Starting phenix.real_space_refine on Thu Mar 21 05:29:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oca_12802/03_2024/7oca_12802_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oca_12802/03_2024/7oca_12802.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oca_12802/03_2024/7oca_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_12802/03_2024/7oca_12802_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oca_12802/03_2024/7oca_12802_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oca_12802/03_2024/7oca_12802.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oca_12802/03_2024/7oca_12802.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oca_12802/03_2024/7oca_12802_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oca_12802/03_2024/7oca_12802_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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: 9 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 dihedrals: 6 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: 199 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: 292 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: 98 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: 164 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: 292 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: 164 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: 199 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: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 14.76, per 1000 atoms: 0.50 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: 12.03 Conformation dependent library (CDL) restraints added in 4.8 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: 6.29 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: 10.49 Time building geometry restraints manager: 13.05 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 - 23.04: 16517 23.04 - 46.07: 1025 46.07 - 69.11: 142 69.11 - 92.14: 61 92.14 - 115.18: 49 Dihedral angle restraints: 17794 sinusoidal: 6810 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 17791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3628 0.052 - 0.105: 906 0.105 - 0.157: 116 0.157 - 0.210: 0 0.210 - 0.262: 6 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=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.72e+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 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: 1.330 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: 8.260 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 75.490 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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= 0.621 Angle : 0.963 30.396 40490 Z= 0.414 Chirality : 0.044 0.262 4656 Planarity : 0.004 0.049 4978 Dihedral : 16.903 115.180 10726 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.15 % Allowed : 0.61 % Favored : 99.24 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 152 HIS 0.016 0.002 HIS E 107 PHE 0.033 0.002 PHE C 82 TYR 0.037 0.002 TYR B 702 ARG 0.007 0.001 ARG D 14 *********************** 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 : 3.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 GLU cc_start: 0.7103 (tp30) cc_final: 0.6877 (tp30) REVERT: B 463 MET cc_start: 0.8264 (mtm) cc_final: 0.8045 (mtp) REVERT: C 482 GLU cc_start: 0.7133 (tp30) cc_final: 0.6894 (tp30) outliers start: 4 outliers final: 3 residues processed: 346 average time/residue: 0.4198 time to fit residues: 229.5529 Evaluate side-chains 256 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 253 time to evaluate : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain C residue 52 MET 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: 0.7702 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29904 Z= 0.176 Angle : 0.518 10.061 40490 Z= 0.259 Chirality : 0.041 0.376 4656 Planarity : 0.004 0.042 4978 Dihedral : 12.874 86.122 5361 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.91 % Allowed : 4.86 % Favored : 94.23 % 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: 2.16 (0.12), residues: 1940 sheet: -0.76 (0.25), residues: 404 loop : -1.06 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 152 HIS 0.007 0.001 HIS D 87 PHE 0.013 0.001 PHE C 217 TYR 0.018 0.001 TYR D 673 ARG 0.005 0.000 ARG B 24 *********************** 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 308 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 284 time to evaluate : 3.365 Fit side-chains revert: symmetry clash REVERT: B 355 MET cc_start: 0.7717 (mtp) cc_final: 0.7383 (mtt) outliers start: 24 outliers final: 16 residues processed: 295 average time/residue: 0.4111 time to fit residues: 195.2951 Evaluate side-chains 265 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 249 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain C residue 99 THR 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: 0.0970 chunk 94 optimal weight: 3.9990 chunk 342 optimal weight: 2.9990 chunk 369 optimal weight: 10.0000 chunk 304 optimal weight: 6.9990 chunk 339 optimal weight: 0.6980 chunk 116 optimal weight: 0.0030 chunk 274 optimal weight: 3.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- 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 106 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 HIS ** G 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 E 132 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29904 Z= 0.233 Angle : 0.509 11.206 40490 Z= 0.255 Chirality : 0.041 0.219 4656 Planarity : 0.004 0.042 4978 Dihedral : 10.658 71.791 5352 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.44 % Allowed : 7.21 % Favored : 91.34 % 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: 1.19 (0.14), residues: 3746 helix: 2.24 (0.12), residues: 1950 sheet: -0.52 (0.25), residues: 413 loop : -0.93 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 152 HIS 0.005 0.001 HIS D 87 PHE 0.012 0.001 PHE A 127 TYR 0.023 0.001 TYR B 367 ARG 0.007 0.000 ARG E 65 *********************** 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 303 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 265 time to evaluate : 3.166 Fit side-chains revert: symmetry clash REVERT: A 499 MET cc_start: 0.8442 (ttm) cc_final: 0.8115 (ttp) REVERT: B 463 MET cc_start: 0.8310 (mtp) cc_final: 0.7979 (mtp) REVERT: D 218 ASN cc_start: 0.8355 (t0) cc_final: 0.7964 (m-40) REVERT: C 195 LEU cc_start: 0.7717 (mt) cc_final: 0.7512 (mt) outliers start: 38 outliers final: 33 residues processed: 293 average time/residue: 0.4104 time to fit residues: 195.1737 Evaluate side-chains 290 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 257 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 484 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 0.7980 chunk 257 optimal weight: 0.2980 chunk 177 optimal weight: 5.9990 chunk 37 optimal weight: 0.0670 chunk 163 optimal weight: 3.9990 chunk 229 optimal weight: 0.8980 chunk 343 optimal weight: 0.0570 chunk 363 optimal weight: 7.9990 chunk 179 optimal weight: 0.6980 chunk 325 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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** D 106 GLN 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 29904 Z= 0.121 Angle : 0.452 8.054 40490 Z= 0.227 Chirality : 0.039 0.164 4656 Planarity : 0.003 0.039 4978 Dihedral : 9.439 67.045 5352 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.10 % Allowed : 8.39 % Favored : 90.51 % 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: 1.46 (0.14), residues: 3746 helix: 2.48 (0.12), residues: 1956 sheet: -0.36 (0.25), residues: 410 loop : -0.87 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 152 HIS 0.003 0.001 HIS B 87 PHE 0.012 0.001 PHE B 546 TYR 0.021 0.001 TYR C 812 ARG 0.010 0.000 ARG E 65 *********************** 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 302 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 273 time to evaluate : 3.365 Fit side-chains revert: symmetry clash REVERT: A 499 MET cc_start: 0.8467 (ttm) cc_final: 0.8091 (ttp) REVERT: B 355 MET cc_start: 0.7689 (mtp) cc_final: 0.7341 (mtt) REVERT: D 218 ASN cc_start: 0.8269 (t0) cc_final: 0.7949 (m-40) REVERT: D 374 MET cc_start: 0.7885 (ttt) cc_final: 0.7683 (ttt) REVERT: C 195 LEU cc_start: 0.7701 (mt) cc_final: 0.7479 (mt) REVERT: C 499 MET cc_start: 0.8452 (ttm) cc_final: 0.8117 (ttp) REVERT: E 65 ARG cc_start: 0.7304 (mtm110) cc_final: 0.6949 (ttm110) REVERT: E 106 PHE cc_start: 0.6453 (m-80) cc_final: 0.6083 (m-80) REVERT: E 123 MET cc_start: 0.5935 (mmm) cc_final: 0.5614 (mmm) outliers start: 29 outliers final: 19 residues processed: 291 average time/residue: 0.4034 time to fit residues: 189.6163 Evaluate side-chains 275 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 256 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain E residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 3.9990 chunk 206 optimal weight: 0.0270 chunk 5 optimal weight: 1.9990 chunk 270 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 310 optimal weight: 3.9990 chunk 251 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 chunk 326 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN B 106 GLN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29904 Z= 0.202 Angle : 0.457 7.494 40490 Z= 0.233 Chirality : 0.039 0.159 4656 Planarity : 0.003 0.039 4978 Dihedral : 9.150 62.054 5352 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.82 % Allowed : 9.04 % Favored : 89.14 % 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: 1.43 (0.14), residues: 3746 helix: 2.42 (0.12), residues: 1962 sheet: -0.36 (0.25), residues: 410 loop : -0.83 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 152 HIS 0.003 0.001 HIS B 87 PHE 0.015 0.001 PHE B 546 TYR 0.021 0.001 TYR A 812 ARG 0.010 0.000 ARG E 65 *********************** 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 312 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 264 time to evaluate : 3.475 Fit side-chains revert: symmetry clash REVERT: A 499 MET cc_start: 0.8505 (ttm) cc_final: 0.8110 (ttp) REVERT: A 804 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8601 (tp) REVERT: B 98 ASP cc_start: 0.6642 (p0) cc_final: 0.6416 (p0) REVERT: B 355 MET cc_start: 0.7771 (mtp) cc_final: 0.7417 (mtt) REVERT: D 92 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8837 (p) REVERT: D 218 ASN cc_start: 0.8432 (t0) cc_final: 0.8122 (m-40) REVERT: D 374 MET cc_start: 0.7888 (ttt) cc_final: 0.7654 (ttt) REVERT: C 52 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6878 (mtp) REVERT: C 195 LEU cc_start: 0.7653 (mt) cc_final: 0.7396 (mt) REVERT: C 499 MET cc_start: 0.8490 (ttm) cc_final: 0.8151 (ttp) REVERT: C 804 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8601 (tp) REVERT: E 106 PHE cc_start: 0.6444 (m-80) cc_final: 0.6065 (m-80) outliers start: 48 outliers final: 35 residues processed: 297 average time/residue: 0.4052 time to fit residues: 195.6370 Evaluate side-chains 290 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 251 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain E residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 4.9990 chunk 327 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 213 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 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: 6.9990 chunk 190 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 349 HIS B 87 HIS B 106 GLN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN D 106 GLN D 329 GLN J 20 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 29904 Z= 0.513 Angle : 0.620 8.144 40490 Z= 0.319 Chirality : 0.045 0.174 4656 Planarity : 0.004 0.049 4978 Dihedral : 9.964 58.876 5352 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.05 % Allowed : 9.79 % Favored : 88.15 % 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: 0.79 (0.14), residues: 3746 helix: 1.78 (0.12), residues: 1961 sheet: -0.48 (0.24), residues: 414 loop : -0.99 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 152 HIS 0.008 0.002 HIS J 83 PHE 0.022 0.002 PHE B 127 TYR 0.024 0.002 TYR A 812 ARG 0.007 0.001 ARG E 65 *********************** 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 304 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 250 time to evaluate : 3.010 Fit side-chains revert: symmetry clash REVERT: A 499 MET cc_start: 0.8437 (ttm) cc_final: 0.8103 (ttp) REVERT: A 751 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.6289 (mp0) REVERT: G 132 GLN cc_start: 0.6265 (pt0) cc_final: 0.6024 (pt0) REVERT: C 751 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.6303 (mp0) outliers start: 54 outliers final: 44 residues processed: 291 average time/residue: 0.4083 time to fit residues: 192.0789 Evaluate side-chains 285 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 239 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 751 GLU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain E residue 90 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.3965 > 50: distance: 36 - 103: 16.316 distance: 39 - 100: 27.731 distance: 82 - 92: 9.180 distance: 92 - 93: 3.983 distance: 93 - 94: 20.040 distance: 93 - 96: 10.506 distance: 94 - 95: 16.373 distance: 94 - 100: 44.420 distance: 96 - 97: 18.007 distance: 97 - 98: 18.395 distance: 97 - 99: 26.649 distance: 100 - 101: 8.816 distance: 101 - 102: 27.813 distance: 101 - 104: 6.184 distance: 102 - 103: 7.699 distance: 102 - 108: 18.747 distance: 104 - 105: 13.420 distance: 105 - 106: 32.661 distance: 105 - 107: 8.605 distance: 109 - 110: 6.844 distance: 109 - 112: 5.507 distance: 112 - 113: 6.131 distance: 113 - 114: 10.522 distance: 114 - 115: 7.659 distance: 114 - 116: 5.644 distance: 118 - 119: 9.422 distance: 118 - 121: 5.898 distance: 119 - 120: 3.675 distance: 119 - 123: 6.154 distance: 120 - 146: 10.353 distance: 121 - 122: 16.694 distance: 123 - 124: 5.283 distance: 124 - 125: 9.090 distance: 124 - 127: 8.665 distance: 125 - 126: 8.058 distance: 125 - 130: 9.795 distance: 126 - 155: 17.897 distance: 127 - 128: 7.897 distance: 127 - 129: 9.544 distance: 130 - 131: 10.755 distance: 131 - 132: 4.655 distance: 131 - 134: 3.375 distance: 132 - 133: 10.781 distance: 132 - 138: 6.456 distance: 133 - 167: 4.538 distance: 134 - 135: 12.229 distance: 135 - 136: 15.921 distance: 136 - 137: 16.934 distance: 138 - 139: 4.859 distance: 139 - 140: 9.258 distance: 140 - 141: 6.576 distance: 140 - 146: 7.629 distance: 141 - 175: 5.471 distance: 142 - 143: 6.879 distance: 143 - 144: 8.648 distance: 143 - 145: 4.891 distance: 146 - 147: 7.071 distance: 147 - 148: 8.057 distance: 147 - 150: 8.708 distance: 148 - 149: 6.884 distance: 148 - 155: 5.788 distance: 150 - 151: 5.313 distance: 151 - 152: 4.781 distance: 152 - 153: 4.124 distance: 155 - 156: 5.525 distance: 156 - 157: 4.824 distance: 156 - 159: 3.218 distance: 157 - 158: 8.601 distance: 157 - 167: 6.572 distance: 159 - 160: 4.416 distance: 160 - 161: 3.748 distance: 160 - 162: 25.074 distance: 162 - 164: 4.495 distance: 163 - 165: 16.997 distance: 164 - 165: 10.903 distance: 165 - 166: 6.599 distance: 167 - 168: 3.955 distance: 168 - 169: 3.127 distance: 168 - 171: 3.855 distance: 169 - 170: 3.820 distance: 169 - 175: 3.608 distance: 171 - 172: 4.522 distance: 171 - 173: 8.531 distance: 172 - 174: 4.663