removed outlier: 3.866A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) 1422 hydrogen bonds defined for protein. 4158 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: 10.67 Time building geometry restraints manager: 13.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4498 1.31 - 1.45: 8491 1.45 - 1.58: 16685 1.58 - 1.71: 8 1.71 - 1.84: 222 Bond restraints: 29904 Sorted by residual: bond pdb=" N15 E2Q D 901 " pdb=" O17 E2Q D 901 " ideal model delta sigma weight residual 1.401 1.186 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" N15 E2Q B2902 " pdb=" O17 E2Q B2902 " ideal model delta sigma weight residual 1.401 1.187 0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" N15 E2Q C2702 " pdb=" O17 E2Q C2702 " ideal model delta sigma weight residual 1.401 1.187 0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" N15 E2Q A 901 " pdb=" O17 E2Q A 901 " ideal model delta sigma weight residual 1.401 1.187 0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C09 E2Q C2702 " pdb=" S11 E2Q C2702 " ideal model delta sigma weight residual 1.820 1.691 0.129 2.00e-02 2.50e+03 4.18e+01 ... (remaining 29899 not shown) Histogram of bond angle deviations from ideal: 98.41 - 107.35: 828 107.35 - 116.29: 19081 116.29 - 125.22: 20140 125.22 - 134.16: 439 134.16 - 143.10: 2 Bond angle restraints: 40490 Sorted by residual: angle pdb=" CB MET C 52 " pdb=" CG MET C 52 " pdb=" SD MET C 52 " ideal model delta sigma weight residual 112.70 143.10 -30.40 3.00e+00 1.11e-01 1.03e+02 angle pdb=" CB MET A 52 " pdb=" CG MET A 52 " pdb=" SD MET A 52 " ideal model delta sigma weight residual 112.70 143.05 -30.35 3.00e+00 1.11e-01 1.02e+02 angle pdb=" O12 E2Q A 901 " pdb=" S11 E2Q A 901 " pdb=" O13 E2Q A 901 " ideal model delta sigma weight residual 101.20 124.23 -23.03 3.00e+00 1.11e-01 5.89e+01 angle pdb=" O12 E2Q B2902 " pdb=" S11 E2Q B2902 " pdb=" O13 E2Q B2902 " ideal model delta sigma weight residual 101.20 124.23 -23.03 3.00e+00 1.11e-01 5.89e+01 angle pdb=" O12 E2Q D 901 " pdb=" S11 E2Q D 901 " pdb=" O13 E2Q D 901 " ideal model delta sigma weight residual 101.20 124.22 -23.02 3.00e+00 1.11e-01 5.89e+01 ... (remaining 40485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.05: 16171 22.05 - 44.10: 1027 44.10 - 66.15: 134 66.15 - 88.20: 28 88.20 - 110.25: 18 Dihedral angle restraints: 17378 sinusoidal: 6394 harmonic: 10984 Sorted by residual: dihedral pdb=" CB CYS I 52 " pdb=" SG CYS I 52 " pdb=" SG CYS I 91 " pdb=" CB CYS I 91 " ideal model delta sinusoidal sigma weight residual -86.00 -163.21 77.21 1 1.00e+01 1.00e-02 7.48e+01 dihedral pdb=" CB CYS J 52 " pdb=" SG CYS J 52 " pdb=" SG CYS J 91 " pdb=" CB CYS J 91 " ideal model delta sinusoidal sigma weight residual -86.00 -163.18 77.18 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS A 714 " pdb=" SG CYS A 714 " pdb=" SG CYS A 769 " pdb=" CB CYS A 769 " ideal model delta sinusoidal sigma weight residual -86.00 -34.84 -51.16 1 1.00e+01 1.00e-02 3.58e+01 ... (remaining 17375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3484 0.048 - 0.095: 987 0.095 - 0.143: 181 0.143 - 0.191: 0 0.191 - 0.238: 4 Chirality restraints: 4656 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 1.98e+00 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 1.81e+00 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 1.58e+00 ... (remaining 4653 not shown) Planarity restraints: 4990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 152 " -0.021 2.00e-02 2.50e+03 1.69e-02 7.14e+00 pdb=" CG TRP C 152 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 152 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP C 152 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 152 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 152 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 152 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 152 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 152 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 152 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 152 " 0.021 2.00e-02 2.50e+03 1.68e-02 7.03e+00 pdb=" CG TRP A 152 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 152 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 152 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 152 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 152 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 152 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 152 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 152 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 152 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 702 " 0.016 2.00e-02 2.50e+03 1.51e-02 4.56e+00 pdb=" CG TYR B 702 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR B 702 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 702 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 702 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 702 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 702 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 702 " 0.001 2.00e-02 2.50e+03 ... (remaining 4987 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 325 2.64 - 3.21: 27907 3.21 - 3.77: 43443 3.77 - 4.34: 60311 4.34 - 4.90: 101670 Nonbonded interactions: 233656 Sorted by model distance: nonbonded pdb=" OG1 THR D 398 " pdb=" OE2 GLU D 466 " model vdw 2.080 2.440 nonbonded pdb=" N LYS B 716 " pdb=" OE1 GLU B 772 " model vdw 2.101 2.520 nonbonded pdb=" N LYS D 716 " pdb=" OE1 GLU D 772 " model vdw 2.101 2.520 nonbonded pdb=" OG SER B 635 " pdb=" OD1 ASP B 638 " model vdw 2.121 2.440 nonbonded pdb=" OG SER D 635 " pdb=" OD1 ASP D 638 " model vdw 2.121 2.440 ... (remaining 233651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 820 or resid 903 or (resid 905 through 907 and ( \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C29 or name C2A or name C2B or name C2C or name C2D or name \ C2E or name C2F or name C2G or name O21 or name O22)))) selection = (chain 'C' and (resid 3 through 820 or resid 2703 or (resid 2705 through 2707 an \ d (name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27 or name C28 or name C29 or name C2A or name C2B or name C2C or name C2D or n \ ame C2E or name C2F or name C2G or name O21 or name O22)))) } ncs_group { reference = (chain 'B' and (resid 4 through 823 or resid 2904 through 2907 or (resid 2908 an \ d (name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27 or name C28 or name C29 or name C2A or name C2B or name C2C or name C2D or n \ ame C2E or name C2F or name C2G or name O21 or name O22)) or resid 2911)) selection = (chain 'D' and (resid 4 through 823 or (resid 904 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name O21 or name \ O22)) or resid 905 through 908 or resid 911)) } ncs_group { reference = (chain 'E' and (resid 2 through 159 or (resid 3101 through 3102 and (name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E or nam \ e C2F or name C2G or name O21 or name O22)) or resid 3103 through 3104)) selection = (chain 'G' and (resid 2 through 159 or (resid 3101 through 3102 and (name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E or nam \ e C2F or name C2G or name O21 or name O22)) or resid 3103 through 3104)) } ncs_group { reference = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'N' } ncs_group { reference = (chain 'I' and (resid 16 through 240 or resid 3001 through 3003 or (resid 3004 t \ hrough 3005 and (name C21 or name C22 or name C23 or name C24 or name C25 or nam \ e C26 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or \ name C2D or name C2E or name C2F or name C2G or name O21 or name O22)))) selection = (chain 'J' and (resid 16 through 240 or (resid 2501 and (name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or nam \ e C2G or name O21 or name O22)) or resid 2502 through 2505)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 19268 2.51 5 N 4660 2.21 5 O 5216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.020 Extract box with map and model: 9.460 Check model and map are aligned: 0.450 Process input model: 76.100 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Set scattering table: 0.260 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 0.009 0.215 29904 Z= 0.617 Angle : 0.950 30.396 40490 Z= 0.413 Chirality : 0.043 0.238 4656 Planarity : 0.004 0.049 4978 Dihedral : 14.770 110.247 10310 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3746 helix: 1.49 (0.12), residues: 1926 sheet: -1.07 (0.26), residues: 380 loop : -1.41 (0.15), residues: 1440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 346 time to evaluate : 3.525 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 346 average time/residue: 0.4286 time to fit residues: 234.1103 Evaluate side-chains 254 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 251 time to evaluate : 3.441 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2983 time to fit residues: 5.8432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 1.9990 chunk 284 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 chunk 97 optimal weight: 0.5980 chunk 192 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 294 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 219 optimal weight: 6.9990 chunk 341 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN D 329 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 756 GLN C 209 HIS C 324 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 29904 Z= 0.182 Angle : 0.488 8.339 40490 Z= 0.256 Chirality : 0.040 0.199 4656 Planarity : 0.004 0.042 4978 Dihedral : 11.159 107.223 4936 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.00 (0.14), residues: 3746 helix: 2.15 (0.12), residues: 1941 sheet: -0.76 (0.25), residues: 404 loop : -1.07 (0.16), residues: 1401 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 280 time to evaluate : 3.324 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 16 residues processed: 293 average time/residue: 0.4803 time to fit residues: 226.9591 Evaluate side-chains 264 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 248 time to evaluate : 3.447 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3109 time to fit residues: 14.3401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 284 optimal weight: 10.0000 chunk 232 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 342 optimal weight: 0.0270 chunk 369 optimal weight: 8.9990 chunk 304 optimal weight: 6.9990 chunk 339 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 274 optimal weight: 3.9990 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN B 59 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 HIS D 18 GLN D 59 GLN D 329 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 29904 Z= 0.289 Angle : 0.506 9.036 40490 Z= 0.267 Chirality : 0.041 0.222 4656 Planarity : 0.004 0.044 4978 Dihedral : 11.019 109.314 4936 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.05 (0.14), residues: 3746 helix: 2.08 (0.12), residues: 1955 sheet: -0.57 (0.25), residues: 414 loop : -0.94 (0.16), residues: 1377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 266 time to evaluate : 3.385 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 21 residues processed: 292 average time/residue: 0.4449 time to fit residues: 208.9199 Evaluate side-chains 275 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 254 time to evaluate : 3.419 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2796 time to fit residues: 15.7568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 163 optimal weight: 6.9990 chunk 229 optimal weight: 0.9980 chunk 343 optimal weight: 0.9980 chunk 363 optimal weight: 7.9990 chunk 179 optimal weight: 0.9980 chunk 325 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 29904 Z= 0.158 Angle : 0.429 7.830 40490 Z= 0.228 Chirality : 0.039 0.233 4656 Planarity : 0.003 0.040 4978 Dihedral : 10.640 107.600 4936 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.31 (0.14), residues: 3746 helix: 2.33 (0.12), residues: 1957 sheet: -0.43 (0.25), residues: 409 loop : -0.90 (0.16), residues: 1380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 266 time to evaluate : 3.433 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 276 average time/residue: 0.4408 time to fit residues: 196.8787 Evaluate side-chains 257 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 252 time to evaluate : 3.561 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2674 time to fit residues: 6.9527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 270 optimal weight: 0.4980 chunk 149 optimal weight: 1.9990 chunk 310 optimal weight: 4.9990 chunk 251 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 chunk 326 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 29904 Z= 0.191 Angle : 0.431 6.154 40490 Z= 0.229 Chirality : 0.039 0.219 4656 Planarity : 0.003 0.040 4978 Dihedral : 10.539 107.408 4936 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.36 (0.14), residues: 3746 helix: 2.35 (0.12), residues: 1963 sheet: -0.39 (0.25), residues: 411 loop : -0.86 (0.17), residues: 1372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 260 time to evaluate : 3.599 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 269 average time/residue: 0.4516 time to fit residues: 194.0523 Evaluate side-chains 256 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 250 time to evaluate : 3.210 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2471 time to fit residues: 7.1051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 5.9990 chunk 327 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 213 optimal weight: 0.0070 chunk 89 optimal weight: 0.7980 chunk 363 optimal weight: 6.9990 chunk 301 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 120 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN D 329 GLN J 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 29904 Z= 0.238 Angle : 0.457 7.960 40490 Z= 0.241 Chirality : 0.040 0.242 4656 Planarity : 0.003 0.040 4978 Dihedral : 10.598 107.033 4936 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.31 (0.14), residues: 3746 helix: 2.29 (0.12), residues: 1964 sheet: -0.38 (0.25), residues: 412 loop : -0.86 (0.17), residues: 1370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 260 time to evaluate : 3.429 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 280 average time/residue: 0.4657 time to fit residues: 209.5186 Evaluate side-chains 258 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 245 time to evaluate : 3.485 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2758 time to fit residues: 11.3868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 0.7980 chunk 41 optimal weight: 0.0980 chunk 207 optimal weight: 1.9990 chunk 265 optimal weight: 6.9990 chunk 205 optimal weight: 0.0370 chunk 306 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 362 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 GLN D 329 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 29904 Z= 0.175 Angle : 0.431 6.702 40490 Z= 0.227 Chirality : 0.039 0.209 4656 Planarity : 0.003 0.040 4978 Dihedral : 10.397 107.026 4936 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.45 (0.14), residues: 3746 helix: 2.41 (0.12), residues: 1964 sheet: -0.29 (0.25), residues: 397 loop : -0.82 (0.17), residues: 1385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 257 time to evaluate : 3.142 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 259 average time/residue: 0.4499 time to fit residues: 188.3985 Evaluate side-chains 245 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 241 time to evaluate : 3.738 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3877 time to fit residues: 7.3869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 230 optimal weight: 0.0010 chunk 246 optimal weight: 0.9990 chunk 179 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 284 optimal weight: 10.0000 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 29904 Z= 0.191 Angle : 0.440 9.346 40490 Z= 0.230 Chirality : 0.039 0.227 4656 Planarity : 0.003 0.039 4978 Dihedral : 10.307 106.900 4936 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.47 (0.14), residues: 3746 helix: 2.41 (0.12), residues: 1964 sheet: -0.20 (0.26), residues: 390 loop : -0.81 (0.17), residues: 1392 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 253 time to evaluate : 3.708 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 260 average time/residue: 0.4473 time to fit residues: 187.7692 Evaluate side-chains 250 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 239 time to evaluate : 3.265 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2730 time to fit residues: 10.3334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 4.9990 chunk 347 optimal weight: 5.9990 chunk 316 optimal weight: 6.9990 chunk 337 optimal weight: 2.9990 chunk 203 optimal weight: 0.4980 chunk 147 optimal weight: 0.0470 chunk 265 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 305 optimal weight: 7.9990 chunk 319 optimal weight: 10.0000 chunk 336 optimal weight: 0.8980 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 29904 Z= 0.189 Angle : 0.441 8.824 40490 Z= 0.231 Chirality : 0.039 0.210 4656 Planarity : 0.003 0.039 4978 Dihedral : 10.233 106.837 4936 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.49 (0.14), residues: 3746 helix: 2.43 (0.12), residues: 1961 sheet: -0.23 (0.25), residues: 401 loop : -0.78 (0.17), residues: 1384 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 246 time to evaluate : 3.328 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 248 average time/residue: 0.4236 time to fit residues: 169.9135 Evaluate side-chains 249 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 242 time to evaluate : 3.285 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2816 time to fit residues: 8.4045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 0.9980 chunk 357 optimal weight: 7.9990 chunk 217 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 374 optimal weight: 0.9990 chunk 344 optimal weight: 9.9990 chunk 298 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 230 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 GLN D 329 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 ASN E 132 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 29904 Z= 0.252 Angle : 0.469 9.046 40490 Z= 0.245 Chirality : 0.040 0.240 4656 Planarity : 0.003 0.039 4978 Dihedral : 10.319 106.775 4936 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.38 (0.14), residues: 3746 helix: 2.31 (0.12), residues: 1962 sheet: -0.19 (0.25), residues: 394 loop : -0.81 (0.17), residues: 1390 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7492 Ramachandran restraints generated. 3746 Oldfield, 0 Emsley, 3746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 245 time to evaluate : 3.601 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 247 average time/residue: 0.4762 time to fit residues: 190.3575 Evaluate side-chains 245 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 241 time to evaluate : 3.300 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3135 time to fit residues: 6.7301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 5.9990 chunk 317 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 275 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 306 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.146870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116385 restraints weight = 41039.906| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.65 r_work: 0.3011 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.056 29904 Z= 0.156 Angle : 0.436 8.890 40490 Z= 0.227 Chirality : 0.038 0.194 4656 Planarity : 0.003 0.039 4978 Dihedral : 10.098 106.688 4936 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.53 (0.14), residues: 3746 helix: 2.49 (0.12), residues: 1964 sheet: -0.28 (0.25), residues: 403 loop : -0.78 (0.17), residues: 1379 =============================================================================== Job complete usr+sys time: 5399.61 seconds wall clock time: 100 minutes 3.02 seconds (6003.02 seconds total)