Starting phenix.real_space_refine on Tue Feb 13 17:43:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yo0_10862/02_2024/6yo0_10862_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yo0_10862/02_2024/6yo0_10862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yo0_10862/02_2024/6yo0_10862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yo0_10862/02_2024/6yo0_10862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yo0_10862/02_2024/6yo0_10862_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yo0_10862/02_2024/6yo0_10862_trim_updated.pdb" } resolution = 2.9 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 101 5.16 5 C 17412 2.51 5 N 4798 2.21 5 O 5349 1.98 5 H 28102 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G1 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G1 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G1 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G1 TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G1 ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G1 ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G1 GLU 154": "OE1" <-> "OE2" Residue "G1 TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G1 ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 GLU 132": "OE1" <-> "OE2" Residue "C1 ARG 174": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 GLU 196": "OE1" <-> "OE2" Residue "C1 TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 ARG 393": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 ARG 454": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C1 ARG 504": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 ARG 513": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C1 PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 GLU 86": "OE1" <-> "OE2" Residue "D1 ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 ARG 167": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 ARG 250": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 ARG 391": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D1 PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D1 ARG 490": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B1 TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B1 GLU 115": "OE1" <-> "OE2" Residue "B1 GLU 132": "OE1" <-> "OE2" Residue "B1 PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 ARG 174": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B1 GLU 196": "OE1" <-> "OE2" Residue "B1 PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 ASP 442": "OD1" <-> "OD2" Residue "B1 ARG 454": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B1 TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B1 ARG 513": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B1 ARG 515": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F1 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F1 ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F1 ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F1 ARG 167": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F1 PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F1 GLU 187": "OE1" <-> "OE2" Residue "F1 PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F1 ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F1 ARG 250": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F1 PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F1 GLU 265": "OE1" <-> "OE2" Residue "F1 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F1 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F1 PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F1 ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F1 ARG 375": not complete - not flipped Residue "F1 TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F1 ARG 425": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F1 PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F1 PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F1 PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F1 TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F1 PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F1 ARG 490": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A1 TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A1 ARG 91": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A1 PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A1 TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A1 PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A1 PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A1 TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A1 TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A1 PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A1 GLU 338": "OE1" <-> "OE2" Residue "A1 ARG 339": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A1 PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A1 PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A1 TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A1 ARG 454": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A1 GLU 457": "OE1" <-> "OE2" Residue "A1 TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A1 GLU 470": "OE1" <-> "OE2" Residue "A1 ARG 504": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A1 ARG 513": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A1 ARG 515": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A1 PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E1 GLU 86": "OE1" <-> "OE2" Residue "E1 ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E1 ARG 167": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E1 GLU 187": "OE1" <-> "OE2" Residue "E1 PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E1 ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E1 ARG 250": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E1 PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E1 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E1 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E1 PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E1 ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E1 PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E1 PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E1 PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E1 GLU 483": "OE1" <-> "OE2" Residue "E1 ARG 490": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "s TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 286": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 350": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 54": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 55780 Number of models: 1 Model: "" Number of chains: 17 Chain: "G1" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 3000 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain: "g1" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1420 Classifications: {'peptide': 90} Link IDs: {'TRANS': 89} Chain breaks: 1 Chain: "C1" Number of atoms: 7980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 7980 Classifications: {'peptide': 513} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 495} Chain: "D1" Number of atoms: 7135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 7135 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "B1" Number of atoms: 7934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 7934 Classifications: {'peptide': 511} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 493} Chain: "F1" Number of atoms: 7112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7112 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 23, 'TRANS': 445} Chain: "A1" Number of atoms: 7946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 7946 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 494} Chain: "E1" Number of atoms: 7135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 7135 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "i1" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 638 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "s" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 486 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "b" Number of atoms: 3227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 3227 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 3, 'TRANS': 201} Chain breaks: 1 Chain: "d" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1615 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "C1" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B1" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A1" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.13, per 1000 atoms: 0.33 Number of scatterers: 55780 At special positions: 0 Unit cell: (135.29, 157.7, 148.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 101 16.00 P 13 15.00 Mg 5 11.99 O 5349 8.00 N 4798 7.00 C 17412 6.00 H 28102 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 36.72 Conformation dependent library (CDL) restraints added in 5.6 seconds 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 23 sheets defined 45.4% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.49 Creating SS restraints... Processing helix chain 'G1' and resid 43 through 57 Processing helix chain 'G1' and resid 62 through 77 Processing helix chain 'G1' and resid 79 through 86 Processing helix chain 'G1' and resid 92 through 102 Processing helix chain 'G1' and resid 109 through 120 Processing helix chain 'G1' and resid 124 through 141 Proline residue: G1 128 - end of helix Processing helix chain 'G1' and resid 157 through 171 Processing helix chain 'G1' and resid 203 through 215 Processing helix chain 'g1' and resid 26 through 60 Processing helix chain 'g1' and resid 248 through 297 Processing helix chain 'C1' and resid 40 through 48 Processing helix chain 'C1' and resid 182 through 187 Processing helix chain 'C1' and resid 206 through 223 removed outlier: 3.948A pdb=" N LYSC1 218 " --> pdb=" O ILEC1 214 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLUC1 219 " --> pdb=" O LEUC1 215 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ALAC1 220 " --> pdb=" O ASNC1 216 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHEC1 221 " --> pdb=" O GLNC1 217 " (cutoff:3.500A) Processing helix chain 'C1' and resid 241 through 253 Processing helix chain 'C1' and resid 271 through 290 Proline residue: C1 278 - end of helix removed outlier: 4.018A pdb=" N PHEC1 288 " --> pdb=" O ILEC1 284 " (cutoff:3.500A) Processing helix chain 'C1' and resid 302 through 315 Processing helix chain 'C1' and resid 322 through 324 No H-bonds generated for 'chain 'C1' and resid 322 through 324' Processing helix chain 'C1' and resid 329 through 339 removed outlier: 3.871A pdb=" N LEUC1 336 " --> pdb=" O LEUC1 332 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARGC1 339 " --> pdb=" O ARGC1 335 " (cutoff:3.500A) Processing helix chain 'C1' and resid 368 through 376 Processing helix chain 'C1' and resid 385 through 389 Processing helix chain 'C1' and resid 406 through 408 No H-bonds generated for 'chain 'C1' and resid 406 through 408' Processing helix chain 'C1' and resid 412 through 434 removed outlier: 4.417A pdb=" N LYSC1 416 " --> pdb=" O LYSC1 412 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILEC1 417 " --> pdb=" O ALAC1 413 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASNC1 420 " --> pdb=" O LYSC1 416 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALAC1 433 " --> pdb=" O ARGC1 429 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N PHEC1 434 " --> pdb=" O GLUC1 430 " (cutoff:3.500A) Processing helix chain 'C1' and resid 446 through 459 Processing helix chain 'C1' and resid 469 through 481 Processing helix chain 'C1' and resid 483 through 485 No H-bonds generated for 'chain 'C1' and resid 483 through 485' Processing helix chain 'C1' and resid 489 through 505 removed outlier: 4.782A pdb=" N LEUC1 493 " --> pdb=" O SERC1 490 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARGC1 504 " --> pdb=" O GLUC1 501 " (cutoff:3.500A) Processing helix chain 'C1' and resid 508 through 517 Processing helix chain 'C1' and resid 522 through 538 Proline residue: C1 533 - end of helix Processing helix chain 'D1' and resid 107 through 109 No H-bonds generated for 'chain 'D1' and resid 107 through 109' Processing helix chain 'D1' and resid 157 through 162 Processing helix chain 'D1' and resid 181 through 192 Processing helix chain 'D1' and resid 209 through 221 Processing helix chain 'D1' and resid 251 through 264 Processing helix chain 'D1' and resid 278 through 291 removed outlier: 3.587A pdb=" N VALD1 287 " --> pdb=" O ALAD1 283 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALAD1 289 " --> pdb=" O SERD1 285 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEUD1 290 " --> pdb=" O GLUD1 286 " (cutoff:3.500A) Processing helix chain 'D1' and resid 304 through 312 removed outlier: 3.667A pdb=" N LEUD1 311 " --> pdb=" O ASPD1 307 " (cutoff:3.500A) Processing helix chain 'D1' and resid 332 through 334 No H-bonds generated for 'chain 'D1' and resid 332 through 334' Processing helix chain 'D1' and resid 339 through 347 removed outlier: 4.342A pdb=" N ALAD1 346 " --> pdb=" O ALAD1 342 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HISD1 347 " --> pdb=" O THRD1 343 " (cutoff:3.500A) Processing helix chain 'D1' and resid 356 through 361 Processing helix chain 'D1' and resid 384 through 410 removed outlier: 4.485A pdb=" N ASPD1 405 " --> pdb=" O LYSD1 401 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILED1 406 " --> pdb=" O SERD1 402 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILED1 409 " --> pdb=" O ASPD1 405 " (cutoff:3.500A) Processing helix chain 'D1' and resid 417 through 432 Processing helix chain 'D1' and resid 438 through 444 removed outlier: 4.843A pdb=" N VALD1 442 " --> pdb=" O METD1 439 " (cutoff:3.500A) Processing helix chain 'D1' and resid 453 through 464 Processing helix chain 'D1' and resid 473 through 475 No H-bonds generated for 'chain 'D1' and resid 473 through 475' Processing helix chain 'D1' and resid 482 through 495 Processing helix chain 'B1' and resid 36 through 49 removed outlier: 3.802A pdb=" N ALAB1 39 " --> pdb=" O THRB1 36 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYB1 49 " --> pdb=" O LYSB1 46 " (cutoff:3.500A) Processing helix chain 'B1' and resid 110 through 112 No H-bonds generated for 'chain 'B1' and resid 110 through 112' Processing helix chain 'B1' and resid 132 through 134 No H-bonds generated for 'chain 'B1' and resid 132 through 134' Processing helix chain 'B1' and resid 182 through 187 Processing helix chain 'B1' and resid 206 through 223 removed outlier: 4.155A pdb=" N ALAB1 210 " --> pdb=" O LYSB1 206 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYSB1 218 " --> pdb=" O ILEB1 214 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLUB1 219 " --> pdb=" O LEUB1 215 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ALAB1 220 " --> pdb=" O ASNB1 216 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHEB1 221 " --> pdb=" O GLNB1 217 " (cutoff:3.500A) Processing helix chain 'B1' and resid 241 through 253 Processing helix chain 'B1' and resid 271 through 290 Proline residue: B1 278 - end of helix removed outlier: 3.984A pdb=" N PHEB1 288 " --> pdb=" O ILEB1 284 " (cutoff:3.500A) Processing helix chain 'B1' and resid 302 through 316 Processing helix chain 'B1' and resid 322 through 324 No H-bonds generated for 'chain 'B1' and resid 322 through 324' Processing helix chain 'B1' and resid 329 through 339 removed outlier: 4.015A pdb=" N LEUB1 336 " --> pdb=" O LEUB1 332 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARGB1 339 " --> pdb=" O ARGB1 335 " (cutoff:3.500A) Processing helix chain 'B1' and resid 368 through 376 Processing helix chain 'B1' and resid 385 through 389 Processing helix chain 'B1' and resid 406 through 408 No H-bonds generated for 'chain 'B1' and resid 406 through 408' Processing helix chain 'B1' and resid 412 through 437 removed outlier: 4.071A pdb=" N LYSB1 416 " --> pdb=" O LYSB1 412 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILEB1 417 " --> pdb=" O ALAB1 413 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASNB1 420 " --> pdb=" O LYSB1 416 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALAB1 433 " --> pdb=" O ARGB1 429 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHEB1 434 " --> pdb=" O GLUB1 430 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SERB1 435 " --> pdb=" O LEUB1 431 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLNB1 436 " --> pdb=" O ALAB1 432 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHEB1 437 " --> pdb=" O ALAB1 433 " (cutoff:3.500A) Processing helix chain 'B1' and resid 446 through 459 Processing helix chain 'B1' and resid 469 through 480 Processing helix chain 'B1' and resid 483 through 485 No H-bonds generated for 'chain 'B1' and resid 483 through 485' Processing helix chain 'B1' and resid 489 through 506 removed outlier: 5.014A pdb=" N LEUB1 493 " --> pdb=" O SERB1 490 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARGB1 504 " --> pdb=" O GLUB1 501 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASNB1 506 " --> pdb=" O VALB1 503 " (cutoff:3.500A) Processing helix chain 'B1' and resid 508 through 517 Processing helix chain 'B1' and resid 522 through 538 Proline residue: B1 533 - end of helix Processing helix chain 'F1' and resid 107 through 109 No H-bonds generated for 'chain 'F1' and resid 107 through 109' Processing helix chain 'F1' and resid 157 through 162 Processing helix chain 'F1' and resid 181 through 194 Processing helix chain 'F1' and resid 209 through 218 Processing helix chain 'F1' and resid 247 through 264 removed outlier: 4.660A pdb=" N GLYF1 252 " --> pdb=" O ARGF1 248 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEUF1 253 " --> pdb=" O ALAF1 249 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHEF1 262 " --> pdb=" O VALF1 258 " (cutoff:3.500A) Processing helix chain 'F1' and resid 277 through 291 Processing helix chain 'F1' and resid 304 through 314 removed outlier: 4.079A pdb=" N LEUF1 311 " --> pdb=" O ASPF1 307 " (cutoff:3.500A) Processing helix chain 'F1' and resid 332 through 334 No H-bonds generated for 'chain 'F1' and resid 332 through 334' Processing helix chain 'F1' and resid 339 through 345 Processing helix chain 'F1' and resid 356 through 360 Processing helix chain 'F1' and resid 384 through 407 Processing helix chain 'F1' and resid 417 through 432 Processing helix chain 'F1' and resid 441 through 444 No H-bonds generated for 'chain 'F1' and resid 441 through 444' Processing helix chain 'F1' and resid 453 through 465 Processing helix chain 'F1' and resid 473 through 475 No H-bonds generated for 'chain 'F1' and resid 473 through 475' Processing helix chain 'F1' and resid 482 through 495 Processing helix chain 'A1' and resid 36 through 48 Processing helix chain 'A1' and resid 182 through 187 Processing helix chain 'A1' and resid 206 through 222 removed outlier: 3.721A pdb=" N ALAA1 210 " --> pdb=" O LYSA1 206 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYSA1 218 " --> pdb=" O ILEA1 214 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLUA1 219 " --> pdb=" O LEUA1 215 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALAA1 220 " --> pdb=" O ASNA1 216 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHEA1 221 " --> pdb=" O GLNA1 217 " (cutoff:3.500A) Processing helix chain 'A1' and resid 226 through 228 No H-bonds generated for 'chain 'A1' and resid 226 through 228' Processing helix chain 'A1' and resid 241 through 253 Processing helix chain 'A1' and resid 271 through 290 Proline residue: A1 278 - end of helix removed outlier: 3.946A pdb=" N PHEA1 288 " --> pdb=" O ILEA1 284 " (cutoff:3.500A) Processing helix chain 'A1' and resid 302 through 314 Processing helix chain 'A1' and resid 322 through 324 No H-bonds generated for 'chain 'A1' and resid 322 through 324' Processing helix chain 'A1' and resid 329 through 339 removed outlier: 4.074A pdb=" N ARGA1 339 " --> pdb=" O ARGA1 335 " (cutoff:3.500A) Processing helix chain 'A1' and resid 345 through 347 No H-bonds generated for 'chain 'A1' and resid 345 through 347' Processing helix chain 'A1' and resid 368 through 376 Processing helix chain 'A1' and resid 385 through 389 Processing helix chain 'A1' and resid 406 through 408 No H-bonds generated for 'chain 'A1' and resid 406 through 408' Processing helix chain 'A1' and resid 412 through 438 removed outlier: 3.742A pdb=" N LYSA1 416 " --> pdb=" O LYSA1 412 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILEA1 417 " --> pdb=" O ALAA1 413 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASNA1 420 " --> pdb=" O LYSA1 416 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALAA1 433 " --> pdb=" O ARGA1 429 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N PHEA1 434 " --> pdb=" O GLUA1 430 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLNA1 436 " --> pdb=" O ALAA1 432 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHEA1 437 " --> pdb=" O ALAA1 433 " (cutoff:3.500A) Processing helix chain 'A1' and resid 443 through 459 Processing helix chain 'A1' and resid 469 through 480 Processing helix chain 'A1' and resid 483 through 485 No H-bonds generated for 'chain 'A1' and resid 483 through 485' Processing helix chain 'A1' and resid 489 through 506 removed outlier: 4.711A pdb=" N LEUA1 493 " --> pdb=" O SERA1 490 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASNA1 506 " --> pdb=" O VALA1 503 " (cutoff:3.500A) Processing helix chain 'A1' and resid 509 through 517 Processing helix chain 'A1' and resid 522 through 538 Proline residue: A1 533 - end of helix Processing helix chain 'E1' and resid 107 through 109 No H-bonds generated for 'chain 'E1' and resid 107 through 109' Processing helix chain 'E1' and resid 157 through 162 Processing helix chain 'E1' and resid 181 through 191 Processing helix chain 'E1' and resid 209 through 222 Processing helix chain 'E1' and resid 251 through 264 removed outlier: 3.665A pdb=" N PHEE1 262 " --> pdb=" O VALE1 258 " (cutoff:3.500A) Processing helix chain 'E1' and resid 278 through 291 removed outlier: 3.830A pdb=" N ALAE1 289 " --> pdb=" O SERE1 285 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEUE1 290 " --> pdb=" O GLUE1 286 " (cutoff:3.500A) Processing helix chain 'E1' and resid 304 through 312 Processing helix chain 'E1' and resid 332 through 334 No H-bonds generated for 'chain 'E1' and resid 332 through 334' Processing helix chain 'E1' and resid 339 through 347 removed outlier: 4.188A pdb=" N ALAE1 346 " --> pdb=" O ALAE1 342 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N HISE1 347 " --> pdb=" O THRE1 343 " (cutoff:3.500A) Processing helix chain 'E1' and resid 356 through 361 Processing helix chain 'E1' and resid 384 through 409 removed outlier: 3.614A pdb=" N LEUE1 403 " --> pdb=" O ASPE1 399 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASPE1 405 " --> pdb=" O LYSE1 401 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ILEE1 406 " --> pdb=" O SERE1 402 " (cutoff:3.500A) Processing helix chain 'E1' and resid 417 through 433 Processing helix chain 'E1' and resid 441 through 444 No H-bonds generated for 'chain 'E1' and resid 441 through 444' Processing helix chain 'E1' and resid 453 through 465 Processing helix chain 'E1' and resid 473 through 476 Processing helix chain 'E1' and resid 482 through 495 Processing helix chain 'i1' and resid 30 through 61 Processing helix chain 's' and resid 116 through 127 removed outlier: 3.595A pdb=" N TYR s 127 " --> pdb=" O ASP s 123 " (cutoff:3.500A) Processing helix chain 's' and resid 130 through 141 Processing helix chain 'b' and resid 28 through 59 removed outlier: 4.093A pdb=" N ALA b 46 " --> pdb=" O ALA b 42 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE b 47 " --> pdb=" O SER b 43 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN b 48 " --> pdb=" O VAL b 44 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN b 49 " --> pdb=" O ALA b 45 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG b 50 " --> pdb=" O ALA b 46 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE b 51 " --> pdb=" O PHE b 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 214 through 275 removed outlier: 3.614A pdb=" N LEU b 245 " --> pdb=" O ALA b 241 " (cutoff:3.500A) Processing helix chain 'b' and resid 281 through 296 Processing helix chain 'b' and resid 306 through 322 Processing helix chain 'b' and resid 326 through 332 removed outlier: 4.008A pdb=" N ALA b 331 " --> pdb=" O ALA b 327 " (cutoff:3.500A) Processing helix chain 'b' and resid 338 through 357 removed outlier: 3.681A pdb=" N ILE b 344 " --> pdb=" O GLN b 340 " (cutoff:3.500A) Processing helix chain 'b' and resid 370 through 377 Processing helix chain 'd' and resid 35 through 47 removed outlier: 3.789A pdb=" N ILE d 41 " --> pdb=" O ILE d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 68 Processing helix chain 'd' and resid 80 through 86 Processing helix chain 'd' and resid 92 through 105 Processing helix chain 'd' and resid 110 through 119 Processing helix chain 'd' and resid 123 through 130 Processing sheet with id= A, first strand: chain 'G1' and resid 177 through 181 Processing sheet with id= B, first strand: chain 'C1' and resid 59 through 61 removed outlier: 6.710A pdb=" N GLYC1 103 " --> pdb=" O LEUC1 95 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHEC1 73 " --> pdb=" O VALC1 62 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VALC1 62 " --> pdb=" O PHEC1 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C1' and resid 127 through 130 removed outlier: 4.401A pdb=" N GLNC1 156 " --> pdb=" O ILEC1 130 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C1' and resid 379 through 383 Processing sheet with id= E, first strand: chain 'C1' and resid 260 through 265 removed outlier: 8.668A pdb=" N ILEC1 261 " --> pdb=" O LEUC1 230 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYSC1 232 " --> pdb=" O ILEC1 261 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VALC1 263 " --> pdb=" O CYSC1 232 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYRC1 234 " --> pdb=" O VALC1 263 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ALAC1 265 " --> pdb=" O TYRC1 234 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALAC1 236 " --> pdb=" O ALAC1 265 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N HISC1 294 " --> pdb=" O TYRC1 231 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILEC1 233 " --> pdb=" O HISC1 294 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEUC1 296 " --> pdb=" O ILEC1 233 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VALC1 235 " --> pdb=" O LEUC1 296 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILEC1 298 " --> pdb=" O VALC1 235 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VALC1 237 " --> pdb=" O ILEC1 298 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASPC1 300 " --> pdb=" O VALC1 237 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N SERC1 351 " --> pdb=" O ALAC1 295 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILEC1 297 " --> pdb=" O SERC1 351 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THRC1 353 " --> pdb=" O ILEC1 297 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N TYRC1 299 " --> pdb=" O THRC1 353 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEUC1 355 " --> pdb=" O TYRC1 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'D1' and resid 31 through 36 removed outlier: 6.679A pdb=" N ASPD1 41 " --> pdb=" O SERD1 33 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VALD1 35 " --> pdb=" O VALD1 39 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VALD1 39 " --> pdb=" O VALD1 35 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILED1 80 " --> pdb=" O VALD1 68 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VALD1 68 " --> pdb=" O ILED1 80 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D1' and resid 102 through 104 Processing sheet with id= H, first strand: chain 'D1' and resid 350 through 353 removed outlier: 6.415A pdb=" N VALD1 270 " --> pdb=" O THRD1 324 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VALD1 326 " --> pdb=" O VALD1 270 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEUD1 272 " --> pdb=" O VALD1 326 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALAD1 328 " --> pdb=" O LEUD1 272 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VALD1 274 " --> pdb=" O ALAD1 328 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N TYRD1 330 " --> pdb=" O VALD1 274 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B1' and resid 59 through 61 Processing sheet with id= J, first strand: chain 'B1' and resid 69 through 73 removed outlier: 6.863A pdb=" N VALB1 105 " --> pdb=" O ALAB1 94 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ALAB1 94 " --> pdb=" O VALB1 105 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B1' and resid 127 through 130 removed outlier: 4.376A pdb=" N GLNB1 156 " --> pdb=" O ILEB1 130 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B1' and resid 379 through 383 Processing sheet with id= M, first strand: chain 'B1' and resid 260 through 265 removed outlier: 6.694A pdb=" N CYSB1 232 " --> pdb=" O ILEB1 261 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VALB1 263 " --> pdb=" O CYSB1 232 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYRB1 234 " --> pdb=" O VALB1 263 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ALAB1 265 " --> pdb=" O TYRB1 234 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALAB1 236 " --> pdb=" O ALAB1 265 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VALB1 237 " --> pdb=" O ASPB1 300 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SERB1 351 " --> pdb=" O ALAB1 295 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILEB1 297 " --> pdb=" O SERB1 351 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THRB1 353 " --> pdb=" O ILEB1 297 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N TYRB1 299 " --> pdb=" O THRB1 353 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEUB1 355 " --> pdb=" O TYRB1 299 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F1' and resid 30 through 36 removed outlier: 6.941A pdb=" N ASPF1 41 " --> pdb=" O SERF1 33 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VALF1 35 " --> pdb=" O VALF1 39 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VALF1 39 " --> pdb=" O VALF1 35 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILEF1 80 " --> pdb=" O VALF1 68 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VALF1 68 " --> pdb=" O ILEF1 80 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F1' and resid 102 through 105 removed outlier: 3.913A pdb=" N LYSF1 131 " --> pdb=" O VALF1 105 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F1' and resid 350 through 353 removed outlier: 3.624A pdb=" N ALAF1 350 " --> pdb=" O LYSF1 170 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILEF1 171 " --> pdb=" O ILEF1 323 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SERF1 325 " --> pdb=" O ILEF1 171 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEUF1 173 " --> pdb=" O SERF1 325 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLNF1 327 " --> pdb=" O LEUF1 173 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VALF1 270 " --> pdb=" O THRF1 324 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VALF1 326 " --> pdb=" O VALF1 270 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEUF1 272 " --> pdb=" O VALF1 326 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALAF1 328 " --> pdb=" O LEUF1 272 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VALF1 274 " --> pdb=" O ALAF1 328 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALAF1 235 " --> pdb=" O PHEF1 202 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N GLYF1 204 " --> pdb=" O ALAF1 235 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILEF1 237 " --> pdb=" O GLYF1 204 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N GLYF1 206 " --> pdb=" O ILEF1 237 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLYF1 239 " --> pdb=" O GLYF1 206 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A1' and resid 118 through 120 removed outlier: 6.561A pdb=" N ARGA1 71 " --> pdb=" O ILEA1 63 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILEA1 65 " --> pdb=" O ILEA1 69 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILEA1 69 " --> pdb=" O ILEA1 65 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VALA1 105 " --> pdb=" O ALAA1 94 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ALAA1 94 " --> pdb=" O VALA1 105 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A1' and resid 127 through 130 removed outlier: 4.087A pdb=" N GLNA1 156 " --> pdb=" O ILEA1 130 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A1' and resid 379 through 383 Processing sheet with id= T, first strand: chain 'A1' and resid 260 through 265 removed outlier: 6.697A pdb=" N CYSA1 232 " --> pdb=" O ILEA1 261 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VALA1 263 " --> pdb=" O CYSA1 232 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYRA1 234 " --> pdb=" O VALA1 263 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ALAA1 265 " --> pdb=" O TYRA1 234 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALAA1 236 " --> pdb=" O ALAA1 265 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SERA1 351 " --> pdb=" O ALAA1 295 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILEA1 297 " --> pdb=" O SERA1 351 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THRA1 353 " --> pdb=" O ILEA1 297 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYRA1 299 " --> pdb=" O THRA1 353 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E1' and resid 30 through 36 removed outlier: 6.714A pdb=" N ASPE1 41 " --> pdb=" O SERE1 33 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VALE1 35 " --> pdb=" O VALE1 39 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VALE1 39 " --> pdb=" O VALE1 35 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILEE1 80 " --> pdb=" O VALE1 68 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VALE1 68 " --> pdb=" O ILEE1 80 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E1' and resid 102 through 105 removed outlier: 4.233A pdb=" N LYSE1 131 " --> pdb=" O VALE1 105 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E1' and resid 350 through 353 removed outlier: 7.097A pdb=" N ILEE1 171 " --> pdb=" O ILEE1 323 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SERE1 325 " --> pdb=" O ILEE1 171 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEUE1 173 " --> pdb=" O SERE1 325 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLNE1 327 " --> pdb=" O LEUE1 173 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLYE1 175 " --> pdb=" O GLNE1 327 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILEE1 329 " --> pdb=" O GLYE1 175 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VALE1 270 " --> pdb=" O THRE1 324 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VALE1 326 " --> pdb=" O VALE1 270 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEUE1 272 " --> pdb=" O VALE1 326 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ALAE1 328 " --> pdb=" O LEUE1 272 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VALE1 274 " --> pdb=" O ALAE1 328 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N TYRE1 330 " --> pdb=" O VALE1 274 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N TYRE1 199 " --> pdb=" O LEUE1 271 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N PHEE1 273 " --> pdb=" O TYRE1 199 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VALE1 201 " --> pdb=" O PHEE1 273 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASPE1 275 " --> pdb=" O VALE1 201 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALAE1 203 " --> pdb=" O ASPE1 275 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALAE1 235 " --> pdb=" O PHEE1 202 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLYE1 204 " --> pdb=" O ALAE1 235 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILEE1 237 " --> pdb=" O GLYE1 204 " (cutoff:3.500A) 1195 hydrogen bonds defined for protein. 3369 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: 18.16 Time building geometry restraints manager: 38.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 28069 1.03 - 1.22: 35 1.22 - 1.42: 11145 1.42 - 1.61: 16731 1.61 - 1.81: 192 Bond restraints: 56172 Sorted by residual: bond pdb=" C3' ATPC1 900 " pdb=" C4' ATPC1 900 " ideal model delta sigma weight residual 1.526 1.281 0.245 1.10e-02 8.26e+03 4.95e+02 bond pdb=" C3' ATPB1 900 " pdb=" C4' ATPB1 900 " ideal model delta sigma weight residual 1.526 1.281 0.245 1.10e-02 8.26e+03 4.95e+02 bond pdb=" C1' ATPA1 900 " pdb=" C2' ATPA1 900 " ideal model delta sigma weight residual 1.531 1.266 0.265 1.20e-02 6.94e+03 4.88e+02 bond pdb=" C3' ATPA1 900 " pdb=" C4' ATPA1 900 " ideal model delta sigma weight residual 1.526 1.284 0.242 1.10e-02 8.26e+03 4.83e+02 bond pdb=" C1' ATPB1 900 " pdb=" C2' ATPB1 900 " ideal model delta sigma weight residual 1.531 1.268 0.263 1.20e-02 6.94e+03 4.79e+02 ... (remaining 56167 not shown) Histogram of bond angle deviations from ideal: 98.25 - 108.91: 28689 108.91 - 119.58: 52056 119.58 - 130.24: 21099 130.24 - 140.91: 68 140.91 - 151.57: 2 Bond angle restraints: 101914 Sorted by residual: angle pdb=" PB ATPA1 900 " pdb=" O3B ATPA1 900 " pdb=" PG ATPA1 900 " ideal model delta sigma weight residual 139.87 120.81 19.06 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PB ATPC1 900 " pdb=" O3B ATPC1 900 " pdb=" PG ATPC1 900 " ideal model delta sigma weight residual 139.87 121.89 17.98 1.00e+00 1.00e+00 3.23e+02 angle pdb=" PB ATPB1 900 " pdb=" O3B ATPB1 900 " pdb=" PG ATPB1 900 " ideal model delta sigma weight residual 139.87 122.82 17.05 1.00e+00 1.00e+00 2.91e+02 angle pdb=" PA ATPA1 900 " pdb=" O3A ATPA1 900 " pdb=" PB ATPA1 900 " ideal model delta sigma weight residual 136.83 121.90 14.93 1.00e+00 1.00e+00 2.23e+02 angle pdb=" PA ATPC1 900 " pdb=" O3A ATPC1 900 " pdb=" PB ATPC1 900 " ideal model delta sigma weight residual 136.83 123.72 13.11 1.00e+00 1.00e+00 1.72e+02 ... (remaining 101909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 25614 35.95 - 71.89: 541 71.89 - 107.84: 16 107.84 - 143.78: 2 143.78 - 179.73: 1 Dihedral angle restraints: 26174 sinusoidal: 14760 harmonic: 11414 Sorted by residual: dihedral pdb=" CD ARGF1 375 " pdb=" NE ARGF1 375 " pdb=" CZ ARGF1 375 " pdb=" NH1 ARGF1 375 " ideal model delta sinusoidal sigma weight residual 0.00 -179.73 179.73 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA TYRF1 364 " pdb=" C TYRF1 364 " pdb=" N PROF1 365 " pdb=" CA PROF1 365 " ideal model delta harmonic sigma weight residual 180.00 131.01 48.99 0 5.00e+00 4.00e-02 9.60e+01 dihedral pdb=" CA ASPB1 300 " pdb=" C ASPB1 300 " pdb=" N ASPB1 301 " pdb=" CA ASPB1 301 " ideal model delta harmonic sigma weight residual -180.00 -135.06 -44.94 0 5.00e+00 4.00e-02 8.08e+01 ... (remaining 26171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3246 0.046 - 0.093: 984 0.093 - 0.139: 176 0.139 - 0.185: 8 0.185 - 0.231: 4 Chirality restraints: 4418 Sorted by residual: chirality pdb=" C2' ATPB1 900 " pdb=" C1' ATPB1 900 " pdb=" C3' ATPB1 900 " pdb=" O2' ATPB1 900 " both_signs ideal model delta sigma weight residual False -2.68 -2.45 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C2' ATPA1 900 " pdb=" C1' ATPA1 900 " pdb=" C3' ATPA1 900 " pdb=" O2' ATPA1 900 " both_signs ideal model delta sigma weight residual False -2.68 -2.46 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C3' ATPB1 900 " pdb=" C2' ATPB1 900 " pdb=" C4' ATPB1 900 " pdb=" O3' ATPB1 900 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 4415 not shown) Planarity restraints: 8360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASNB1 216 " 0.023 2.00e-02 2.50e+03 4.03e-02 2.43e+01 pdb=" CG ASNB1 216 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASNB1 216 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASNB1 216 " 0.070 2.00e-02 2.50e+03 pdb="HD21 ASNB1 216 " 0.002 2.00e-02 2.50e+03 pdb="HD22 ASNB1 216 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYRF1 364 " 0.056 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PROF1 365 " -0.148 5.00e-02 4.00e+02 pdb=" CA PROF1 365 " 0.045 5.00e-02 4.00e+02 pdb=" CD PROF1 365 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HISE1 386 " 0.012 2.00e-02 2.50e+03 1.30e-02 3.79e+00 pdb=" CG HISE1 386 " -0.030 2.00e-02 2.50e+03 pdb=" ND1 HISE1 386 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 HISE1 386 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 HISE1 386 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 HISE1 386 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 HISE1 386 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 HISE1 386 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 HISE1 386 " 0.007 2.00e-02 2.50e+03 ... (remaining 8357 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 1544 2.10 - 2.72: 101749 2.72 - 3.35: 163364 3.35 - 3.97: 208489 3.97 - 4.60: 335997 Nonbonded interactions: 811143 Sorted by model distance: nonbonded pdb="HH22 ARGE1 112 " pdb=" O GLYE1 125 " model vdw 1.473 1.850 nonbonded pdb=" OE1 GLNE1 301 " pdb=" H GLNE1 301 " model vdw 1.484 1.850 nonbonded pdb=" OE1 GLNF1 301 " pdb=" H GLNF1 301 " model vdw 1.487 1.850 nonbonded pdb=" OE1 GLND1 301 " pdb=" H GLND1 301 " model vdw 1.513 1.850 nonbonded pdb=" OE2 GLUF1 150 " pdb=" HE ARGF1 167 " model vdw 1.528 1.850 ... (remaining 811138 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 'A1' and (resid 34 through 205 or (resid 206 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 207 through 403 \ or (resid 404 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE \ or name HH11 or name HH12 or name HH22)) or resid 405 through 544 or resid 900 t \ hrough 1001)) selection = chain 'B1' selection = (chain 'C1' and ((resid 34 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 35 through 205 or (resid 206 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name CE or name NZ or name HA or name HB2 \ or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name \ HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 207 through 403 or (resid 40 \ 4 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or \ name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 \ or name HH12 or name HH22)) or resid 405 through 544 or resid 900 through 1001) \ ) } ncs_group { reference = (chain 'D1' and ((resid 28 and (name N or name CA or name C or name O or name CB \ or name HA or name HB1 or name HB2 or name HB3)) or resid 29 through 374 or (re \ sid 375 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name H \ B2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or nam \ e HH21 or name HH22)) or resid 376 through 496)) selection = (chain 'E1' and ((resid 28 and (name N or name CA or name C or name O or name CB \ or name HA or name HB1 or name HB2 or name HB3)) or resid 29 through 374 or (re \ sid 375 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name H \ B2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or nam \ e HH21 or name HH22)) or resid 376 through 496)) selection = (chain 'F1' and (resid 28 through 181 or (resid 182 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 183 through 496)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.270 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: 0.680 Extract box with map and model: 41.280 Check model and map are aligned: 0.630 Set scattering table: 0.400 Process input model: 143.820 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.200 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: 0.000 Load rotamer database and sin/cos tables:9.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 208.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.292 28070 Z= 0.615 Angle : 0.755 25.572 37949 Z= 0.449 Chirality : 0.043 0.231 4418 Planarity : 0.003 0.085 4907 Dihedral : 9.972 179.730 10621 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.27 % Allowed : 5.04 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.09 % 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: -0.60 (0.14), residues: 3570 helix: 0.59 (0.12), residues: 1648 sheet: -0.84 (0.24), residues: 452 loop : -1.34 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP b 379 HIS 0.021 0.002 HISE1 386 PHE 0.021 0.002 PHED1 437 TYR 0.018 0.002 TYRB1 368 ARG 0.011 0.001 ARG b 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 536 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 528 time to evaluate : 3.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g1 46 MET cc_start: 0.8810 (mtm) cc_final: 0.8573 (mtp) REVERT: g1 259 MET cc_start: 0.8157 (mmp) cc_final: 0.7706 (mmp) REVERT: g1 268 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7485 (mt-10) REVERT: C1 380 GLN cc_start: 0.8150 (pm20) cc_final: 0.7912 (pp30) REVERT: C1 522 GLU cc_start: 0.7795 (tp30) cc_final: 0.7576 (tp30) REVERT: C1 534 LEU cc_start: 0.8715 (tt) cc_final: 0.8098 (tm) REVERT: i1 36 LYS cc_start: 0.8641 (mttm) cc_final: 0.8332 (mtmt) REVERT: b 229 GLU cc_start: 0.7757 (tp30) cc_final: 0.7473 (tp30) REVERT: d 87 ILE cc_start: 0.7556 (tp) cc_final: 0.7312 (pp) REVERT: d 97 LYS cc_start: 0.8938 (tttp) cc_final: 0.8440 (ttmm) outliers start: 8 outliers final: 1 residues processed: 531 average time/residue: 2.8999 time to fit residues: 1769.8002 Evaluate side-chains 256 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 255 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G1 residue 165 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 0.6980 chunk 269 optimal weight: 0.3980 chunk 149 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 279 optimal weight: 0.0670 chunk 107 optimal weight: 0.6980 chunk 169 optimal weight: 0.9980 chunk 207 optimal weight: 0.0870 chunk 323 optimal weight: 9.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1 113 ASN G1 165 GLN C1 109 ASN C1 253 GLN C1 436 GLN C1 472 GLN C1 502 HIS B1 216 ASN A1 502 HIS ** E1 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1 404 GLN E1 452 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 28070 Z= 0.174 Angle : 0.560 8.961 37949 Z= 0.288 Chirality : 0.040 0.165 4418 Planarity : 0.004 0.084 4907 Dihedral : 7.114 179.786 3982 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.04 % Allowed : 12.19 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3570 helix: 1.16 (0.13), residues: 1646 sheet: -0.61 (0.24), residues: 444 loop : -0.73 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRPi1 33 HIS 0.018 0.001 HISE1 62 PHE 0.014 0.001 PHEA1 287 TYR 0.014 0.001 TYRB1 428 ARG 0.012 0.000 ARGB1 404 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 313 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 282 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G1 161 GLN cc_start: 0.8339 (tm130) cc_final: 0.7593 (tp40) REVERT: G1 165 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7894 (mm110) REVERT: C1 380 GLN cc_start: 0.8166 (pm20) cc_final: 0.7907 (pp30) REVERT: C1 384 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7618 (mm-30) REVERT: C1 522 GLU cc_start: 0.7915 (tp30) cc_final: 0.7696 (tm-30) REVERT: B1 522 GLU cc_start: 0.7871 (tp30) cc_final: 0.7543 (tp30) REVERT: B1 526 ASN cc_start: 0.8497 (m-40) cc_final: 0.7746 (m-40) REVERT: E1 82 MET cc_start: 0.8221 (mmt) cc_final: 0.7613 (mmt) REVERT: i1 36 LYS cc_start: 0.8527 (mttm) cc_final: 0.8258 (mtmt) REVERT: i1 47 ASP cc_start: 0.7823 (m-30) cc_final: 0.7623 (m-30) REVERT: b 37 ARG cc_start: 0.9056 (mmm160) cc_final: 0.8682 (mmp-170) REVERT: b 361 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7875 (pmmt) REVERT: d 34 GLN cc_start: 0.7850 (mt0) cc_final: 0.7617 (mt0) REVERT: d 36 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7352 (tptp) REVERT: d 101 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8315 (mp0) outliers start: 31 outliers final: 10 residues processed: 303 average time/residue: 2.5451 time to fit residues: 906.3114 Evaluate side-chains 256 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 243 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G1 residue 213 GLU Chi-restraints excluded: chain C1 residue 172 SER Chi-restraints excluded: chain C1 residue 242 SER Chi-restraints excluded: chain C1 residue 537 GLN Chi-restraints excluded: chain C1 residue 538 GLU Chi-restraints excluded: chain F1 residue 349 ASP Chi-restraints excluded: chain F1 residue 422 VAL Chi-restraints excluded: chain A1 residue 93 MET Chi-restraints excluded: chain A1 residue 435 SER Chi-restraints excluded: chain A1 residue 508 SER Chi-restraints excluded: chain b residue 361 LYS Chi-restraints excluded: chain d residue 36 LYS Chi-restraints excluded: chain d residue 101 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 269 optimal weight: 0.2980 chunk 220 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 323 optimal weight: 10.0000 chunk 349 optimal weight: 5.9990 chunk 288 optimal weight: 2.9990 chunk 321 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 79 GLN ** B1 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1 502 HIS E1 404 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28070 Z= 0.354 Angle : 0.575 15.565 37949 Z= 0.298 Chirality : 0.042 0.339 4418 Planarity : 0.005 0.170 4907 Dihedral : 7.339 179.804 3979 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.65 % Allowed : 11.85 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.09 % 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: 0.44 (0.14), residues: 3570 helix: 1.32 (0.13), residues: 1657 sheet: -0.52 (0.23), residues: 457 loop : -0.56 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 83 HIS 0.017 0.001 HISE1 62 PHE 0.023 0.001 PHEA1 434 TYR 0.014 0.001 TYR d 100 ARG 0.026 0.001 ARGB1 404 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 294 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 245 time to evaluate : 4.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G1 161 GLN cc_start: 0.8351 (tm130) cc_final: 0.7643 (tp40) REVERT: G1 165 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7883 (mm110) REVERT: g1 46 MET cc_start: 0.8833 (mtp) cc_final: 0.8625 (mtp) REVERT: g1 268 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7507 (mt-10) REVERT: g1 272 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7881 (mptt) REVERT: C1 380 GLN cc_start: 0.8323 (pm20) cc_final: 0.7984 (pm20) REVERT: C1 522 GLU cc_start: 0.7973 (tp30) cc_final: 0.7671 (tm-30) REVERT: D1 360 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: F1 449 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8074 (mmp-170) REVERT: A1 56 ILE cc_start: 0.9213 (pt) cc_final: 0.8891 (pp) REVERT: A1 435 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.8121 (p) REVERT: E1 82 MET cc_start: 0.8635 (mmt) cc_final: 0.7825 (mmt) REVERT: i1 36 LYS cc_start: 0.8618 (mttm) cc_final: 0.8362 (mtmt) REVERT: s 129 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7437 (p0) REVERT: b 37 ARG cc_start: 0.9043 (mmm160) cc_final: 0.8756 (mmp-170) REVERT: b 361 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7956 (pmmt) REVERT: d 34 GLN cc_start: 0.8300 (mt0) cc_final: 0.8095 (mt0) REVERT: d 101 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8145 (mp0) outliers start: 49 outliers final: 14 residues processed: 279 average time/residue: 2.5150 time to fit residues: 827.3522 Evaluate side-chains 242 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 221 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g1 residue 272 LYS Chi-restraints excluded: chain C1 residue 172 SER Chi-restraints excluded: chain C1 residue 242 SER Chi-restraints excluded: chain C1 residue 537 GLN Chi-restraints excluded: chain C1 residue 543 LEU Chi-restraints excluded: chain D1 residue 360 GLU Chi-restraints excluded: chain B1 residue 366 SER Chi-restraints excluded: chain B1 residue 496 GLU Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 317 THR Chi-restraints excluded: chain F1 residue 422 VAL Chi-restraints excluded: chain F1 residue 449 ARG Chi-restraints excluded: chain A1 residue 435 SER Chi-restraints excluded: chain A1 residue 508 SER Chi-restraints excluded: chain E1 residue 219 MET Chi-restraints excluded: chain s residue 129 ASP Chi-restraints excluded: chain b residue 212 THR Chi-restraints excluded: chain b residue 361 LYS Chi-restraints excluded: chain d residue 79 ASP Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 101 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 3.9990 chunk 243 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 chunk 217 optimal weight: 0.9980 chunk 325 optimal weight: 8.9990 chunk 344 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 308 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1 73 GLN C1 79 GLN C1 420 ASN B1 448 GLN B1 502 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28070 Z= 0.169 Angle : 0.508 11.520 37949 Z= 0.259 Chirality : 0.039 0.151 4418 Planarity : 0.003 0.082 4907 Dihedral : 6.844 179.643 3979 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.18 % Allowed : 13.23 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.14), residues: 3570 helix: 1.60 (0.13), residues: 1652 sheet: -0.40 (0.24), residues: 461 loop : -0.33 (0.17), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 83 HIS 0.014 0.001 HISE1 62 PHE 0.012 0.001 PHED1 437 TYR 0.013 0.001 TYRB1 428 ARG 0.013 0.000 ARGB1 404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 243 time to evaluate : 3.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g1 260 GLU cc_start: 0.8334 (tt0) cc_final: 0.8113 (tp30) REVERT: C1 109 ASN cc_start: 0.7661 (m-40) cc_final: 0.7461 (m110) REVERT: C1 380 GLN cc_start: 0.8288 (pm20) cc_final: 0.7968 (pm20) REVERT: C1 522 GLU cc_start: 0.7986 (tp30) cc_final: 0.7682 (tm-30) REVERT: D1 360 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: B1 360 THR cc_start: 0.8380 (m) cc_final: 0.8067 (p) REVERT: B1 522 GLU cc_start: 0.7914 (tp30) cc_final: 0.7585 (tp30) REVERT: B1 526 ASN cc_start: 0.8491 (m-40) cc_final: 0.7878 (m-40) REVERT: A1 56 ILE cc_start: 0.9204 (pt) cc_final: 0.8908 (pp) REVERT: A1 435 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.8047 (p) REVERT: E1 82 MET cc_start: 0.8649 (mmt) cc_final: 0.7942 (mmt) REVERT: E1 410 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7497 (pp) REVERT: i1 36 LYS cc_start: 0.8601 (mttm) cc_final: 0.8345 (mtmt) REVERT: b 37 ARG cc_start: 0.9066 (mmm160) cc_final: 0.8714 (mmp-170) REVERT: d 34 GLN cc_start: 0.8272 (mt0) cc_final: 0.8071 (mt0) REVERT: d 101 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8285 (mp0) outliers start: 35 outliers final: 13 residues processed: 269 average time/residue: 2.5373 time to fit residues: 814.4668 Evaluate side-chains 243 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 226 time to evaluate : 3.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 58 GLU Chi-restraints excluded: chain C1 residue 172 SER Chi-restraints excluded: chain C1 residue 537 GLN Chi-restraints excluded: chain C1 residue 543 LEU Chi-restraints excluded: chain D1 residue 360 GLU Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 317 THR Chi-restraints excluded: chain F1 residue 422 VAL Chi-restraints excluded: chain A1 residue 93 MET Chi-restraints excluded: chain A1 residue 300 ASP Chi-restraints excluded: chain A1 residue 417 ILE Chi-restraints excluded: chain A1 residue 435 SER Chi-restraints excluded: chain E1 residue 219 MET Chi-restraints excluded: chain E1 residue 376 MET Chi-restraints excluded: chain E1 residue 410 LEU Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 101 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 chunk 237 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 308 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 79 GLN E1 404 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28070 Z= 0.272 Angle : 0.521 8.267 37949 Z= 0.271 Chirality : 0.040 0.152 4418 Planarity : 0.004 0.082 4907 Dihedral : 6.993 179.666 3979 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.38 % Allowed : 13.13 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.06 % 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 (0.14), residues: 3570 helix: 1.63 (0.13), residues: 1648 sheet: -0.44 (0.24), residues: 462 loop : -0.30 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRPi1 33 HIS 0.014 0.001 HISE1 62 PHE 0.013 0.001 PHEi1 46 TYR 0.014 0.001 TYR d 100 ARG 0.008 0.000 ARGE1 490 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 279 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 238 time to evaluate : 3.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 380 GLN cc_start: 0.8347 (pm20) cc_final: 0.8013 (pm20) REVERT: C1 384 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7821 (mm-30) REVERT: C1 522 GLU cc_start: 0.8074 (tp30) cc_final: 0.7735 (tm-30) REVERT: D1 360 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: B1 83 MET cc_start: 0.8221 (tpp) cc_final: 0.8013 (ttp) REVERT: B1 522 GLU cc_start: 0.7931 (tp30) cc_final: 0.7556 (tp30) REVERT: B1 526 ASN cc_start: 0.8592 (m-40) cc_final: 0.7835 (m-40) REVERT: A1 56 ILE cc_start: 0.9253 (pt) cc_final: 0.8953 (pp) REVERT: A1 435 SER cc_start: 0.8208 (OUTLIER) cc_final: 0.8006 (p) REVERT: E1 82 MET cc_start: 0.8746 (mmt) cc_final: 0.8088 (mmt) REVERT: E1 410 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7418 (pp) REVERT: i1 36 LYS cc_start: 0.8642 (mttm) cc_final: 0.8391 (mtmt) REVERT: b 37 ARG cc_start: 0.9065 (mmm160) cc_final: 0.8725 (mmp-170) REVERT: d 101 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8296 (mp0) outliers start: 41 outliers final: 18 residues processed: 268 average time/residue: 2.4467 time to fit residues: 773.0688 Evaluate side-chains 245 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 223 time to evaluate : 3.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g1 residue 272 LYS Chi-restraints excluded: chain C1 residue 172 SER Chi-restraints excluded: chain C1 residue 242 SER Chi-restraints excluded: chain C1 residue 537 GLN Chi-restraints excluded: chain C1 residue 543 LEU Chi-restraints excluded: chain D1 residue 360 GLU Chi-restraints excluded: chain D1 residue 414 ASP Chi-restraints excluded: chain B1 residue 366 SER Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 317 THR Chi-restraints excluded: chain F1 residue 422 VAL Chi-restraints excluded: chain A1 residue 300 ASP Chi-restraints excluded: chain A1 residue 417 ILE Chi-restraints excluded: chain A1 residue 435 SER Chi-restraints excluded: chain A1 residue 508 SER Chi-restraints excluded: chain E1 residue 219 MET Chi-restraints excluded: chain E1 residue 410 LEU Chi-restraints excluded: chain b residue 212 THR Chi-restraints excluded: chain b residue 361 LYS Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 101 GLU Chi-restraints excluded: chain d residue 105 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 2.9990 chunk 309 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 344 optimal weight: 0.9990 chunk 285 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 79 GLN ** d 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28070 Z= 0.220 Angle : 0.510 8.260 37949 Z= 0.263 Chirality : 0.040 0.152 4418 Planarity : 0.003 0.081 4907 Dihedral : 6.911 179.835 3979 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.38 % Allowed : 13.47 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.06 % 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: 0.94 (0.14), residues: 3570 helix: 1.75 (0.13), residues: 1650 sheet: -0.38 (0.24), residues: 454 loop : -0.27 (0.17), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 83 HIS 0.012 0.001 HISE1 62 PHE 0.016 0.001 PHED1 437 TYR 0.018 0.001 TYRB1 428 ARG 0.006 0.000 ARGB1 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 240 time to evaluate : 3.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C1 380 GLN cc_start: 0.8326 (pm20) cc_final: 0.7996 (pm20) REVERT: C1 522 GLU cc_start: 0.8098 (tp30) cc_final: 0.7747 (tm-30) REVERT: D1 360 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: B1 516 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8617 (m-30) REVERT: B1 522 GLU cc_start: 0.7928 (tp30) cc_final: 0.7561 (tp30) REVERT: B1 526 ASN cc_start: 0.8591 (m-40) cc_final: 0.7808 (m-40) REVERT: A1 56 ILE cc_start: 0.9257 (pt) cc_final: 0.8963 (pp) REVERT: E1 82 MET cc_start: 0.8791 (mmt) cc_final: 0.8097 (mmt) REVERT: i1 36 LYS cc_start: 0.8649 (mttm) cc_final: 0.8409 (mtmt) REVERT: b 37 ARG cc_start: 0.9050 (mmm160) cc_final: 0.8745 (mmp-170) REVERT: d 101 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8330 (mp0) outliers start: 41 outliers final: 16 residues processed: 267 average time/residue: 2.5205 time to fit residues: 802.7602 Evaluate side-chains 240 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 221 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g1 residue 272 LYS Chi-restraints excluded: chain C1 residue 58 GLU Chi-restraints excluded: chain C1 residue 172 SER Chi-restraints excluded: chain C1 residue 242 SER Chi-restraints excluded: chain C1 residue 537 GLN Chi-restraints excluded: chain C1 residue 543 LEU Chi-restraints excluded: chain D1 residue 360 GLU Chi-restraints excluded: chain B1 residue 516 ASP Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 317 THR Chi-restraints excluded: chain F1 residue 422 VAL Chi-restraints excluded: chain A1 residue 300 ASP Chi-restraints excluded: chain A1 residue 417 ILE Chi-restraints excluded: chain A1 residue 508 SER Chi-restraints excluded: chain E1 residue 219 MET Chi-restraints excluded: chain b residue 212 THR Chi-restraints excluded: chain b residue 361 LYS Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 101 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 chunk 251 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 289 optimal weight: 0.1980 chunk 192 optimal weight: 1.9990 chunk 343 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 209 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1 73 GLN C1 420 ASN E1 404 GLN ** d 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28070 Z= 0.185 Angle : 0.506 8.474 37949 Z= 0.259 Chirality : 0.039 0.152 4418 Planarity : 0.004 0.113 4907 Dihedral : 6.810 179.698 3979 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.07 % Allowed : 13.87 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.06 % 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: 1.09 (0.14), residues: 3570 helix: 1.87 (0.13), residues: 1643 sheet: -0.32 (0.24), residues: 448 loop : -0.18 (0.17), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 83 HIS 0.011 0.001 HISE1 62 PHE 0.012 0.001 PHEi1 46 TYR 0.020 0.001 TYRB1 428 ARG 0.012 0.000 ARGB1 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 231 time to evaluate : 3.466 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: C1 380 GLN cc_start: 0.8324 (pm20) cc_final: 0.7998 (pm20) REVERT: D1 360 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: B1 516 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8617 (m-30) REVERT: B1 522 GLU cc_start: 0.7950 (tp30) cc_final: 0.7550 (tp30) REVERT: B1 526 ASN cc_start: 0.8594 (m-40) cc_final: 0.7786 (m-40) REVERT: F1 404 GLN cc_start: 0.8147 (mt0) cc_final: 0.7884 (mt0) REVERT: A1 56 ILE cc_start: 0.9262 (pt) cc_final: 0.8971 (pp) REVERT: E1 82 MET cc_start: 0.8821 (mmt) cc_final: 0.8124 (mmt) REVERT: E1 376 MET cc_start: 0.8616 (mmm) cc_final: 0.8405 (mmm) REVERT: E1 410 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7367 (pp) REVERT: i1 36 LYS cc_start: 0.8628 (mttm) cc_final: 0.8389 (mtmt) REVERT: b 37 ARG cc_start: 0.9064 (mmm160) cc_final: 0.8705 (mmp-170) REVERT: d 101 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8394 (mp0) outliers start: 32 outliers final: 15 residues processed: 252 average time/residue: 2.4814 time to fit residues: 736.8411 Evaluate side-chains 243 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 224 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g1 residue 272 LYS Chi-restraints excluded: chain C1 residue 58 GLU Chi-restraints excluded: chain C1 residue 172 SER Chi-restraints excluded: chain C1 residue 242 SER Chi-restraints excluded: chain C1 residue 420 ASN Chi-restraints excluded: chain D1 residue 360 GLU Chi-restraints excluded: chain B1 residue 516 ASP Chi-restraints excluded: chain F1 residue 317 THR Chi-restraints excluded: chain F1 residue 422 VAL Chi-restraints excluded: chain A1 residue 300 ASP Chi-restraints excluded: chain A1 residue 417 ILE Chi-restraints excluded: chain A1 residue 508 SER Chi-restraints excluded: chain E1 residue 219 MET Chi-restraints excluded: chain E1 residue 410 LEU Chi-restraints excluded: chain b residue 212 THR Chi-restraints excluded: chain b residue 361 LYS Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 101 GLU Chi-restraints excluded: chain d residue 105 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 204 optimal weight: 0.0020 chunk 103 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 28070 Z= 0.257 Angle : 0.519 9.141 37949 Z= 0.269 Chirality : 0.040 0.150 4418 Planarity : 0.004 0.081 4907 Dihedral : 6.866 179.771 3979 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.11 % Allowed : 14.27 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.06 % 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: 1.03 (0.14), residues: 3570 helix: 1.84 (0.13), residues: 1645 sheet: -0.37 (0.24), residues: 455 loop : -0.23 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP d 83 HIS 0.009 0.001 HISE1 62 PHE 0.013 0.001 PHEi1 46 TYR 0.025 0.001 TYRB1 428 ARG 0.006 0.000 ARGE1 490 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 229 time to evaluate : 3.565 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: g1 259 MET cc_start: 0.8620 (mmp) cc_final: 0.8116 (mmp) REVERT: C1 380 GLN cc_start: 0.8368 (pm20) cc_final: 0.8009 (pm20) REVERT: D1 360 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: B1 522 GLU cc_start: 0.7992 (tp30) cc_final: 0.7644 (tp30) REVERT: B1 526 ASN cc_start: 0.8613 (m-40) cc_final: 0.7854 (m-40) REVERT: A1 56 ILE cc_start: 0.9271 (pt) cc_final: 0.8981 (pp) REVERT: E1 82 MET cc_start: 0.8880 (mmt) cc_final: 0.8117 (mmt) REVERT: E1 410 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7381 (pp) REVERT: E1 490 ARG cc_start: 0.8386 (ttp-110) cc_final: 0.8146 (ttm-80) REVERT: i1 36 LYS cc_start: 0.8657 (mttm) cc_final: 0.8426 (mtmt) REVERT: b 37 ARG cc_start: 0.9069 (mmm160) cc_final: 0.8721 (mmp-170) REVERT: d 101 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8399 (mp0) outliers start: 33 outliers final: 19 residues processed: 250 average time/residue: 2.6220 time to fit residues: 775.6651 Evaluate side-chains 245 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 223 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g1 residue 272 LYS Chi-restraints excluded: chain C1 residue 58 GLU Chi-restraints excluded: chain C1 residue 172 SER Chi-restraints excluded: chain C1 residue 242 SER Chi-restraints excluded: chain D1 residue 360 GLU Chi-restraints excluded: chain D1 residue 414 ASP Chi-restraints excluded: chain D1 residue 485 SER Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 317 THR Chi-restraints excluded: chain F1 residue 422 VAL Chi-restraints excluded: chain A1 residue 93 MET Chi-restraints excluded: chain A1 residue 300 ASP Chi-restraints excluded: chain A1 residue 417 ILE Chi-restraints excluded: chain A1 residue 508 SER Chi-restraints excluded: chain E1 residue 219 MET Chi-restraints excluded: chain E1 residue 410 LEU Chi-restraints excluded: chain b residue 212 THR Chi-restraints excluded: chain b residue 332 ASN Chi-restraints excluded: chain b residue 361 LYS Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 101 GLU Chi-restraints excluded: chain d residue 105 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 2.9990 chunk 328 optimal weight: 4.9990 chunk 299 optimal weight: 0.7980 chunk 319 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 251 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 288 optimal weight: 1.9990 chunk 302 optimal weight: 0.3980 chunk 318 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28070 Z= 0.187 Angle : 0.503 9.545 37949 Z= 0.258 Chirality : 0.039 0.151 4418 Planarity : 0.003 0.080 4907 Dihedral : 6.733 179.607 3979 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.91 % Allowed : 14.54 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.06 % 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: 1.14 (0.14), residues: 3570 helix: 1.92 (0.13), residues: 1645 sheet: -0.31 (0.24), residues: 455 loop : -0.15 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP d 83 HIS 0.007 0.001 HISE1 62 PHE 0.013 0.001 PHEi1 46 TYR 0.026 0.001 TYRB1 428 ARG 0.006 0.000 ARGF1 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 232 time to evaluate : 3.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g1 259 MET cc_start: 0.8547 (mmp) cc_final: 0.8086 (mmp) REVERT: C1 380 GLN cc_start: 0.8349 (pm20) cc_final: 0.7995 (pm20) REVERT: D1 360 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: B1 516 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8630 (m-30) REVERT: B1 522 GLU cc_start: 0.7989 (tp30) cc_final: 0.7638 (tp30) REVERT: B1 526 ASN cc_start: 0.8611 (m-40) cc_final: 0.7846 (m-40) REVERT: A1 56 ILE cc_start: 0.9267 (pt) cc_final: 0.8982 (pp) REVERT: A1 430 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7772 (mt-10) REVERT: E1 82 MET cc_start: 0.8886 (mmt) cc_final: 0.8227 (mmt) REVERT: E1 376 MET cc_start: 0.8604 (mmm) cc_final: 0.8391 (mmm) REVERT: E1 490 ARG cc_start: 0.8396 (ttp-110) cc_final: 0.8187 (ttm-80) REVERT: i1 36 LYS cc_start: 0.8662 (mttm) cc_final: 0.8449 (mtmt) REVERT: b 37 ARG cc_start: 0.9074 (mmm160) cc_final: 0.8742 (mmp-170) REVERT: d 101 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8415 (mp0) outliers start: 27 outliers final: 15 residues processed: 251 average time/residue: 2.5522 time to fit residues: 762.6691 Evaluate side-chains 241 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 223 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g1 residue 272 LYS Chi-restraints excluded: chain C1 residue 58 GLU Chi-restraints excluded: chain C1 residue 172 SER Chi-restraints excluded: chain C1 residue 242 SER Chi-restraints excluded: chain C1 residue 537 GLN Chi-restraints excluded: chain D1 residue 360 GLU Chi-restraints excluded: chain B1 residue 516 ASP Chi-restraints excluded: chain F1 residue 317 THR Chi-restraints excluded: chain F1 residue 422 VAL Chi-restraints excluded: chain A1 residue 300 ASP Chi-restraints excluded: chain A1 residue 417 ILE Chi-restraints excluded: chain A1 residue 508 SER Chi-restraints excluded: chain E1 residue 219 MET Chi-restraints excluded: chain E1 residue 465 GLU Chi-restraints excluded: chain b residue 332 ASN Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 101 GLU Chi-restraints excluded: chain d residue 105 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 0.9990 chunk 338 optimal weight: 6.9990 chunk 206 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 235 optimal weight: 1.9990 chunk 354 optimal weight: 5.9990 chunk 326 optimal weight: 9.9990 chunk 282 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 253 GLN ** d 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28070 Z= 0.223 Angle : 0.516 11.188 37949 Z= 0.266 Chirality : 0.039 0.150 4418 Planarity : 0.003 0.080 4907 Dihedral : 6.764 179.676 3979 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.87 % Allowed : 14.61 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.06 % 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: 1.13 (0.14), residues: 3570 helix: 1.92 (0.13), residues: 1646 sheet: -0.30 (0.24), residues: 461 loop : -0.17 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 83 HIS 0.006 0.001 HISE1 386 PHE 0.013 0.001 PHED1 437 TYR 0.023 0.001 TYRB1 428 ARG 0.007 0.000 ARGF1 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 230 time to evaluate : 3.593 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: g1 259 MET cc_start: 0.8493 (mmp) cc_final: 0.8001 (mmp) REVERT: C1 380 GLN cc_start: 0.8367 (pm20) cc_final: 0.8010 (pm20) REVERT: D1 360 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: B1 516 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8676 (m-30) REVERT: B1 522 GLU cc_start: 0.8006 (tp30) cc_final: 0.7615 (tp30) REVERT: B1 526 ASN cc_start: 0.8619 (m-40) cc_final: 0.7818 (m-40) REVERT: F1 404 GLN cc_start: 0.8107 (mt0) cc_final: 0.7854 (mt0) REVERT: A1 56 ILE cc_start: 0.9271 (pt) cc_final: 0.8986 (pp) REVERT: A1 430 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7820 (mt-10) REVERT: E1 82 MET cc_start: 0.8891 (mmt) cc_final: 0.8175 (mmt) REVERT: E1 490 ARG cc_start: 0.8397 (ttp-110) cc_final: 0.8197 (ttm-80) REVERT: i1 36 LYS cc_start: 0.8655 (mttm) cc_final: 0.8440 (mtmt) REVERT: b 37 ARG cc_start: 0.9079 (mmm160) cc_final: 0.8779 (mmp-170) REVERT: d 101 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8417 (mp0) outliers start: 26 outliers final: 16 residues processed: 249 average time/residue: 2.4998 time to fit residues: 734.5818 Evaluate side-chains 243 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 224 time to evaluate : 3.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g1 residue 272 LYS Chi-restraints excluded: chain C1 residue 58 GLU Chi-restraints excluded: chain C1 residue 172 SER Chi-restraints excluded: chain C1 residue 242 SER Chi-restraints excluded: chain D1 residue 360 GLU Chi-restraints excluded: chain B1 residue 105 VAL Chi-restraints excluded: chain B1 residue 516 ASP Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 317 THR Chi-restraints excluded: chain F1 residue 422 VAL Chi-restraints excluded: chain A1 residue 300 ASP Chi-restraints excluded: chain A1 residue 417 ILE Chi-restraints excluded: chain A1 residue 508 SER Chi-restraints excluded: chain E1 residue 219 MET Chi-restraints excluded: chain E1 residue 465 GLU Chi-restraints excluded: chain b residue 212 THR Chi-restraints excluded: chain b residue 332 ASN Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 101 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 0.7980 chunk 300 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 78 optimal weight: 3.9990 chunk 282 optimal weight: 0.0970 chunk 118 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 GLN ** 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 = 0.3403 r_free = 0.3403 target = 0.084325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.062135 restraints weight = 181727.215| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.39 r_work: 0.2846 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28070 Z= 0.168 Angle : 0.505 11.401 37949 Z= 0.257 Chirality : 0.039 0.152 4418 Planarity : 0.004 0.193 4907 Dihedral : 6.961 179.487 3979 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.71 % Allowed : 14.94 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.03 % 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: 1.25 (0.15), residues: 3570 helix: 2.00 (0.13), residues: 1644 sheet: -0.25 (0.24), residues: 461 loop : -0.09 (0.17), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP d 83 HIS 0.005 0.000 HISE1 386 PHE 0.024 0.001 PHEA1 434 TYR 0.023 0.001 TYRB1 428 ARG 0.006 0.000 ARGF1 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15500.14 seconds wall clock time: 267 minutes 41.99 seconds (16061.99 seconds total)