Starting phenix.real_space_refine on Fri Dec 8 05:04:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nps_12518/12_2023/7nps_12518.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nps_12518/12_2023/7nps_12518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nps_12518/12_2023/7nps_12518.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nps_12518/12_2023/7nps_12518.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nps_12518/12_2023/7nps_12518.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nps_12518/12_2023/7nps_12518.pdb" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 87 5.16 5 C 17460 2.51 5 N 4851 2.21 5 O 5271 1.98 5 H 27681 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B1 TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 ARG 127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B1 ASP 163": "OD1" <-> "OD2" Residue "B1 ASP 183": "OD1" <-> "OD2" Residue "B1 ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B1 ASP 208": "OD1" <-> "OD2" Residue "B1 ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B1 GLU 214": "OE1" <-> "OE2" Residue "B1 ARG 242": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B1 GLU 257": "OE1" <-> "OE2" Residue "B1 PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 ASP 300": "OD1" <-> "OD2" Residue "B1 GLU 328": "OE1" <-> "OE2" Residue "B1 ARG 340": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B1 ASP 355": "OD1" <-> "OD2" Residue "B1 ASP 409": "OD1" <-> "OD2" Residue "B1 ASP 416": "OD1" <-> "OD2" Residue "B1 PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 ASP 441": "OD1" <-> "OD2" Residue "B1 GLU 449": "OE1" <-> "OE2" Residue "B1 ARG 473": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B1 ASP 485": "OD1" <-> "OD2" Residue "B1 GLU 501": "OE1" <-> "OE2" Residue "B2 ASP 92": "OD1" <-> "OD2" Residue "B2 ASP 163": "OD1" <-> "OD2" Residue "B2 ASP 183": "OD1" <-> "OD2" Residue "B2 ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B2 ASP 208": "OD1" <-> "OD2" Residue "B2 ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B2 ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B2 ARG 242": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B2 PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B2 TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B2 GLU 328": "OE1" <-> "OE2" Residue "B2 ARG 340": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B2 ASP 409": "OD1" <-> "OD2" Residue "B2 PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B2 ASP 416": "OD1" <-> "OD2" Residue "B2 PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B2 ASP 441": "OD1" <-> "OD2" Residue "B2 ARG 473": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B2 ASP 485": "OD1" <-> "OD2" Residue "B2 GLU 501": "OE1" <-> "OE2" Residue "B3 GLU 84": "OE1" <-> "OE2" Residue "B3 ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B3 ASP 92": "OD1" <-> "OD2" Residue "B3 ARG 127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B3 ASP 163": "OD1" <-> "OD2" Residue "B3 ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B3 ASP 208": "OD1" <-> "OD2" Residue "B3 ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B3 GLU 214": "OE1" <-> "OE2" Residue "B3 ARG 242": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B3 GLU 257": "OE1" <-> "OE2" Residue "B3 PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B3 GLU 328": "OE1" <-> "OE2" Residue "B3 ASP 342": "OD1" <-> "OD2" Residue "B3 ASP 409": "OD1" <-> "OD2" Residue "B3 PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B3 ASP 416": "OD1" <-> "OD2" Residue "B3 PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B3 ASP 441": "OD1" <-> "OD2" Residue "B3 GLU 449": "OE1" <-> "OE2" Residue "B3 ARG 473": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B3 GLU 489": "OE1" <-> "OE2" Residue "B3 ASP 491": "OD1" <-> "OD2" Residue "B3 GLU 501": "OE1" <-> "OE2" Residue "B4 GLU 84": "OE1" <-> "OE2" Residue "B4 ASP 92": "OD1" <-> "OD2" Residue "B4 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B4 ASP 163": "OD1" <-> "OD2" Residue "B4 ASP 183": "OD1" <-> "OD2" Residue "B4 ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B4 ASP 208": "OD1" <-> "OD2" Residue "B4 ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B4 ARG 242": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B4 PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B4 GLU 328": "OE1" <-> "OE2" Residue "B4 TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B4 GLU 358": "OE1" <-> "OE2" Residue "B4 GLU 391": "OE1" <-> "OE2" Residue "B4 ASP 409": "OD1" <-> "OD2" Residue "B4 PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B4 ASP 416": "OD1" <-> "OD2" Residue "B4 PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B4 GLU 434": "OE1" <-> "OE2" Residue "B4 GLU 449": "OE1" <-> "OE2" Residue "B4 ARG 473": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B4 ASP 485": "OD1" <-> "OD2" Residue "B4 ASP 491": "OD1" <-> "OD2" Residue "B5 GLU 84": "OE1" <-> "OE2" Residue "B5 ASP 92": "OD1" <-> "OD2" Residue "B5 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B5 ASP 163": "OD1" <-> "OD2" Residue "B5 ASP 183": "OD1" <-> "OD2" Residue "B5 ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B5 ASP 208": "OD1" <-> "OD2" Residue "B5 ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B5 GLU 214": "OE1" <-> "OE2" Residue "B5 ARG 242": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B5 GLU 328": "OE1" <-> "OE2" Residue "B5 ASP 342": "OD1" <-> "OD2" Residue "B5 TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B5 ASP 355": "OD1" <-> "OD2" Residue "B5 GLU 367": "OE1" <-> "OE2" Residue "B5 GLU 391": "OE1" <-> "OE2" Residue "B5 ASP 409": "OD1" <-> "OD2" Residue "B5 PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B5 ASP 416": "OD1" <-> "OD2" Residue "B5 PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B5 GLU 434": "OE1" <-> "OE2" Residue "B5 ASP 441": "OD1" <-> "OD2" Residue "B5 GLU 449": "OE1" <-> "OE2" Residue "B5 ARG 473": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B6 GLU 84": "OE1" <-> "OE2" Residue "B6 ASP 92": "OD1" <-> "OD2" Residue "B6 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B6 ASP 163": "OD1" <-> "OD2" Residue "B6 ASP 183": "OD1" <-> "OD2" Residue "B6 ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B6 ASP 208": "OD1" <-> "OD2" Residue "B6 ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B6 ARG 242": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B6 GLU 257": "OE1" <-> "OE2" Residue "B6 PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B6 GLU 328": "OE1" <-> "OE2" Residue "B6 ASP 342": "OD1" <-> "OD2" Residue "B6 TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B6 GLU 391": "OE1" <-> "OE2" Residue "B6 ARG 406": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B6 ASP 409": "OD1" <-> "OD2" Residue "B6 PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B6 ASP 416": "OD1" <-> "OD2" Residue "B6 PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B6 ASP 441": "OD1" <-> "OD2" Residue "B6 ASP 450": "OD1" <-> "OD2" Residue "B6 GLU 453": "OE1" <-> "OE2" Residue "B6 ARG 473": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P1 ASP 46": "OD1" <-> "OD2" Residue "P1 PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P1 ASP 101": "OD1" <-> "OD2" Residue "P1 ASP 109": "OD1" <-> "OD2" Residue "P1 ASP 126": "OD1" <-> "OD2" Residue "P1 ASP 133": "OD1" <-> "OD2" Residue "P1 ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P1 ASP 267": "OD1" <-> "OD2" Residue "P1 TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P1 ASP 297": "OD1" <-> "OD2" Residue "P1 GLU 310": "OE1" <-> "OE2" Residue "P1 ARG 314": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P1 ARG 344": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P1 ASP 386": "OD1" <-> "OD2" Residue "P1 PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P1 ASP 404": "OD1" <-> "OD2" Residue "P1 ASP 413": "OD1" <-> "OD2" Residue "P1 ASP 445": "OD1" <-> "OD2" Residue "P1 ASP 446": "OD1" <-> "OD2" Residue "P1 ASP 456": "OD1" <-> "OD2" Residue "P1 PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P1 ARG 494": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P1 TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P2 ASP 46": "OD1" <-> "OD2" Residue "P2 GLU 70": "OE1" <-> "OE2" Residue "P2 PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P2 GLU 93": "OE1" <-> "OE2" Residue "P2 ASP 109": "OD1" <-> "OD2" Residue "P2 ASP 126": "OD1" <-> "OD2" Residue "P2 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P2 ASP 139": "OD1" <-> "OD2" Residue "P2 ARG 165": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P2 ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P2 ASP 267": "OD1" <-> "OD2" Residue "P2 TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P2 ASP 297": "OD1" <-> "OD2" Residue "P2 GLU 298": "OE1" <-> "OE2" Residue "P2 GLU 310": "OE1" <-> "OE2" Residue "P2 ARG 314": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P2 ASP 342": "OD1" <-> "OD2" Residue "P2 ARG 344": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P2 PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P2 ASP 404": "OD1" <-> "OD2" Residue "P2 ASP 413": "OD1" <-> "OD2" Residue "P2 ARG 444": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P2 ASP 445": "OD1" <-> "OD2" Residue "P2 ASP 446": "OD1" <-> "OD2" Residue "P2 ASP 453": "OD1" <-> "OD2" Residue "P2 ASP 456": "OD1" <-> "OD2" Residue "P2 ARG 494": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P2 TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P3 ASP 46": "OD1" <-> "OD2" Residue "P3 PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P3 GLU 93": "OE1" <-> "OE2" Residue "P3 ASP 101": "OD1" <-> "OD2" Residue "P3 ASP 126": "OD1" <-> "OD2" Residue "P3 ASP 139": "OD1" <-> "OD2" Residue "P3 ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P3 ASP 267": "OD1" <-> "OD2" Residue "P3 TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P3 ASP 297": "OD1" <-> "OD2" Residue "P3 GLU 310": "OE1" <-> "OE2" Residue "P3 ARG 314": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P3 ASP 342": "OD1" <-> "OD2" Residue "P3 ARG 344": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P3 PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P3 ASP 404": "OD1" <-> "OD2" Residue "P3 ASP 413": "OD1" <-> "OD2" Residue "P3 ASP 445": "OD1" <-> "OD2" Residue "P3 ASP 446": "OD1" <-> "OD2" Residue "P3 ASP 453": "OD1" <-> "OD2" Residue "P3 ASP 456": "OD1" <-> "OD2" Residue "P3 PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P3 ARG 494": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P3 TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P3 GLU 531": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 55350 Number of models: 1 Model: "" Number of chains: 9 Chain: "B1" Number of atoms: 6214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6214 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 44, 'TRANS': 369} Chain breaks: 3 Chain: "B2" Number of atoms: 6214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6214 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 44, 'TRANS': 369} Chain breaks: 3 Chain: "B3" Number of atoms: 6214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6214 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 44, 'TRANS': 369} Chain breaks: 3 Chain: "B4" Number of atoms: 6208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6208 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 44, 'TRANS': 371} Chain breaks: 1 Chain: "B5" Number of atoms: 6208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6208 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 44, 'TRANS': 371} Chain breaks: 1 Chain: "B6" Number of atoms: 6208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6208 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 44, 'TRANS': 371} Chain breaks: 1 Chain: "P1" Number of atoms: 6028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6028 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 365} Chain breaks: 1 Chain: "P2" Number of atoms: 6028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6028 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 365} Chain breaks: 1 Chain: "P3" Number of atoms: 6028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6028 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 365} Chain breaks: 1 Time building chain proxies: 17.65, per 1000 atoms: 0.32 Number of scatterers: 55350 At special positions: 0 Unit cell: (210.1, 202.4, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 87 16.00 O 5271 8.00 N 4851 7.00 C 17460 6.00 H 27681 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYSB1 162 " - pdb=" SG CYSB1 363 " distance=2.03 Simple disulfide: pdb=" SG CYSB2 162 " - pdb=" SG CYSB2 363 " distance=2.02 Simple disulfide: pdb=" SG CYSB3 162 " - pdb=" SG CYSB3 363 " distance=2.03 Simple disulfide: pdb=" SG CYSB4 162 " - pdb=" SG CYSB4 363 " distance=2.02 Simple disulfide: pdb=" SG CYSB5 162 " - pdb=" SG CYSB5 363 " distance=2.02 Simple disulfide: pdb=" SG CYSB6 162 " - pdb=" SG CYSB6 363 " distance=2.03 Simple disulfide: pdb=" SG CYSP1 68 " - pdb=" SG CYSP1 138 " distance=2.04 Simple disulfide: pdb=" SG CYSP1 334 " - pdb=" SG CYSP1 373 " distance=2.03 Simple disulfide: pdb=" SG CYSP2 68 " - pdb=" SG CYSP2 138 " distance=2.04 Simple disulfide: pdb=" SG CYSP2 334 " - pdb=" SG CYSP2 373 " distance=2.03 Simple disulfide: pdb=" SG CYSP3 68 " - pdb=" SG CYSP3 138 " distance=2.04 Simple disulfide: pdb=" SG CYSP3 334 " - pdb=" SG CYSP3 373 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 31.57 Conformation dependent library (CDL) restraints added in 5.3 seconds 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6828 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 51 sheets defined 22.8% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'B1' and resid 109 through 118 Processing helix chain 'B1' and resid 127 through 132 removed outlier: 3.523A pdb=" N ILEB1 131 " --> pdb=" O ARGB1 127 " (cutoff:3.500A) Processing helix chain 'B1' and resid 224 through 232 Proline residue: B1 230 - end of helix Processing helix chain 'B1' and resid 234 through 240 Processing helix chain 'B1' and resid 245 through 252 Processing helix chain 'B1' and resid 306 through 316 Processing helix chain 'B1' and resid 328 through 335 Processing helix chain 'B1' and resid 390 through 395 removed outlier: 4.217A pdb=" N ASNB1 393 " --> pdb=" O THRB1 390 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VALB1 395 " --> pdb=" O METB1 392 " (cutoff:3.500A) Processing helix chain 'B1' and resid 451 through 458 Processing helix chain 'B1' and resid 468 through 473 Processing helix chain 'B1' and resid 482 through 487 removed outlier: 3.843A pdb=" N LEUB1 487 " --> pdb=" O ARGB1 483 " (cutoff:3.500A) Processing helix chain 'B2' and resid 109 through 118 Processing helix chain 'B2' and resid 127 through 132 removed outlier: 3.576A pdb=" N ILEB2 131 " --> pdb=" O ARGB2 127 " (cutoff:3.500A) Processing helix chain 'B2' and resid 224 through 232 Proline residue: B2 230 - end of helix Processing helix chain 'B2' and resid 234 through 240 Processing helix chain 'B2' and resid 245 through 252 removed outlier: 3.869A pdb=" N ALAB2 251 " --> pdb=" O ALAB2 247 " (cutoff:3.500A) Processing helix chain 'B2' and resid 306 through 314 Processing helix chain 'B2' and resid 328 through 335 Processing helix chain 'B2' and resid 391 through 395 removed outlier: 3.731A pdb=" N VALB2 395 " --> pdb=" O METB2 392 " (cutoff:3.500A) Processing helix chain 'B2' and resid 453 through 458 Processing helix chain 'B2' and resid 468 through 473 Processing helix chain 'B2' and resid 482 through 487 removed outlier: 3.603A pdb=" N LEUB2 487 " --> pdb=" O ARGB2 483 " (cutoff:3.500A) Processing helix chain 'B3' and resid 109 through 118 Processing helix chain 'B3' and resid 127 through 132 removed outlier: 3.612A pdb=" N ALAB3 132 " --> pdb=" O SERB3 128 " (cutoff:3.500A) Processing helix chain 'B3' and resid 224 through 232 Proline residue: B3 230 - end of helix Processing helix chain 'B3' and resid 234 through 240 Processing helix chain 'B3' and resid 245 through 252 Processing helix chain 'B3' and resid 306 through 314 Processing helix chain 'B3' and resid 328 through 335 Processing helix chain 'B3' and resid 391 through 395 removed outlier: 3.770A pdb=" N VALB3 395 " --> pdb=" O METB3 392 " (cutoff:3.500A) Processing helix chain 'B3' and resid 451 through 459 Processing helix chain 'B3' and resid 468 through 473 Processing helix chain 'B3' and resid 482 through 487 removed outlier: 3.855A pdb=" N LEUB3 487 " --> pdb=" O ARGB3 483 " (cutoff:3.500A) Processing helix chain 'B4' and resid 109 through 118 Processing helix chain 'B4' and resid 127 through 132 removed outlier: 3.612A pdb=" N ILEB4 131 " --> pdb=" O ARGB4 127 " (cutoff:3.500A) Processing helix chain 'B4' and resid 224 through 232 Proline residue: B4 230 - end of helix Processing helix chain 'B4' and resid 234 through 240 Processing helix chain 'B4' and resid 245 through 252 removed outlier: 3.510A pdb=" N ALAB4 251 " --> pdb=" O ALAB4 247 " (cutoff:3.500A) Processing helix chain 'B4' and resid 286 through 290 removed outlier: 3.501A pdb=" N SERB4 289 " --> pdb=" O PROB4 286 " (cutoff:3.500A) Processing helix chain 'B4' and resid 306 through 317 removed outlier: 3.612A pdb=" N GLNB4 311 " --> pdb=" O PROB4 307 " (cutoff:3.500A) Processing helix chain 'B4' and resid 328 through 333 Processing helix chain 'B4' and resid 342 through 346 removed outlier: 4.325A pdb=" N ALAB4 345 " --> pdb=" O ASPB4 342 " (cutoff:3.500A) Processing helix chain 'B4' and resid 388 through 395 removed outlier: 4.099A pdb=" N ASNB4 393 " --> pdb=" O THRB4 390 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VALB4 395 " --> pdb=" O METB4 392 " (cutoff:3.500A) Processing helix chain 'B4' and resid 451 through 459 Processing helix chain 'B4' and resid 469 through 473 Processing helix chain 'B4' and resid 482 through 487 Processing helix chain 'B5' and resid 109 through 118 Processing helix chain 'B5' and resid 127 through 132 removed outlier: 3.702A pdb=" N ILEB5 131 " --> pdb=" O ARGB5 127 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALAB5 132 " --> pdb=" O SERB5 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'B5' and resid 127 through 132' Processing helix chain 'B5' and resid 224 through 232 Proline residue: B5 230 - end of helix Processing helix chain 'B5' and resid 234 through 240 Processing helix chain 'B5' and resid 245 through 252 removed outlier: 3.506A pdb=" N ALAB5 251 " --> pdb=" O ALAB5 247 " (cutoff:3.500A) Processing helix chain 'B5' and resid 286 through 290 removed outlier: 3.572A pdb=" N GLYB5 290 " --> pdb=" O GLNB5 287 " (cutoff:3.500A) Processing helix chain 'B5' and resid 306 through 317 removed outlier: 3.516A pdb=" N GLNB5 311 " --> pdb=" O PROB5 307 " (cutoff:3.500A) Processing helix chain 'B5' and resid 328 through 333 Processing helix chain 'B5' and resid 390 through 395 removed outlier: 4.225A pdb=" N ASNB5 393 " --> pdb=" O THRB5 390 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VALB5 395 " --> pdb=" O METB5 392 " (cutoff:3.500A) Processing helix chain 'B5' and resid 451 through 458 Processing helix chain 'B5' and resid 469 through 473 Processing helix chain 'B5' and resid 482 through 487 removed outlier: 3.615A pdb=" N LEUB5 487 " --> pdb=" O ARGB5 483 " (cutoff:3.500A) Processing helix chain 'B6' and resid 109 through 118 Processing helix chain 'B6' and resid 127 through 132 removed outlier: 3.853A pdb=" N ILEB6 131 " --> pdb=" O ARGB6 127 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALAB6 132 " --> pdb=" O SERB6 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'B6' and resid 127 through 132' Processing helix chain 'B6' and resid 224 through 232 Proline residue: B6 230 - end of helix Processing helix chain 'B6' and resid 234 through 240 Processing helix chain 'B6' and resid 245 through 252 removed outlier: 3.589A pdb=" N ALAB6 251 " --> pdb=" O ALAB6 247 " (cutoff:3.500A) Processing helix chain 'B6' and resid 306 through 317 removed outlier: 3.543A pdb=" N GLNB6 311 " --> pdb=" O PROB6 307 " (cutoff:3.500A) Processing helix chain 'B6' and resid 328 through 333 Processing helix chain 'B6' and resid 390 through 395 removed outlier: 4.125A pdb=" N ASNB6 393 " --> pdb=" O THRB6 390 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VALB6 395 " --> pdb=" O METB6 392 " (cutoff:3.500A) Processing helix chain 'B6' and resid 451 through 459 Processing helix chain 'B6' and resid 469 through 473 Processing helix chain 'B6' and resid 482 through 487 removed outlier: 3.547A pdb=" N LEUB6 487 " --> pdb=" O ARGB6 483 " (cutoff:3.500A) Processing helix chain 'P1' and resid 46 through 50 removed outlier: 3.814A pdb=" N LEUP1 50 " --> pdb=" O PROP1 47 " (cutoff:3.500A) Processing helix chain 'P1' and resid 85 through 90 removed outlier: 4.035A pdb=" N LEUP1 89 " --> pdb=" O TYRP1 85 " (cutoff:3.500A) Processing helix chain 'P1' and resid 90 through 95 Processing helix chain 'P1' and resid 96 through 98 No H-bonds generated for 'chain 'P1' and resid 96 through 98' Processing helix chain 'P1' and resid 141 through 151 removed outlier: 3.531A pdb=" N VALP1 145 " --> pdb=" O HISP1 141 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILEP1 149 " --> pdb=" O VALP1 145 " (cutoff:3.500A) Processing helix chain 'P1' and resid 299 through 322 removed outlier: 3.648A pdb=" N GLNP1 304 " --> pdb=" O PROP1 300 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYSP1 305 " --> pdb=" O GLNP1 301 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILEP1 306 " --> pdb=" O THRP1 302 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASPP1 307 " --> pdb=" O ALAP1 303 " (cutoff:3.500A) Processing helix chain 'P1' and resid 343 through 356 Processing helix chain 'P1' and resid 464 through 483 removed outlier: 3.699A pdb=" N SERP1 468 " --> pdb=" O GLYP1 464 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALAP1 470 " --> pdb=" O SERP1 466 " (cutoff:3.500A) Processing helix chain 'P1' and resid 487 through 499 removed outlier: 3.719A pdb=" N THRP1 498 " --> pdb=" O ARGP1 494 " (cutoff:3.500A) Processing helix chain 'P1' and resid 516 through 523 Processing helix chain 'P2' and resid 46 through 50 removed outlier: 3.952A pdb=" N LEUP2 50 " --> pdb=" O PROP2 47 " (cutoff:3.500A) Processing helix chain 'P2' and resid 85 through 90 removed outlier: 3.999A pdb=" N LEUP2 89 " --> pdb=" O TYRP2 85 " (cutoff:3.500A) Processing helix chain 'P2' and resid 90 through 95 Processing helix chain 'P2' and resid 96 through 98 No H-bonds generated for 'chain 'P2' and resid 96 through 98' Processing helix chain 'P2' and resid 140 through 151 removed outlier: 4.052A pdb=" N LEUP2 144 " --> pdb=" O ALAP2 140 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VALP2 145 " --> pdb=" O HISP2 141 " (cutoff:3.500A) Processing helix chain 'P2' and resid 299 through 322 removed outlier: 3.956A pdb=" N LYSP2 305 " --> pdb=" O GLNP2 301 " (cutoff:3.500A) Processing helix chain 'P2' and resid 343 through 356 Processing helix chain 'P2' and resid 389 through 393 removed outlier: 3.720A pdb=" N ALAP2 392 " --> pdb=" O ALAP2 389 " (cutoff:3.500A) Processing helix chain 'P2' and resid 464 through 483 removed outlier: 3.593A pdb=" N SERP2 468 " --> pdb=" O GLYP2 464 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ALAP2 470 " --> pdb=" O SERP2 466 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILEP2 471 " --> pdb=" O PHEP2 467 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALAP2 481 " --> pdb=" O ALAP2 477 " (cutoff:3.500A) Processing helix chain 'P2' and resid 487 through 498 removed outlier: 3.539A pdb=" N THRP2 498 " --> pdb=" O ARGP2 494 " (cutoff:3.500A) Processing helix chain 'P2' and resid 516 through 523 Processing helix chain 'P3' and resid 46 through 50 removed outlier: 3.734A pdb=" N LEUP3 50 " --> pdb=" O PROP3 47 " (cutoff:3.500A) Processing helix chain 'P3' and resid 85 through 90 removed outlier: 3.995A pdb=" N LEUP3 89 " --> pdb=" O TYRP3 85 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASNP3 90 " --> pdb=" O METP3 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'P3' and resid 85 through 90' Processing helix chain 'P3' and resid 90 through 95 Processing helix chain 'P3' and resid 96 through 98 No H-bonds generated for 'chain 'P3' and resid 96 through 98' Processing helix chain 'P3' and resid 141 through 151 removed outlier: 3.590A pdb=" N ILEP3 149 " --> pdb=" O VALP3 145 " (cutoff:3.500A) Processing helix chain 'P3' and resid 299 through 322 removed outlier: 3.653A pdb=" N GLNP3 304 " --> pdb=" O PROP3 300 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYSP3 305 " --> pdb=" O GLNP3 301 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASPP3 307 " --> pdb=" O ALAP3 303 " (cutoff:3.500A) Processing helix chain 'P3' and resid 343 through 356 Processing helix chain 'P3' and resid 464 through 483 removed outlier: 3.634A pdb=" N SERP3 468 " --> pdb=" O GLYP3 464 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALAP3 470 " --> pdb=" O SERP3 466 " (cutoff:3.500A) Processing helix chain 'P3' and resid 487 through 499 removed outlier: 3.656A pdb=" N THRP3 498 " --> pdb=" O ARGP3 494 " (cutoff:3.500A) Processing helix chain 'P3' and resid 516 through 523 Processing sheet with id=AA1, first strand: chain 'B1' and resid 103 through 106 Processing sheet with id=AA2, first strand: chain 'B1' and resid 139 through 140 removed outlier: 3.668A pdb=" N ALAP3 538 " --> pdb=" O GLUB1 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B1' and resid 193 through 194 removed outlier: 3.743A pdb=" N THRB1 362 " --> pdb=" O ASPB1 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B1' and resid 216 through 220 removed outlier: 4.349A pdb=" N ALAB1 209 " --> pdb=" O ILEB1 220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B1' and resid 301 through 305 removed outlier: 4.424A pdb=" N TYRB1 294 " --> pdb=" O LEUB1 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B1' and resid 445 through 448 removed outlier: 4.568A pdb=" N LEUB1 436 " --> pdb=" O VALB1 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B1' and resid 500 through 501 Processing sheet with id=AA8, first strand: chain 'B2' and resid 103 through 106 removed outlier: 6.872A pdb=" N ILEB2 87 " --> pdb=" O HISB2 124 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VALB2 126 " --> pdb=" O ILEB2 87 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ALAB2 89 " --> pdb=" O VALB2 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B2' and resid 139 through 140 Processing sheet with id=AB1, first strand: chain 'B2' and resid 193 through 194 removed outlier: 3.520A pdb=" N THRB2 362 " --> pdb=" O ASPB2 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B2' and resid 216 through 220 removed outlier: 4.135A pdb=" N ALAB2 209 " --> pdb=" O ILEB2 220 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B2' and resid 302 through 305 removed outlier: 4.383A pdb=" N TYRB2 294 " --> pdb=" O LEUB2 305 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VALB2 282 " --> pdb=" O LEUB2 325 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B2' and resid 445 through 448 removed outlier: 4.309A pdb=" N LEUB2 436 " --> pdb=" O VALB2 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B2' and resid 500 through 501 Processing sheet with id=AB6, first strand: chain 'B3' and resid 103 through 106 removed outlier: 6.929A pdb=" N ILEB3 87 " --> pdb=" O HISB3 124 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VALB3 126 " --> pdb=" O ILEB3 87 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALAB3 89 " --> pdb=" O VALB3 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B3' and resid 139 through 140 removed outlier: 3.520A pdb=" N LEUB3 139 " --> pdb=" O HISB3 490 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B3' and resid 193 through 194 Processing sheet with id=AB9, first strand: chain 'B3' and resid 216 through 220 removed outlier: 4.277A pdb=" N ALAB3 209 " --> pdb=" O ILEB3 220 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B3' and resid 301 through 305 removed outlier: 4.481A pdb=" N TYRB3 294 " --> pdb=" O LEUB3 305 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B3' and resid 445 through 448 removed outlier: 4.602A pdb=" N LEUB3 436 " --> pdb=" O VALB3 448 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B3' and resid 500 through 501 removed outlier: 3.531A pdb=" N LEUB6 139 " --> pdb=" O HISB6 490 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B4' and resid 103 through 106 Processing sheet with id=AC5, first strand: chain 'B4' and resid 193 through 194 removed outlier: 3.517A pdb=" N SERB4 361 " --> pdb=" O GLYB4 382 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B4' and resid 216 through 220 removed outlier: 4.091A pdb=" N ALAB4 209 " --> pdb=" O ILEB4 220 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B4' and resid 302 through 305 removed outlier: 4.477A pdb=" N TYRB4 294 " --> pdb=" O LEUB4 305 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B4' and resid 445 through 447 Processing sheet with id=AC9, first strand: chain 'B5' and resid 103 through 106 removed outlier: 6.786A pdb=" N ILEB5 87 " --> pdb=" O HISB5 124 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VALB5 126 " --> pdb=" O ILEB5 87 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ALAB5 89 " --> pdb=" O VALB5 126 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B5' and resid 193 through 194 Processing sheet with id=AD2, first strand: chain 'B5' and resid 216 through 220 removed outlier: 4.355A pdb=" N ALAB5 209 " --> pdb=" O ILEB5 220 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALAB5 200 " --> pdb=" O GLUB5 352 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B5' and resid 301 through 305 removed outlier: 4.514A pdb=" N TYRB5 294 " --> pdb=" O LEUB5 305 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B5' and resid 445 through 447 Processing sheet with id=AD5, first strand: chain 'B6' and resid 103 through 106 Processing sheet with id=AD6, first strand: chain 'B6' and resid 193 through 194 Processing sheet with id=AD7, first strand: chain 'B6' and resid 216 through 220 removed outlier: 4.191A pdb=" N ALAB6 209 " --> pdb=" O ILEB6 220 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B6' and resid 302 through 305 removed outlier: 4.475A pdb=" N TYRB6 294 " --> pdb=" O LEUB6 305 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B6' and resid 445 through 448 removed outlier: 4.680A pdb=" N LEUB6 436 " --> pdb=" O VALB6 448 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P1' and resid 62 through 64 Processing sheet with id=AE2, first strand: chain 'P1' and resid 71 through 72 Processing sheet with id=AE3, first strand: chain 'P1' and resid 121 through 126 removed outlier: 7.055A pdb=" N ARGP1 282 " --> pdb=" O GLYP1 124 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASPP1 126 " --> pdb=" O ARGP1 282 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P1' and resid 333 through 336 Processing sheet with id=AE5, first strand: chain 'P1' and resid 440 through 441 removed outlier: 3.714A pdb=" N GLYP1 440 " --> pdb=" O ILEP1 449 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P2' and resid 62 through 64 Processing sheet with id=AE7, first strand: chain 'P2' and resid 71 through 72 Processing sheet with id=AE8, first strand: chain 'P2' and resid 121 through 126 removed outlier: 6.874A pdb=" N ILEP2 122 " --> pdb=" O SERP2 280 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ARGP2 282 " --> pdb=" O ILEP2 122 " (cutoff:3.500A) removed outlier: 9.360A pdb=" N GLYP2 124 " --> pdb=" O ARGP2 282 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VALP2 326 " --> pdb=" O LYSP2 104 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P2' and resid 333 through 336 Processing sheet with id=AF1, first strand: chain 'P2' and resid 440 through 441 removed outlier: 3.659A pdb=" N GLYP2 440 " --> pdb=" O ILEP2 449 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P3' and resid 62 through 64 Processing sheet with id=AF3, first strand: chain 'P3' and resid 71 through 72 Processing sheet with id=AF4, first strand: chain 'P3' and resid 121 through 126 removed outlier: 6.818A pdb=" N ILEP3 122 " --> pdb=" O SERP3 280 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N ARGP3 282 " --> pdb=" O ILEP3 122 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N GLYP3 124 " --> pdb=" O ARGP3 282 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYSP3 104 " --> pdb=" O VALP3 326 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASNP3 328 " --> pdb=" O LYSP3 104 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALAP3 106 " --> pdb=" O ASNP3 328 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILEP3 327 " --> pdb=" O VALP3 362 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ALAP3 364 " --> pdb=" O ILEP3 327 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILEP3 329 " --> pdb=" O ALAP3 364 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILEP3 361 " --> pdb=" O LEUP3 407 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VALP3 409 " --> pdb=" O ILEP3 361 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ALAP3 363 " --> pdb=" O VALP3 409 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N ALAP3 411 " --> pdb=" O ALAP3 363 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P3' and resid 333 through 336 removed outlier: 3.693A pdb=" N METP3 333 " --> pdb=" O THRP3 398 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P3' and resid 440 through 441 removed outlier: 3.722A pdb=" N GLYP3 440 " --> pdb=" O ILEP3 449 " (cutoff:3.500A) 885 hydrogen bonds defined for protein. 2349 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: 17.69 Time building geometry restraints manager: 33.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 27361 1.03 - 1.23: 459 1.23 - 1.43: 11188 1.43 - 1.62: 16876 1.62 - 1.82: 150 Bond restraints: 56034 Sorted by residual: bond pdb=" CZ ARGB2 103 " pdb=" NH2 ARGB2 103 " ideal model delta sigma weight residual 1.330 1.224 0.106 1.30e-02 5.92e+03 6.62e+01 bond pdb=" CA ALAP3 538 " pdb=" CB ALAP3 538 " ideal model delta sigma weight residual 1.537 1.426 0.111 1.38e-02 5.25e+03 6.47e+01 bond pdb=" CZ ARGB1 103 " pdb=" NH2 ARGB1 103 " ideal model delta sigma weight residual 1.330 1.226 0.104 1.30e-02 5.92e+03 6.40e+01 bond pdb=" CZ ARGB2 483 " pdb=" NH2 ARGB2 483 " ideal model delta sigma weight residual 1.330 1.230 0.100 1.30e-02 5.92e+03 5.87e+01 bond pdb=" N GLUB2 489 " pdb=" H GLUB2 489 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 56029 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.47: 2222 106.47 - 113.58: 68204 113.58 - 120.69: 16779 120.69 - 127.80: 14315 127.80 - 134.90: 555 Bond angle restraints: 102075 Sorted by residual: angle pdb=" C LEUP2 540 " pdb=" N VALP2 541 " pdb=" CA VALP2 541 " ideal model delta sigma weight residual 122.22 130.82 -8.60 1.15e+00 7.56e-01 5.59e+01 angle pdb=" N VALP3 542 " pdb=" CA VALP3 542 " pdb=" CB VALP3 542 " ideal model delta sigma weight residual 110.08 116.55 -6.47 9.30e-01 1.16e+00 4.83e+01 angle pdb=" C VALB2 488 " pdb=" N GLUB2 489 " pdb=" CA GLUB2 489 " ideal model delta sigma weight residual 122.93 132.93 -10.00 1.45e+00 4.76e-01 4.75e+01 angle pdb=" C ARGB3 99 " pdb=" N VALB3 100 " pdb=" CA VALB3 100 " ideal model delta sigma weight residual 123.17 131.59 -8.42 1.28e+00 6.10e-01 4.32e+01 angle pdb=" C PROP3 539 " pdb=" N LEUP3 540 " pdb=" CA LEUP3 540 " ideal model delta sigma weight residual 121.72 131.15 -9.43 1.45e+00 4.76e-01 4.23e+01 ... (remaining 102070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 23889 17.60 - 35.20: 1271 35.20 - 52.79: 327 52.79 - 70.39: 515 70.39 - 87.99: 35 Dihedral angle restraints: 26037 sinusoidal: 14343 harmonic: 11694 Sorted by residual: dihedral pdb=" C VALP2 541 " pdb=" N VALP2 541 " pdb=" CA VALP2 541 " pdb=" CB VALP2 541 " ideal model delta harmonic sigma weight residual -122.00 -134.84 12.84 0 2.50e+00 1.60e-01 2.64e+01 dihedral pdb=" N VALP2 541 " pdb=" C VALP2 541 " pdb=" CA VALP2 541 " pdb=" CB VALP2 541 " ideal model delta harmonic sigma weight residual 123.40 135.86 -12.46 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" C LEUB2 487 " pdb=" N LEUB2 487 " pdb=" CA LEUB2 487 " pdb=" CB LEUB2 487 " ideal model delta harmonic sigma weight residual -122.60 -134.56 11.96 0 2.50e+00 1.60e-01 2.29e+01 ... (remaining 26034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 4429 0.144 - 0.287: 43 0.287 - 0.431: 21 0.431 - 0.574: 17 0.574 - 0.718: 17 Chirality restraints: 4527 Sorted by residual: chirality pdb=" CG LEUB2 487 " pdb=" CB LEUB2 487 " pdb=" CD1 LEUB2 487 " pdb=" CD2 LEUB2 487 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CB VALB3 100 " pdb=" CA VALB3 100 " pdb=" CG1 VALB3 100 " pdb=" CG2 VALB3 100 " both_signs ideal model delta sigma weight residual False -2.63 -1.92 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CB VALP2 541 " pdb=" CA VALP2 541 " pdb=" CG1 VALP2 541 " pdb=" CG2 VALP2 541 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.70 2.00e-01 2.50e+01 1.23e+01 ... (remaining 4524 not shown) Planarity restraints: 8484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARGB2 406 " -0.108 9.50e-02 1.11e+02 5.31e-02 3.56e+01 pdb=" NE ARGB2 406 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARGB2 406 " -0.094 2.00e-02 2.50e+03 pdb=" NH1 ARGB2 406 " 0.032 2.00e-02 2.50e+03 pdb=" NH2 ARGB2 406 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARGB2 406 " -0.015 2.00e-02 2.50e+03 pdb="HH12 ARGB2 406 " 0.012 2.00e-02 2.50e+03 pdb="HH21 ARGB2 406 " -0.005 2.00e-02 2.50e+03 pdb="HH22 ARGB2 406 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGB2 192 " 0.199 9.50e-02 1.11e+02 7.50e-02 3.21e+01 pdb=" NE ARGB2 192 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARGB2 192 " -0.034 2.00e-02 2.50e+03 pdb=" NH1 ARGB2 192 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARGB2 192 " 0.074 2.00e-02 2.50e+03 pdb="HH11 ARGB2 192 " 0.030 2.00e-02 2.50e+03 pdb="HH12 ARGB2 192 " -0.027 2.00e-02 2.50e+03 pdb="HH21 ARGB2 192 " 0.005 2.00e-02 2.50e+03 pdb="HH22 ARGB2 192 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGB3 192 " -0.208 9.50e-02 1.11e+02 7.54e-02 2.44e+01 pdb=" NE ARGB3 192 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ARGB3 192 " 0.066 2.00e-02 2.50e+03 pdb=" NH1 ARGB3 192 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARGB3 192 " -0.024 2.00e-02 2.50e+03 pdb="HH11 ARGB3 192 " -0.031 2.00e-02 2.50e+03 pdb="HH12 ARGB3 192 " 0.035 2.00e-02 2.50e+03 pdb="HH21 ARGB3 192 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARGB3 192 " -0.018 2.00e-02 2.50e+03 ... (remaining 8481 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.04: 612 2.04 - 2.68: 81603 2.68 - 3.32: 148581 3.32 - 3.96: 184690 3.96 - 4.60: 294574 Nonbonded interactions: 710060 Sorted by model distance: nonbonded pdb=" HG1 THRP2 113 " pdb=" OD1 ASPP2 137 " model vdw 1.406 1.850 nonbonded pdb=" O LEUB6 259 " pdb=" HH TYRB6 346 " model vdw 1.498 1.850 nonbonded pdb=" O LEUB4 259 " pdb=" HH TYRB4 346 " model vdw 1.502 1.850 nonbonded pdb=" O LEUB5 259 " pdb=" HH TYRB5 346 " model vdw 1.525 1.850 nonbonded pdb=" HG SERP2 336 " pdb=" OD1 ASNP3 457 " model vdw 1.595 1.850 ... (remaining 710055 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 'B1' and resid 74 through 496) selection = (chain 'B2' and resid 74 through 496) selection = (chain 'B3' and resid 74 through 496) selection = (chain 'B4' and (resid 74 through 316 or resid 319 through 424 or resid 433 thro \ ugh 496)) selection = (chain 'B5' and (resid 74 through 316 or resid 319 through 424 or resid 433 thro \ ugh 496)) selection = (chain 'B6' and (resid 74 through 316 or resid 319 through 424 or resid 433 thro \ ugh 496)) } ncs_group { reference = chain 'P1' selection = chain 'P2' selection = chain 'P3' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 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: 0.640 Extract box with map and model: 5.300 Check model and map are aligned: 0.630 Set scattering table: 0.360 Process input model: 129.050 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.190 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:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 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 : 0.010 0.134 28353 Z= 0.664 Angle : 1.146 12.994 38931 Z= 0.685 Chirality : 0.078 0.718 4527 Planarity : 0.007 0.127 5181 Dihedral : 11.025 87.991 10410 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.74 % 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: -1.44 (0.12), residues: 3684 helix: -1.98 (0.15), residues: 720 sheet: 0.26 (0.19), residues: 618 loop : -0.96 (0.11), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.005 TRPB5 437 HIS 0.036 0.004 HISP1 141 PHE 0.022 0.003 PHEB3 420 TYR 0.050 0.006 TYRB4 412 ARG 0.093 0.008 ARGB2 406 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 3.532 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 outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.8257 time to fit residues: 519.0081 Evaluate side-chains 190 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 3.190 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 0.0470 chunk 279 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 chunk 149 optimal weight: 0.1980 chunk 289 optimal weight: 0.4980 chunk 111 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 335 optimal weight: 2.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 339 ASN B4 130 GLN ** B6 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1 391 ASN P1 450 ASN P2 391 ASN P3 391 ASN P3 450 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28353 Z= 0.181 Angle : 0.613 8.107 38931 Z= 0.314 Chirality : 0.046 0.173 4527 Planarity : 0.006 0.053 5181 Dihedral : 4.246 24.210 3975 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.50 % Allowed : 5.00 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 3684 helix: -0.69 (0.18), residues: 702 sheet: 0.60 (0.20), residues: 594 loop : -0.58 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPB2 364 HIS 0.014 0.001 HISB6 359 PHE 0.009 0.001 PHEB6 420 TYR 0.012 0.001 TYRB3 205 ARG 0.006 0.001 ARGB3 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 223 time to evaluate : 3.225 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 outliers start: 15 outliers final: 11 residues processed: 236 average time/residue: 0.7487 time to fit residues: 283.9801 Evaluate side-chains 197 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 186 time to evaluate : 3.210 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4914 time to fit residues: 14.0419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 186 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 278 optimal weight: 0.2980 chunk 228 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 335 optimal weight: 0.9990 chunk 362 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 chunk 332 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 269 optimal weight: 7.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1 359 HIS ** B6 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 28353 Z= 0.177 Angle : 0.545 10.614 38931 Z= 0.266 Chirality : 0.045 0.179 4527 Planarity : 0.005 0.054 5181 Dihedral : 4.000 19.814 3975 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.30 % Allowed : 5.86 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.13), residues: 3684 helix: -0.11 (0.20), residues: 702 sheet: 0.74 (0.20), residues: 606 loop : -0.48 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPB1 366 HIS 0.005 0.001 HISB6 359 PHE 0.010 0.001 PHEP1 467 TYR 0.008 0.001 TYRB3 205 ARG 0.006 0.000 ARGB3 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 196 time to evaluate : 3.256 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 outliers start: 9 outliers final: 8 residues processed: 200 average time/residue: 0.7253 time to fit residues: 236.2058 Evaluate side-chains 182 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 3.257 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5643 time to fit residues: 11.8420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 331 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 174 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 225 optimal weight: 9.9990 chunk 336 optimal weight: 4.9990 chunk 356 optimal weight: 0.0270 chunk 176 optimal weight: 5.9990 chunk 319 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 overall best weight: 2.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3 287 GLN ** B6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 28353 Z= 0.215 Angle : 0.528 10.709 38931 Z= 0.257 Chirality : 0.045 0.175 4527 Planarity : 0.005 0.062 5181 Dihedral : 3.999 19.680 3975 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.17 % Allowed : 6.23 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 3684 helix: 0.04 (0.20), residues: 705 sheet: 0.67 (0.20), residues: 612 loop : -0.50 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPB5 366 HIS 0.007 0.001 HISB6 359 PHE 0.010 0.001 PHEP1 467 TYR 0.009 0.001 TYRP2 85 ARG 0.004 0.000 ARGB3 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 184 time to evaluate : 3.883 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 outliers start: 5 outliers final: 3 residues processed: 186 average time/residue: 0.7362 time to fit residues: 220.8498 Evaluate side-chains 168 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 3.287 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4681 time to fit residues: 6.6124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 297 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 265 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 320 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 28353 Z= 0.261 Angle : 0.537 10.736 38931 Z= 0.262 Chirality : 0.045 0.186 4527 Planarity : 0.005 0.064 5181 Dihedral : 4.064 20.278 3975 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.23 % Allowed : 6.76 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 3684 helix: 0.00 (0.20), residues: 723 sheet: 0.68 (0.20), residues: 600 loop : -0.59 (0.12), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPB4 366 HIS 0.004 0.001 HISB2 417 PHE 0.012 0.001 PHEB1 272 TYR 0.015 0.001 TYRP1 127 ARG 0.005 0.000 ARGB3 374 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 174 time to evaluate : 3.427 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 outliers start: 7 outliers final: 7 residues processed: 174 average time/residue: 0.7640 time to fit residues: 214.9932 Evaluate side-chains 170 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 163 time to evaluate : 3.275 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5420 time to fit residues: 11.0582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 120 optimal weight: 0.7980 chunk 321 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 357 optimal weight: 2.9990 chunk 296 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28353 Z= 0.272 Angle : 0.540 10.776 38931 Z= 0.263 Chirality : 0.046 0.183 4527 Planarity : 0.005 0.046 5181 Dihedral : 4.120 20.656 3975 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.20 % Allowed : 6.93 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.13), residues: 3684 helix: 0.07 (0.20), residues: 726 sheet: 0.44 (0.20), residues: 627 loop : -0.63 (0.12), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPB5 364 HIS 0.005 0.001 HISB6 359 PHE 0.010 0.001 PHEP3 467 TYR 0.014 0.001 TYRP1 127 ARG 0.003 0.000 ARGB2 374 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 165 time to evaluate : 3.231 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 outliers start: 6 outliers final: 5 residues processed: 167 average time/residue: 0.7134 time to fit residues: 195.0691 Evaluate side-chains 165 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 160 time to evaluate : 3.217 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5785 time to fit residues: 8.9842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 344 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 202 optimal weight: 0.6980 chunk 300 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 355 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P3 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 28353 Z= 0.328 Angle : 0.556 10.734 38931 Z= 0.274 Chirality : 0.046 0.189 4527 Planarity : 0.005 0.051 5181 Dihedral : 4.257 22.451 3975 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.20 % Allowed : 7.39 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 3684 helix: -0.04 (0.19), residues: 729 sheet: 0.39 (0.20), residues: 609 loop : -0.76 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPB4 366 HIS 0.006 0.001 HISB2 417 PHE 0.012 0.001 PHEP3 467 TYR 0.014 0.001 TYRP1 127 ARG 0.004 0.000 ARGB3 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 159 time to evaluate : 3.282 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 outliers start: 6 outliers final: 4 residues processed: 164 average time/residue: 0.7678 time to fit residues: 202.7395 Evaluate side-chains 158 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 3.219 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5131 time to fit residues: 7.6930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 220 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 226 optimal weight: 7.9990 chunk 242 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 279 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 28353 Z= 0.379 Angle : 0.576 10.746 38931 Z= 0.286 Chirality : 0.047 0.190 4527 Planarity : 0.005 0.054 5181 Dihedral : 4.408 22.386 3975 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.20 % Allowed : 7.65 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 3684 helix: -0.18 (0.19), residues: 735 sheet: 0.29 (0.21), residues: 591 loop : -0.90 (0.12), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPB4 366 HIS 0.005 0.001 HISB2 417 PHE 0.012 0.001 PHEP3 467 TYR 0.012 0.001 TYRB5 412 ARG 0.005 0.000 ARGB5 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 3.290 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 outliers start: 6 outliers final: 5 residues processed: 157 average time/residue: 0.7745 time to fit residues: 195.3664 Evaluate side-chains 154 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 3.261 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5210 time to fit residues: 8.6940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 323 optimal weight: 3.9990 chunk 340 optimal weight: 1.9990 chunk 310 optimal weight: 8.9990 chunk 331 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 299 optimal weight: 0.0470 chunk 313 optimal weight: 2.9990 chunk 330 optimal weight: 5.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28353 Z= 0.184 Angle : 0.522 10.868 38931 Z= 0.253 Chirality : 0.045 0.176 4527 Planarity : 0.005 0.049 5181 Dihedral : 4.146 20.711 3975 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.13), residues: 3684 helix: 0.25 (0.20), residues: 699 sheet: 0.50 (0.21), residues: 591 loop : -0.73 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPB1 366 HIS 0.004 0.001 HISB2 490 PHE 0.009 0.001 PHEP1 288 TYR 0.009 0.001 TYRP1 294 ARG 0.005 0.000 ARGB3 374 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 3.842 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 outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.7897 time to fit residues: 206.4011 Evaluate side-chains 158 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 3.325 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 217 optimal weight: 3.9990 chunk 350 optimal weight: 4.9990 chunk 213 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 367 optimal weight: 4.9990 chunk 338 optimal weight: 4.9990 chunk 292 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 226 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 28353 Z= 0.266 Angle : 0.535 10.653 38931 Z= 0.260 Chirality : 0.045 0.180 4527 Planarity : 0.005 0.050 5181 Dihedral : 4.153 20.673 3975 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.03 % Allowed : 8.15 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.13), residues: 3684 helix: 0.09 (0.19), residues: 735 sheet: 0.47 (0.21), residues: 591 loop : -0.77 (0.12), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPB5 366 HIS 0.003 0.001 HISB2 417 PHE 0.019 0.001 PHEB1 272 TYR 0.014 0.001 TYRP1 127 ARG 0.004 0.000 ARGB3 374 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 3.288 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 outliers start: 1 outliers final: 1 residues processed: 164 average time/residue: 0.8135 time to fit residues: 217.3956 Evaluate side-chains 160 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 3.298 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5061 time to fit residues: 5.2313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 232 optimal weight: 1.9990 chunk 311 optimal weight: 8.9990 chunk 89 optimal weight: 0.5980 chunk 269 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 293 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 301 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B6 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.084487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.062823 restraints weight = 195889.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.066012 restraints weight = 83540.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.068140 restraints weight = 49361.434| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 28353 Z= 0.149 Angle : 0.507 10.688 38931 Z= 0.241 Chirality : 0.045 0.169 4527 Planarity : 0.005 0.046 5181 Dihedral : 3.886 18.690 3975 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.07 % Allowed : 8.18 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3684 helix: 0.58 (0.21), residues: 681 sheet: 0.52 (0.20), residues: 612 loop : -0.60 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPB5 366 HIS 0.004 0.001 HISB2 490 PHE 0.019 0.001 PHEB1 272 TYR 0.009 0.001 TYRP1 127 ARG 0.004 0.000 ARGB3 374 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6721.39 seconds wall clock time: 118 minutes 0.37 seconds (7080.37 seconds total)