Starting phenix.real_space_refine on Sat Feb 24 21:46:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7laa_23246/02_2024/7laa_23246_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7laa_23246/02_2024/7laa_23246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7laa_23246/02_2024/7laa_23246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7laa_23246/02_2024/7laa_23246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7laa_23246/02_2024/7laa_23246_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7laa_23246/02_2024/7laa_23246_trim.pdb" } resolution = 3.42 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= -0.001 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 98 5.16 5 C 15075 2.51 5 N 3877 2.21 5 O 4662 1.98 5 H 22222 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1084": "OD1" <-> "OD2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1084": "OD1" <-> "OD2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 54": "OD1" <-> "OD2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "H ASP 208": "OD1" <-> "OD2" Residue "H GLU 212": "OE1" <-> "OE2" Residue "L TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 85": "OD1" <-> "OD2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 125": "OE1" <-> "OE2" Residue "L TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 184": "OE1" <-> "OE2" Residue "L TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 199": "OE1" <-> "OE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 1084": "OD1" <-> "OD2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 45934 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 14998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 14998 Classifications: {'peptide': 991} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 48, 'TRANS': 942} Chain breaks: 9 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 7, 'ASN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 11871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 11871 Classifications: {'peptide': 788} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 37, 'TRANS': 750} Chain breaks: 11 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "H" Number of atoms: 3227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3227 Classifications: {'peptide': 217} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 205} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3182 Classifications: {'peptide': 217} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 200} Chain: "C" Number of atoms: 11876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 11876 Classifications: {'peptide': 789} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 37, 'TRANS': 751} Chain breaks: 11 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 84 Chain: "D" 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: "E" 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: "F" 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: "G" 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: "I" 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: "J" 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: "K" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 19.72, per 1000 atoms: 0.43 Number of scatterers: 45934 At special positions: 0 Unit cell: (129.076, 139.656, 232.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 O 4662 8.00 N 3877 7.00 C 15075 6.00 H 22222 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.99 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1201 " - " ASN A 125 " " NAG A1202 " - " ASN A 331 " " NAG A1203 " - " ASN A 343 " " NAG A1204 " - " ASN A 616 " " NAG A1205 " - " ASN A 657 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 122 " " NAG B1203 " - " ASN B 234 " " NAG B1204 " - " ASN B 616 " " NAG B1205 " - " ASN B 709 " " NAG B1206 " - " ASN B 801 " " NAG C1201 " - " ASN C 61 " " NAG C1202 " - " ASN C 122 " " NAG C1203 " - " ASN C 234 " " NAG C1204 " - " ASN C 616 " " NAG C1205 " - " ASN C 709 " " NAG C1206 " - " ASN C 801 " " NAG D 1 " - " ASN A 282 " " NAG E 1 " - " ASN A 709 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 282 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B1074 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 282 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Time building additional restraints: 36.35 Conformation dependent library (CDL) restraints added in 4.6 seconds 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5620 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 52 sheets defined 25.3% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.149A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.727A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.625A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.851A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.501A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.521A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.198A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.684A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.688A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.629A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.955A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.536A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.875A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.581A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.937A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.863A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.946A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.320A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.797A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.133A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 159 through 161 No H-bonds generated for 'chain 'H' and resid 159 through 161' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 122 through 129 Processing helix chain 'L' and resid 182 through 189 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.276A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.921A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.620A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.835A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.584A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.959A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 891' Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.681A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.771A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.636A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.442A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 4.034A pdb=" N LEU C1145 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.123A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.508A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.839A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 84 Processing sheet with id=AA5, first strand: chain 'A' and resid 126 through 130 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.405A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.477A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.600A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.653A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.756A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.046A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.776A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.515A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.323A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.384A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.449A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.565A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.866A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.409A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 327 removed outlier: 4.213A pdb=" N LYS B 537 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 552 " --> pdb=" O LYS B 537 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.852A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.367A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.299A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.146A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.146A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.439A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 861 " --> pdb=" O LYS B 733 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.601A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.557A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.228A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'H' and resid 45 through 46 removed outlier: 4.265A pdb=" N ARG H 38 " --> pdb=" O GLU H 46 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 139 through 141 Processing sheet with id=AD8, first strand: chain 'H' and resid 152 through 154 Processing sheet with id=AD9, first strand: chain 'H' and resid 169 through 171 removed outlier: 3.654A pdb=" N LEU H 175 " --> pdb=" O GLN H 171 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.721A pdb=" N VAL L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.721A pdb=" N VAL L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 18 through 20 Processing sheet with id=AE4, first strand: chain 'L' and resid 18 through 20 Processing sheet with id=AE5, first strand: chain 'L' and resid 115 through 118 removed outlier: 5.551A pdb=" N LEU L 136 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N SER L 177 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER L 138 " --> pdb=" O ALA L 175 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA L 175 " --> pdb=" O SER L 138 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE L 140 " --> pdb=" O TYR L 173 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 154 through 155 Processing sheet with id=AE7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.192A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 50 through 55 removed outlier: 4.003A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AF1, first strand: chain 'C' and resid 117 through 122 Processing sheet with id=AF2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.373A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.083A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.328A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.328A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.732A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 974 hydrogen bonds defined for protein. 2649 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: 22.02 Time building geometry restraints manager: 37.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.88: 11 0.88 - 1.12: 22201 1.12 - 1.35: 7601 1.35 - 1.59: 16494 1.59 - 1.83: 124 Bond restraints: 46431 Sorted by residual: bond pdb=" OG SER H 115 " pdb=" HG SER H 115 " ideal model delta sigma weight residual 0.840 0.646 0.194 2.00e-02 2.50e+03 9.43e+01 bond pdb=" CE2 TYR A 707 " pdb=" HE2 TYR A 707 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" N ARG A1107 " pdb=" H ARG A1107 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" N GLN L 89 " pdb=" H GLN L 89 " ideal model delta sigma weight residual 0.860 1.009 -0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" N LEU C 981 " pdb=" H LEU C 981 " ideal model delta sigma weight residual 0.860 1.009 -0.149 2.00e-02 2.50e+03 5.58e+01 ... (remaining 46426 not shown) Histogram of bond angle deviations from ideal: 95.74 - 103.74: 306 103.74 - 111.74: 48462 111.74 - 119.75: 19179 119.75 - 127.75: 15134 127.75 - 135.76: 169 Bond angle restraints: 83250 Sorted by residual: angle pdb=" CA PHE A 168 " pdb=" CB PHE A 168 " pdb=" CG PHE A 168 " ideal model delta sigma weight residual 113.80 122.03 -8.23 1.00e+00 1.00e+00 6.78e+01 angle pdb=" CA ASP B 228 " pdb=" CB ASP B 228 " pdb=" CG ASP B 228 " ideal model delta sigma weight residual 112.60 120.39 -7.79 1.00e+00 1.00e+00 6.07e+01 angle pdb=" CA PHE B 32 " pdb=" CB PHE B 32 " pdb=" CG PHE B 32 " ideal model delta sigma weight residual 113.80 121.39 -7.59 1.00e+00 1.00e+00 5.77e+01 angle pdb=" CA PHE L 119 " pdb=" CB PHE L 119 " pdb=" CG PHE L 119 " ideal model delta sigma weight residual 113.80 121.06 -7.26 1.00e+00 1.00e+00 5.27e+01 angle pdb=" N ILE C 231 " pdb=" CA ILE C 231 " pdb=" C ILE C 231 " ideal model delta sigma weight residual 110.62 118.05 -7.43 1.14e+00 7.69e-01 4.25e+01 ... (remaining 83245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 21316 21.48 - 42.96: 1093 42.96 - 64.43: 569 64.43 - 85.91: 145 85.91 - 107.39: 32 Dihedral angle restraints: 23155 sinusoidal: 12812 harmonic: 10343 Sorted by residual: dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual 93.00 176.34 -83.34 1 1.00e+01 1.00e-02 8.49e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -168.98 82.98 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CA TYR A 453 " pdb=" C TYR A 453 " pdb=" N ARG A 454 " pdb=" CA ARG A 454 " ideal model delta harmonic sigma weight residual 180.00 150.17 29.83 0 5.00e+00 4.00e-02 3.56e+01 ... (remaining 23152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2568 0.095 - 0.190: 1179 0.190 - 0.286: 211 0.286 - 0.381: 25 0.381 - 0.476: 14 Chirality restraints: 3997 Sorted by residual: chirality pdb=" C1 BMA U 3 " pdb=" O4 NAG U 2 " pdb=" C2 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.57e+02 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.03e+02 ... (remaining 3994 not shown) Planarity restraints: 7012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 122 " -0.231 2.00e-02 2.50e+03 1.76e-01 4.64e+02 pdb=" CG ASN C 122 " 0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN C 122 " 0.146 2.00e-02 2.50e+03 pdb=" ND2 ASN C 122 " 0.110 2.00e-02 2.50e+03 pdb="HD21 ASN C 122 " 0.178 2.00e-02 2.50e+03 pdb=" C1 NAG C1202 " -0.255 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.220 2.00e-02 2.50e+03 1.65e-01 4.09e+02 pdb=" CG ASN A 343 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.123 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.096 2.00e-02 2.50e+03 pdb="HD21 ASN A 343 " 0.185 2.00e-02 2.50e+03 pdb=" C1 NAG A1203 " -0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " 0.222 2.00e-02 2.50e+03 1.64e-01 4.02e+02 pdb=" CG ASN C 234 " -0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.126 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " -0.057 2.00e-02 2.50e+03 pdb="HD21 ASN C 234 " -0.201 2.00e-02 2.50e+03 pdb=" C1 NAG C1203 " 0.221 2.00e-02 2.50e+03 ... (remaining 7009 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 2681 2.17 - 2.78: 78451 2.78 - 3.39: 127670 3.39 - 3.99: 172474 3.99 - 4.60: 250607 Nonbonded interactions: 631883 Sorted by model distance: nonbonded pdb=" OE2 GLU A 918 " pdb=" HG SER C1123 " model vdw 1.569 1.850 nonbonded pdb=" OE2 GLU B 298 " pdb=" HG1 THR B 315 " model vdw 1.576 1.850 nonbonded pdb=" OD1 ASP C 294 " pdb=" HG SER C 297 " model vdw 1.578 1.850 nonbonded pdb=" HG SER B 813 " pdb=" OE1 GLU B 868 " model vdw 1.587 1.850 nonbonded pdb=" OE2 GLU A 819 " pdb=" HG SER A1055 " model vdw 1.592 1.850 ... (remaining 631878 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 'B' and (resid 27 through 290 or (resid 291 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 292 through 300 or (resid 301 and (name N or name CA or name C or na \ me O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or res \ id 302 through 1147 or resid 1201 through 1206)) selection = (chain 'C' and (resid 27 through 211 or resid 216 through 1147 or resid 1201 thr \ ough 1206)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'V' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'P' selection = chain 'S' selection = chain 'U' } 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: 4.110 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: 0.670 Extract box with map and model: 11.540 Check model and map are aligned: 0.680 Set scattering table: 0.360 Process input model: 142.640 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.430 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 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 : 0.014 0.079 24209 Z= 0.905 Angle : 1.926 9.012 32972 Z= 1.282 Chirality : 0.105 0.476 3997 Planarity : 0.015 0.144 4161 Dihedral : 15.170 107.390 9397 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.00 % Favored : 92.49 % Rotamer: Outliers : 1.87 % Allowed : 4.49 % Favored : 93.64 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 2.03 % 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: -2.08 (0.14), residues: 2928 helix: -1.33 (0.17), residues: 617 sheet: -0.84 (0.22), residues: 481 loop : -1.60 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.150 0.032 TRP L 149 HIS 0.014 0.003 HIS C1101 PHE 0.122 0.016 PHE A 65 TYR 0.154 0.022 TYR C 265 ARG 0.014 0.002 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 1073 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Evaluate side-chains 500 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 453 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 THR cc_start: 0.6827 (p) cc_final: 0.6415 (t) REVERT: A 878 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8415 (mm) REVERT: B 66 HIS cc_start: 0.6368 (OUTLIER) cc_final: 0.5990 (m90) REVERT: B 675 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6840 (mm-40) REVERT: B 902 MET cc_start: 0.8357 (mmm) cc_final: 0.8003 (mmm) REVERT: H 100 TYR cc_start: 0.3555 (OUTLIER) cc_final: 0.2794 (t80) REVERT: L 194 CYS cc_start: 0.3774 (OUTLIER) cc_final: 0.3057 (m) REVERT: C 808 ASP cc_start: 0.6111 (t0) cc_final: 0.5195 (m-30) REVERT: C 983 ARG cc_start: 0.6686 (mtp-110) cc_final: 0.6425 (ttm-80) REVERT: C 1103 PHE cc_start: 0.7327 (m-80) cc_final: 0.6925 (m-10) REVERT: C 1137 VAL cc_start: 0.7768 (t) cc_final: 0.7454 (m) outliers start: 47 outliers final: 23 residues processed: 491 average time/residue: 0.8333 time to fit residues: 635.3521 Evaluate side-chains 322 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 294 time to evaluate : 4.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 463 PRO Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.9980 chunk 225 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 173 optimal weight: 0.8980 chunk 269 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A1054 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C 87 ASN C 211 ASN C 675 GLN C 762 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 24209 Z= 0.226 Angle : 0.748 8.369 32972 Z= 0.399 Chirality : 0.047 0.367 3997 Planarity : 0.005 0.061 4161 Dihedral : 11.348 77.867 4414 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.36 % Rotamer: Outliers : 2.54 % Allowed : 8.90 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 2928 helix: 0.31 (0.20), residues: 621 sheet: -0.91 (0.19), residues: 618 loop : -1.61 (0.13), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 47 HIS 0.010 0.001 HIS B 207 PHE 0.026 0.002 PHE A 168 TYR 0.024 0.002 TYR A 453 ARG 0.005 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 1073 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Evaluate side-chains 382 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 318 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 GLU cc_start: 0.2476 (OUTLIER) cc_final: 0.2251 (pm20) REVERT: B 66 HIS cc_start: 0.6235 (OUTLIER) cc_final: 0.5610 (m90) REVERT: B 84 LEU cc_start: 0.7921 (mp) cc_final: 0.7702 (mt) REVERT: B 902 MET cc_start: 0.8254 (mmm) cc_final: 0.8026 (tpt) REVERT: H 100 TYR cc_start: 0.3186 (OUTLIER) cc_final: 0.2391 (t80) REVERT: H 100 HIS cc_start: 0.2366 (t70) cc_final: 0.1746 (t-170) REVERT: L 49 TYR cc_start: 0.3371 (OUTLIER) cc_final: 0.2694 (t80) REVERT: L 194 CYS cc_start: 0.3393 (OUTLIER) cc_final: 0.2565 (m) REVERT: C 856 ASN cc_start: 0.6906 (m110) cc_final: 0.6651 (m110) outliers start: 64 outliers final: 44 residues processed: 362 average time/residue: 0.8388 time to fit residues: 477.8737 Evaluate side-chains 315 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 266 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 0.0050 chunk 83 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 270 optimal weight: 2.9990 chunk 291 optimal weight: 0.7980 chunk 240 optimal weight: 4.9990 chunk 267 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 216 optimal weight: 8.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A1002 GLN A1054 GLN A1083 HIS ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 690 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 24209 Z= 0.204 Angle : 0.635 7.696 32972 Z= 0.335 Chirality : 0.045 0.297 3997 Planarity : 0.004 0.051 4161 Dihedral : 9.256 59.986 4394 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.29 % Favored : 94.64 % Rotamer: Outliers : 2.46 % Allowed : 10.17 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 2928 helix: 0.73 (0.20), residues: 636 sheet: -0.99 (0.19), residues: 618 loop : -1.57 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.004 0.001 HIS B 207 PHE 0.021 0.001 PHE L 119 TYR 0.020 0.001 TYR C1067 ARG 0.007 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 1073 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Evaluate side-chains 334 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 272 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.5922 (m-80) cc_final: 0.5713 (m-80) REVERT: B 66 HIS cc_start: 0.6035 (OUTLIER) cc_final: 0.5367 (m90) REVERT: B 84 LEU cc_start: 0.8202 (mp) cc_final: 0.7997 (mt) REVERT: B 902 MET cc_start: 0.8277 (mmm) cc_final: 0.8075 (tpt) REVERT: H 100 TYR cc_start: 0.2728 (OUTLIER) cc_final: 0.1970 (t80) REVERT: C 856 ASN cc_start: 0.6984 (m110) cc_final: 0.6640 (m110) outliers start: 62 outliers final: 43 residues processed: 314 average time/residue: 0.8029 time to fit residues: 395.0785 Evaluate side-chains 293 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 248 time to evaluate : 3.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 0.0070 chunk 203 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24209 Z= 0.254 Angle : 0.625 12.667 32972 Z= 0.329 Chirality : 0.045 0.334 3997 Planarity : 0.004 0.052 4161 Dihedral : 8.335 59.813 4385 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.64 % Favored : 94.33 % Rotamer: Outliers : 2.54 % Allowed : 11.16 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.15), residues: 2928 helix: 0.94 (0.21), residues: 630 sheet: -1.14 (0.19), residues: 646 loop : -1.63 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.008 0.001 HIS B 207 PHE 0.019 0.002 PHE B 643 TYR 0.019 0.002 TYR C1067 ARG 0.011 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 1073 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Evaluate side-chains 319 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 255 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 HIS cc_start: 0.6056 (OUTLIER) cc_final: 0.5429 (m90) REVERT: B 1094 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8421 (m) REVERT: H 100 TYR cc_start: 0.2861 (OUTLIER) cc_final: 0.2142 (t80) REVERT: L 54 ARG cc_start: 0.4974 (mtm-85) cc_final: 0.4245 (mtm-85) REVERT: C 856 ASN cc_start: 0.6990 (m110) cc_final: 0.6618 (m110) outliers start: 64 outliers final: 47 residues processed: 300 average time/residue: 0.7675 time to fit residues: 361.6218 Evaluate side-chains 289 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 239 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 4 optimal weight: 0.0040 chunk 213 optimal weight: 0.0170 chunk 118 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.8036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN A 926 GLN A1054 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN H 100 ASN C 762 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 24209 Z= 0.229 Angle : 0.595 8.871 32972 Z= 0.315 Chirality : 0.045 0.321 3997 Planarity : 0.004 0.054 4161 Dihedral : 7.828 59.510 4383 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.26 % Allowed : 11.96 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.15), residues: 2928 helix: 1.22 (0.21), residues: 618 sheet: -1.19 (0.18), residues: 670 loop : -1.61 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.008 0.001 HIS B 207 PHE 0.018 0.001 PHE L 119 TYR 0.027 0.001 TYR B 904 ARG 0.014 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 1073 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 236 time to evaluate : 3.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.7982 (mmt) cc_final: 0.7737 (mmt) REVERT: B 66 HIS cc_start: 0.6180 (OUTLIER) cc_final: 0.5539 (m90) REVERT: H 100 TYR cc_start: 0.3083 (OUTLIER) cc_final: 0.2466 (t80) REVERT: L 54 ARG cc_start: 0.5043 (mtm-85) cc_final: 0.4483 (mtm-85) REVERT: C 856 ASN cc_start: 0.7014 (m110) cc_final: 0.6638 (m110) outliers start: 57 outliers final: 44 residues processed: 281 average time/residue: 0.7855 time to fit residues: 350.1694 Evaluate side-chains 274 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 228 time to evaluate : 3.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 3.9990 chunk 258 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 287 optimal weight: 3.9990 chunk 238 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 0.0970 chunk 150 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24209 Z= 0.198 Angle : 0.566 7.971 32972 Z= 0.299 Chirality : 0.044 0.316 3997 Planarity : 0.004 0.048 4161 Dihedral : 7.559 59.681 4381 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.19 % Allowed : 12.16 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -1.21 (0.15), residues: 2928 helix: 1.43 (0.21), residues: 618 sheet: -1.16 (0.18), residues: 660 loop : -1.57 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS B 207 PHE 0.017 0.001 PHE L 119 TYR 0.020 0.001 TYR A1110 ARG 0.009 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 1073 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 238 time to evaluate : 3.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 HIS cc_start: 0.6211 (OUTLIER) cc_final: 0.5516 (m90) REVERT: H 100 TYR cc_start: 0.3381 (OUTLIER) cc_final: 0.2653 (t80) REVERT: H 200 HIS cc_start: 0.3974 (OUTLIER) cc_final: 0.2903 (m-70) REVERT: C 856 ASN cc_start: 0.6938 (m110) cc_final: 0.6565 (m110) outliers start: 55 outliers final: 48 residues processed: 277 average time/residue: 0.7837 time to fit residues: 343.5926 Evaluate side-chains 278 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 227 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 200 HIS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 160 optimal weight: 0.5980 chunk 286 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 24209 Z= 0.349 Angle : 0.657 7.932 32972 Z= 0.347 Chirality : 0.047 0.393 3997 Planarity : 0.005 0.077 4161 Dihedral : 7.924 59.702 4380 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 2.74 % Allowed : 12.28 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.15), residues: 2928 helix: 1.17 (0.21), residues: 624 sheet: -1.30 (0.18), residues: 671 loop : -1.83 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 96 HIS 0.007 0.002 HIS A1048 PHE 0.019 0.002 PHE L 119 TYR 0.035 0.002 TYR B 904 ARG 0.015 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 1073 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Evaluate side-chains 303 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 234 time to evaluate : 3.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 HIS cc_start: 0.6304 (OUTLIER) cc_final: 0.5639 (m90) REVERT: H 100 TYR cc_start: 0.3834 (OUTLIER) cc_final: 0.3078 (t80) REVERT: H 200 HIS cc_start: 0.4086 (OUTLIER) cc_final: 0.3018 (m-70) outliers start: 69 outliers final: 60 residues processed: 288 average time/residue: 0.7435 time to fit residues: 340.5773 Evaluate side-chains 289 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 226 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 200 HIS Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 170 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 195 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24209 Z= 0.331 Angle : 0.637 7.503 32972 Z= 0.337 Chirality : 0.046 0.377 3997 Planarity : 0.005 0.065 4161 Dihedral : 7.920 58.761 4380 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.62 % Allowed : 13.11 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.15), residues: 2928 helix: 1.16 (0.21), residues: 624 sheet: -1.37 (0.18), residues: 667 loop : -1.88 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 64 HIS 0.006 0.001 HIS A1048 PHE 0.019 0.002 PHE L 119 TYR 0.023 0.002 TYR C1067 ARG 0.011 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 1073 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Evaluate side-chains 295 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 229 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 HIS cc_start: 0.6316 (OUTLIER) cc_final: 0.5638 (m90) REVERT: H 200 HIS cc_start: 0.4075 (OUTLIER) cc_final: 0.3029 (m-70) outliers start: 66 outliers final: 57 residues processed: 277 average time/residue: 0.7851 time to fit residues: 345.4554 Evaluate side-chains 285 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 226 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 200 HIS Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 3.9990 chunk 274 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 266 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 209 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 241 optimal weight: 0.4980 chunk 252 optimal weight: 0.9980 chunk 265 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24209 Z= 0.195 Angle : 0.573 6.828 32972 Z= 0.301 Chirality : 0.044 0.336 3997 Planarity : 0.004 0.051 4161 Dihedral : 7.616 59.970 4380 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.11 % Allowed : 13.91 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.15), residues: 2928 helix: 1.44 (0.21), residues: 619 sheet: -1.32 (0.18), residues: 651 loop : -1.74 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.004 0.001 HIS B 207 PHE 0.017 0.001 PHE L 119 TYR 0.021 0.001 TYR B 904 ARG 0.009 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 1073 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Evaluate side-chains 290 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 237 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 739 THR cc_start: 0.7784 (OUTLIER) cc_final: 0.7491 (t) REVERT: A 902 MET cc_start: 0.7950 (mmt) cc_final: 0.7696 (mmt) REVERT: B 66 HIS cc_start: 0.6325 (OUTLIER) cc_final: 0.5586 (m90) REVERT: H 200 HIS cc_start: 0.4001 (OUTLIER) cc_final: 0.2949 (m-70) REVERT: C 227 VAL cc_start: 0.5934 (OUTLIER) cc_final: 0.5481 (m) outliers start: 53 outliers final: 48 residues processed: 276 average time/residue: 0.7742 time to fit residues: 339.1941 Evaluate side-chains 280 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 228 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 200 HIS Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 5.9990 chunk 282 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 196 optimal weight: 8.9990 chunk 295 optimal weight: 4.9990 chunk 272 optimal weight: 0.6980 chunk 235 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24209 Z= 0.222 Angle : 0.572 6.961 32972 Z= 0.301 Chirality : 0.044 0.345 3997 Planarity : 0.004 0.066 4161 Dihedral : 7.446 59.533 4380 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.07 % Allowed : 14.18 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.15), residues: 2928 helix: 1.49 (0.21), residues: 620 sheet: -1.32 (0.18), residues: 650 loop : -1.71 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.004 0.001 HIS A1048 PHE 0.018 0.001 PHE L 119 TYR 0.021 0.001 TYR B 904 ARG 0.013 0.001 ARG H 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 921 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 1073 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 231 time to evaluate : 3.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 739 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7678 (t) REVERT: B 66 HIS cc_start: 0.6369 (OUTLIER) cc_final: 0.5500 (m90) REVERT: H 200 HIS cc_start: 0.3977 (OUTLIER) cc_final: 0.2918 (m-70) REVERT: C 227 VAL cc_start: 0.5936 (OUTLIER) cc_final: 0.5485 (m) REVERT: C 617 CYS cc_start: 0.4218 (t) cc_final: 0.3730 (t) outliers start: 52 outliers final: 46 residues processed: 270 average time/residue: 0.8192 time to fit residues: 348.1174 Evaluate side-chains 279 residues out of total 2617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 229 time to evaluate : 3.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 33 TRP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 200 HIS Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 8.9990 chunk 250 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 217 optimal weight: 30.0000 chunk 34 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.151825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.126722 restraints weight = 116474.099| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.85 r_work: 0.3626 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24209 Z= 0.328 Angle : 0.632 7.305 32972 Z= 0.332 Chirality : 0.046 0.391 3997 Planarity : 0.005 0.050 4161 Dihedral : 7.836 59.941 4380 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.42 % Allowed : 14.14 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -1.56 (0.15), residues: 2928 helix: 1.28 (0.21), residues: 617 sheet: -1.39 (0.18), residues: 644 loop : -1.86 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 436 HIS 0.005 0.001 HIS C 655 PHE 0.019 0.002 PHE L 119 TYR 0.023 0.002 TYR C1067 ARG 0.007 0.001 ARG H 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10088.04 seconds wall clock time: 180 minutes 1.22 seconds (10801.22 seconds total)