Starting phenix.real_space_refine on Fri Feb 16 14:01:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz6_0312/02_2024/6hz6_0312_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz6_0312/02_2024/6hz6_0312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz6_0312/02_2024/6hz6_0312.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz6_0312/02_2024/6hz6_0312.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz6_0312/02_2024/6hz6_0312_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz6_0312/02_2024/6hz6_0312_trim_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 30 5.49 5 Mg 6 5.21 5 S 156 5.16 5 C 21872 2.51 5 N 5748 2.21 5 O 6402 1.98 5 H 33368 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ARG 226": not complete - not flipped Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 387": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 314": "OE1" <-> "OE2" Residue "B ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 348": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B GLU 438": "OE1" <-> "OE2" Residue "B GLU 439": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 280": "OE1" <-> "OE2" Residue "C ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "D ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 365": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 387": "OE1" <-> "OE2" Residue "D ARG 404": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 181": "OE1" <-> "OE2" Residue "E ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 226": not complete - not flipped Residue "E ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 304": "OE1" <-> "OE2" Residue "E GLU 317": "OE1" <-> "OE2" Residue "E ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 356": "OE1" <-> "OE2" Residue "E GLU 391": "OE1" <-> "OE2" Residue "E ARG 404": not complete - not flipped Residue "E GLU 415": "OE1" <-> "OE2" Residue "F ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 317": "OE1" <-> "OE2" Residue "F PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 324": "OE1" <-> "OE2" Residue "F ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 348": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 374": "OE1" <-> "OE2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F GLU 427": "OE1" <-> "OE2" Residue "M TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 191": "OE1" <-> "OE2" Residue "M GLU 194": "OE1" <-> "OE2" Residue "M GLU 196": "OE1" <-> "OE2" Residue "M PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 242": "OE1" <-> "OE2" Residue "M GLU 251": "OE1" <-> "OE2" Residue "M TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 331": "OE1" <-> "OE2" Residue "M GLU 338": "OE1" <-> "OE2" Residue "G GLU 185": "OE1" <-> "OE2" Residue "G ARG 226": not complete - not flipped Residue "G GLU 280": "OE1" <-> "OE2" Residue "G GLU 292": "OE1" <-> "OE2" Residue "G ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 317": "OE1" <-> "OE2" Residue "G ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 387": "OE1" <-> "OE2" Residue "H GLU 185": "OE1" <-> "OE2" Residue "H ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 221": "OE1" <-> "OE2" Residue "H ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 239": "OE1" <-> "OE2" Residue "H GLU 271": "OE1" <-> "OE2" Residue "H GLU 280": "OE1" <-> "OE2" Residue "H ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 314": "OE1" <-> "OE2" Residue "H ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 348": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 395": "OE1" <-> "OE2" Residue "H GLU 427": "OE1" <-> "OE2" Residue "H GLU 438": "OE1" <-> "OE2" Residue "H GLU 439": "OE1" <-> "OE2" Residue "I GLU 171": "OE1" <-> "OE2" Residue "I GLU 181": "OE1" <-> "OE2" Residue "I GLU 185": "OE1" <-> "OE2" Residue "I ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 280": "OE1" <-> "OE2" Residue "I ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 292": "OE1" <-> "OE2" Residue "I ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 304": "OE1" <-> "OE2" Residue "I GLU 317": "OE1" <-> "OE2" Residue "I ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 324": "OE1" <-> "OE2" Residue "I ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 438": "OE1" <-> "OE2" Residue "I GLU 439": "OE1" <-> "OE2" Residue "J GLU 181": "OE1" <-> "OE2" Residue "J PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 268": "OE1" <-> "OE2" Residue "J ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 304": "OE1" <-> "OE2" Residue "J GLU 318": "OE1" <-> "OE2" Residue "J ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 365": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 387": "OE1" <-> "OE2" Residue "J ARG 404": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 181": "OE1" <-> "OE2" Residue "K ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 226": not complete - not flipped Residue "K ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 304": "OE1" <-> "OE2" Residue "K GLU 317": "OE1" <-> "OE2" Residue "K ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 356": "OE1" <-> "OE2" Residue "K GLU 391": "OE1" <-> "OE2" Residue "K ARG 404": not complete - not flipped Residue "K GLU 415": "OE1" <-> "OE2" Residue "L ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 271": "OE1" <-> "OE2" Residue "L ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 317": "OE1" <-> "OE2" Residue "L PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 324": "OE1" <-> "OE2" Residue "L ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 348": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 374": "OE1" <-> "OE2" Residue "L GLU 379": "OE1" <-> "OE2" Residue "L GLU 427": "OE1" <-> "OE2" Residue "N TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 191": "OE1" <-> "OE2" Residue "N GLU 194": "OE1" <-> "OE2" Residue "N GLU 196": "OE1" <-> "OE2" Residue "N PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 242": "OE1" <-> "OE2" Residue "N GLU 251": "OE1" <-> "OE2" Residue "N TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 331": "OE1" <-> "OE2" Residue "N GLU 338": "OE1" <-> "OE2" 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: 67582 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4720 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "B" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4719 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "C" Number of atoms: 4717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4717 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "D" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4633 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "E" Number of atoms: 4637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4637 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain: "F" Number of atoms: 4644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4644 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain: "M" Number of atoms: 5538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5538 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 323} Chain breaks: 2 Chain: "G" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4720 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "H" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4719 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "I" Number of atoms: 4717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4717 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "J" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4633 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "K" Number of atoms: 4637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4637 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain: "L" Number of atoms: 4644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4644 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain: "N" Number of atoms: 5538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5538 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 323} Chain breaks: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.41, per 1000 atoms: 0.32 Number of scatterers: 67582 At special positions: 0 Unit cell: (183.75, 133.35, 123.9, 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 156 16.00 P 30 15.00 Mg 6 11.99 O 6402 8.00 N 5748 7.00 C 21872 6.00 H 33368 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=0, symmetry=0 Time building additional restraints: 43.85 Conformation dependent library (CDL) restraints added in 5.8 seconds 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 200 helices and 32 sheets defined 44.5% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.29 Creating SS restraints... Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 207 through 219 removed outlier: 3.761A pdb=" N ARG A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 258 through 268 removed outlier: 3.694A pdb=" N GLU A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 286 through 289 No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 291 through 297 removed outlier: 3.736A pdb=" N MET A 297 " --> pdb=" O MET A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 337 through 340 Processing helix chain 'A' and resid 344 through 349 removed outlier: 3.760A pdb=" N ARG A 348 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 344 through 349' Processing helix chain 'A' and resid 362 through 370 Processing helix chain 'A' and resid 375 through 394 Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 422 through 440 removed outlier: 4.821A pdb=" N ALA A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Proline residue: A 435 - end of helix Processing helix chain 'A' and resid 445 through 456 removed outlier: 3.652A pdb=" N LEU A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.821A pdb=" N ILE B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 219 removed outlier: 3.810A pdb=" N ARG B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 No H-bonds generated for 'chain 'B' and resid 238 through 241' Processing helix chain 'B' and resid 258 through 266 removed outlier: 3.615A pdb=" N GLN B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 removed outlier: 6.780A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N MET B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N MET B 295 " --> pdb=" O GLY B 291 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 344 through 347 No H-bonds generated for 'chain 'B' and resid 344 through 347' Processing helix chain 'B' and resid 362 through 370 removed outlier: 3.602A pdb=" N LEU B 368 " --> pdb=" O PHE B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 394 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 408 through 411 No H-bonds generated for 'chain 'B' and resid 408 through 411' Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 433 through 441 Processing helix chain 'B' and resid 445 through 456 Processing helix chain 'C' and resid 170 through 174 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.570A pdb=" N ILE C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 219 removed outlier: 3.820A pdb=" N ARG C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR C 216 " --> pdb=" O ARG C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 241 No H-bonds generated for 'chain 'C' and resid 238 through 241' Processing helix chain 'C' and resid 258 through 268 Processing helix chain 'C' and resid 286 through 296 removed outlier: 6.578A pdb=" N GLU C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET C 294 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N MET C 295 " --> pdb=" O GLY C 291 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 344 through 349 removed outlier: 3.671A pdb=" N ARG C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 370 Processing helix chain 'C' and resid 375 through 394 Processing helix chain 'C' and resid 401 through 403 No H-bonds generated for 'chain 'C' and resid 401 through 403' Processing helix chain 'C' and resid 408 through 411 No H-bonds generated for 'chain 'C' and resid 408 through 411' Processing helix chain 'C' and resid 422 through 431 removed outlier: 3.509A pdb=" N MET C 430 " --> pdb=" O ASN C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 440 Processing helix chain 'C' and resid 445 through 456 Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 207 through 219 Processing helix chain 'D' and resid 238 through 241 No H-bonds generated for 'chain 'D' and resid 238 through 241' Processing helix chain 'D' and resid 258 through 268 Processing helix chain 'D' and resid 281 through 283 No H-bonds generated for 'chain 'D' and resid 281 through 283' Processing helix chain 'D' and resid 286 through 296 removed outlier: 6.299A pdb=" N GLU D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N MET D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N MET D 295 " --> pdb=" O GLY D 291 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 346 through 349 No H-bonds generated for 'chain 'D' and resid 346 through 349' Processing helix chain 'D' and resid 362 through 371 removed outlier: 3.698A pdb=" N LEU D 368 " --> pdb=" O PHE D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 394 Processing helix chain 'D' and resid 408 through 411 No H-bonds generated for 'chain 'D' and resid 408 through 411' Processing helix chain 'D' and resid 422 through 431 removed outlier: 3.518A pdb=" N ILE D 428 " --> pdb=" O TRP D 424 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET D 430 " --> pdb=" O ASN D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 440 Processing helix chain 'D' and resid 445 through 456 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.603A pdb=" N LEU E 188 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE E 193 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 219 Processing helix chain 'E' and resid 238 through 241 No H-bonds generated for 'chain 'E' and resid 238 through 241' Processing helix chain 'E' and resid 258 through 267 removed outlier: 3.580A pdb=" N GLN E 264 " --> pdb=" O TYR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 283 No H-bonds generated for 'chain 'E' and resid 281 through 283' Processing helix chain 'E' and resid 286 through 294 removed outlier: 6.952A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL E 293 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N MET E 294 " --> pdb=" O PHE E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 344 through 349 removed outlier: 3.605A pdb=" N ARG E 348 " --> pdb=" O TYR E 344 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG E 349 " --> pdb=" O ALA E 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 344 through 349' Processing helix chain 'E' and resid 362 through 369 Processing helix chain 'E' and resid 375 through 394 removed outlier: 3.684A pdb=" N LEU E 388 " --> pdb=" O LYS E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 403 No H-bonds generated for 'chain 'E' and resid 401 through 403' Processing helix chain 'E' and resid 408 through 411 No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 422 through 431 Processing helix chain 'E' and resid 433 through 441 Processing helix chain 'E' and resid 445 through 456 Processing helix chain 'F' and resid 181 through 194 Processing helix chain 'F' and resid 207 through 219 removed outlier: 3.599A pdb=" N TYR F 216 " --> pdb=" O ARG F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 241 No H-bonds generated for 'chain 'F' and resid 238 through 241' Processing helix chain 'F' and resid 259 through 268 removed outlier: 3.737A pdb=" N GLU F 268 " --> pdb=" O GLN F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 295 removed outlier: 6.735A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL F 293 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET F 294 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N MET F 295 " --> pdb=" O GLY F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 306 No H-bonds generated for 'chain 'F' and resid 304 through 306' Processing helix chain 'F' and resid 344 through 347 No H-bonds generated for 'chain 'F' and resid 344 through 347' Processing helix chain 'F' and resid 362 through 370 Processing helix chain 'F' and resid 375 through 394 Processing helix chain 'F' and resid 401 through 403 No H-bonds generated for 'chain 'F' and resid 401 through 403' Processing helix chain 'F' and resid 408 through 411 No H-bonds generated for 'chain 'F' and resid 408 through 411' Processing helix chain 'F' and resid 422 through 431 removed outlier: 4.214A pdb=" N GLU F 427 " --> pdb=" O GLN F 423 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE F 428 " --> pdb=" O TRP F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 440 Processing helix chain 'F' and resid 445 through 456 removed outlier: 3.619A pdb=" N LYS F 454 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU F 456 " --> pdb=" O THR F 452 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 19 removed outlier: 3.803A pdb=" N TYR M 12 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR M 13 " --> pdb=" O ARG M 9 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET M 14 " --> pdb=" O ASN M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 56 removed outlier: 3.734A pdb=" N LEU M 51 " --> pdb=" O ASN M 47 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG M 56 " --> pdb=" O GLN M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 84 Processing helix chain 'M' and resid 104 through 118 removed outlier: 3.664A pdb=" N ILE M 109 " --> pdb=" O ALA M 105 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE M 115 " --> pdb=" O SER M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 136 Processing helix chain 'M' and resid 147 through 155 removed outlier: 3.784A pdb=" N LEU M 153 " --> pdb=" O HIS M 149 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN M 154 " --> pdb=" O PHE M 150 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLY M 155 " --> pdb=" O SER M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 174 Processing helix chain 'M' and resid 194 through 212 removed outlier: 3.738A pdb=" N TYR M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG M 210 " --> pdb=" O TYR M 206 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG M 211 " --> pdb=" O GLU M 207 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 265 No H-bonds generated for 'chain 'M' and resid 263 through 265' Processing helix chain 'M' and resid 277 through 288 removed outlier: 4.071A pdb=" N MET M 283 " --> pdb=" O TYR M 280 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER M 288 " --> pdb=" O TYR M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 332 through 347 Processing helix chain 'G' and resid 170 through 174 Processing helix chain 'G' and resid 181 through 193 Processing helix chain 'G' and resid 207 through 219 removed outlier: 3.761A pdb=" N ARG G 212 " --> pdb=" O THR G 208 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG G 213 " --> pdb=" O PHE G 209 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA G 215 " --> pdb=" O ALA G 211 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR G 216 " --> pdb=" O ARG G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 241 No H-bonds generated for 'chain 'G' and resid 238 through 241' Processing helix chain 'G' and resid 258 through 268 removed outlier: 3.694A pdb=" N GLU G 268 " --> pdb=" O GLN G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 283 No H-bonds generated for 'chain 'G' and resid 281 through 283' Processing helix chain 'G' and resid 286 through 289 No H-bonds generated for 'chain 'G' and resid 286 through 289' Processing helix chain 'G' and resid 291 through 297 removed outlier: 3.736A pdb=" N MET G 297 " --> pdb=" O MET G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 306 No H-bonds generated for 'chain 'G' and resid 304 through 306' Processing helix chain 'G' and resid 337 through 340 Processing helix chain 'G' and resid 344 through 349 removed outlier: 3.760A pdb=" N ARG G 348 " --> pdb=" O TYR G 344 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG G 349 " --> pdb=" O ALA G 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 344 through 349' Processing helix chain 'G' and resid 362 through 370 Processing helix chain 'G' and resid 375 through 394 Processing helix chain 'G' and resid 401 through 403 No H-bonds generated for 'chain 'G' and resid 401 through 403' Processing helix chain 'G' and resid 422 through 440 removed outlier: 4.821A pdb=" N ALA G 434 " --> pdb=" O MET G 430 " (cutoff:3.500A) Proline residue: G 435 - end of helix Processing helix chain 'G' and resid 445 through 456 removed outlier: 3.652A pdb=" N LEU G 456 " --> pdb=" O THR G 452 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 175 Processing helix chain 'H' and resid 181 through 194 removed outlier: 3.821A pdb=" N ILE H 193 " --> pdb=" O LYS H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 219 removed outlier: 3.810A pdb=" N ARG H 212 " --> pdb=" O THR H 208 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG H 213 " --> pdb=" O PHE H 209 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA H 215 " --> pdb=" O ALA H 211 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR H 216 " --> pdb=" O ARG H 212 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU H 217 " --> pdb=" O ARG H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 241 No H-bonds generated for 'chain 'H' and resid 238 through 241' Processing helix chain 'H' and resid 258 through 266 removed outlier: 3.615A pdb=" N GLN H 265 " --> pdb=" O ASN H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 296 removed outlier: 6.781A pdb=" N GLU H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL H 293 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET H 294 " --> pdb=" O PHE H 290 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N MET H 295 " --> pdb=" O GLY H 291 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU H 296 " --> pdb=" O GLU H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 306 No H-bonds generated for 'chain 'H' and resid 304 through 306' Processing helix chain 'H' and resid 344 through 347 No H-bonds generated for 'chain 'H' and resid 344 through 347' Processing helix chain 'H' and resid 362 through 370 removed outlier: 3.602A pdb=" N LEU H 368 " --> pdb=" O PHE H 364 " (cutoff:3.500A) Processing helix chain 'H' and resid 375 through 394 Processing helix chain 'H' and resid 401 through 403 No H-bonds generated for 'chain 'H' and resid 401 through 403' Processing helix chain 'H' and resid 408 through 411 No H-bonds generated for 'chain 'H' and resid 408 through 411' Processing helix chain 'H' and resid 422 through 431 Processing helix chain 'H' and resid 433 through 441 Processing helix chain 'H' and resid 445 through 456 Processing helix chain 'I' and resid 170 through 174 Processing helix chain 'I' and resid 181 through 194 removed outlier: 3.569A pdb=" N ILE I 193 " --> pdb=" O LYS I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 219 removed outlier: 3.819A pdb=" N ARG I 212 " --> pdb=" O THR I 208 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG I 213 " --> pdb=" O PHE I 209 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR I 216 " --> pdb=" O ARG I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 241 No H-bonds generated for 'chain 'I' and resid 238 through 241' Processing helix chain 'I' and resid 258 through 268 Processing helix chain 'I' and resid 286 through 296 removed outlier: 6.577A pdb=" N GLU I 292 " --> pdb=" O LYS I 288 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET I 294 " --> pdb=" O PHE I 290 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N MET I 295 " --> pdb=" O GLY I 291 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU I 296 " --> pdb=" O GLU I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 306 No H-bonds generated for 'chain 'I' and resid 304 through 306' Processing helix chain 'I' and resid 344 through 349 removed outlier: 3.671A pdb=" N ARG I 349 " --> pdb=" O ALA I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 370 Processing helix chain 'I' and resid 375 through 394 Processing helix chain 'I' and resid 401 through 403 No H-bonds generated for 'chain 'I' and resid 401 through 403' Processing helix chain 'I' and resid 408 through 411 No H-bonds generated for 'chain 'I' and resid 408 through 411' Processing helix chain 'I' and resid 422 through 431 removed outlier: 3.510A pdb=" N MET I 430 " --> pdb=" O ASN I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 440 Processing helix chain 'I' and resid 445 through 456 Processing helix chain 'J' and resid 181 through 194 Processing helix chain 'J' and resid 207 through 219 Processing helix chain 'J' and resid 238 through 241 No H-bonds generated for 'chain 'J' and resid 238 through 241' Processing helix chain 'J' and resid 258 through 268 Processing helix chain 'J' and resid 281 through 283 No H-bonds generated for 'chain 'J' and resid 281 through 283' Processing helix chain 'J' and resid 286 through 296 removed outlier: 6.298A pdb=" N GLU J 292 " --> pdb=" O LYS J 288 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL J 293 " --> pdb=" O VAL J 289 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N MET J 294 " --> pdb=" O PHE J 290 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N MET J 295 " --> pdb=" O GLY J 291 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU J 296 " --> pdb=" O GLU J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 304 through 306 No H-bonds generated for 'chain 'J' and resid 304 through 306' Processing helix chain 'J' and resid 346 through 349 No H-bonds generated for 'chain 'J' and resid 346 through 349' Processing helix chain 'J' and resid 362 through 371 removed outlier: 3.699A pdb=" N LEU J 368 " --> pdb=" O PHE J 364 " (cutoff:3.500A) Processing helix chain 'J' and resid 375 through 394 Processing helix chain 'J' and resid 408 through 411 No H-bonds generated for 'chain 'J' and resid 408 through 411' Processing helix chain 'J' and resid 422 through 431 removed outlier: 3.519A pdb=" N ILE J 428 " --> pdb=" O TRP J 424 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET J 430 " --> pdb=" O ASN J 426 " (cutoff:3.500A) Processing helix chain 'J' and resid 433 through 440 Processing helix chain 'J' and resid 445 through 456 Processing helix chain 'K' and resid 181 through 194 removed outlier: 3.603A pdb=" N LEU K 188 " --> pdb=" O ILE K 184 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE K 193 " --> pdb=" O LYS K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 219 Processing helix chain 'K' and resid 238 through 241 No H-bonds generated for 'chain 'K' and resid 238 through 241' Processing helix chain 'K' and resid 258 through 267 removed outlier: 3.580A pdb=" N GLN K 264 " --> pdb=" O TYR K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 283 No H-bonds generated for 'chain 'K' and resid 281 through 283' Processing helix chain 'K' and resid 286 through 294 removed outlier: 6.952A pdb=" N GLU K 292 " --> pdb=" O LYS K 288 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL K 293 " --> pdb=" O VAL K 289 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N MET K 294 " --> pdb=" O PHE K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 306 No H-bonds generated for 'chain 'K' and resid 304 through 306' Processing helix chain 'K' and resid 344 through 349 removed outlier: 3.605A pdb=" N ARG K 348 " --> pdb=" O TYR K 344 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG K 349 " --> pdb=" O ALA K 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 344 through 349' Processing helix chain 'K' and resid 362 through 369 Processing helix chain 'K' and resid 375 through 394 removed outlier: 3.684A pdb=" N LEU K 388 " --> pdb=" O LYS K 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 401 through 403 No H-bonds generated for 'chain 'K' and resid 401 through 403' Processing helix chain 'K' and resid 408 through 411 No H-bonds generated for 'chain 'K' and resid 408 through 411' Processing helix chain 'K' and resid 422 through 431 Processing helix chain 'K' and resid 433 through 441 Processing helix chain 'K' and resid 445 through 456 Processing helix chain 'L' and resid 181 through 194 Processing helix chain 'L' and resid 207 through 219 removed outlier: 3.600A pdb=" N TYR L 216 " --> pdb=" O ARG L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 238 through 241 No H-bonds generated for 'chain 'L' and resid 238 through 241' Processing helix chain 'L' and resid 259 through 268 removed outlier: 3.737A pdb=" N GLU L 268 " --> pdb=" O GLN L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 295 removed outlier: 6.736A pdb=" N GLU L 292 " --> pdb=" O LYS L 288 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL L 293 " --> pdb=" O VAL L 289 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET L 294 " --> pdb=" O PHE L 290 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N MET L 295 " --> pdb=" O GLY L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 306 No H-bonds generated for 'chain 'L' and resid 304 through 306' Processing helix chain 'L' and resid 344 through 347 No H-bonds generated for 'chain 'L' and resid 344 through 347' Processing helix chain 'L' and resid 362 through 370 Processing helix chain 'L' and resid 375 through 394 Processing helix chain 'L' and resid 401 through 403 No H-bonds generated for 'chain 'L' and resid 401 through 403' Processing helix chain 'L' and resid 408 through 411 No H-bonds generated for 'chain 'L' and resid 408 through 411' Processing helix chain 'L' and resid 422 through 431 removed outlier: 4.214A pdb=" N GLU L 427 " --> pdb=" O GLN L 423 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE L 428 " --> pdb=" O TRP L 424 " (cutoff:3.500A) Processing helix chain 'L' and resid 433 through 440 Processing helix chain 'L' and resid 445 through 456 removed outlier: 3.619A pdb=" N LYS L 454 " --> pdb=" O LYS L 450 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU L 456 " --> pdb=" O THR L 452 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 19 removed outlier: 3.803A pdb=" N TYR N 12 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR N 13 " --> pdb=" O ARG N 9 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET N 14 " --> pdb=" O ASN N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 56 removed outlier: 3.735A pdb=" N LEU N 51 " --> pdb=" O ASN N 47 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG N 56 " --> pdb=" O GLN N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 84 Processing helix chain 'N' and resid 104 through 118 removed outlier: 3.664A pdb=" N ILE N 109 " --> pdb=" O ALA N 105 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE N 115 " --> pdb=" O SER N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 136 Processing helix chain 'N' and resid 147 through 155 removed outlier: 3.784A pdb=" N LEU N 153 " --> pdb=" O HIS N 149 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN N 154 " --> pdb=" O PHE N 150 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLY N 155 " --> pdb=" O SER N 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 174 Processing helix chain 'N' and resid 194 through 212 removed outlier: 3.738A pdb=" N TYR N 206 " --> pdb=" O GLN N 202 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG N 210 " --> pdb=" O TYR N 206 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG N 211 " --> pdb=" O GLU N 207 " (cutoff:3.500A) Processing helix chain 'N' and resid 263 through 265 No H-bonds generated for 'chain 'N' and resid 263 through 265' Processing helix chain 'N' and resid 277 through 288 removed outlier: 4.071A pdb=" N MET N 283 " --> pdb=" O TYR N 280 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER N 288 " --> pdb=" O TYR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 332 through 347 Processing sheet with id= A, first strand: chain 'A' and resid 351 through 354 removed outlier: 8.780A pdb=" N ILE A 197 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 328 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU A 199 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY A 330 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR A 274 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE A 329 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE A 276 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU A 331 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE A 278 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 243 through 247 Processing sheet with id= C, first strand: chain 'B' and resid 351 through 354 removed outlier: 8.699A pdb=" N ILE B 197 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 328 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU B 199 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY B 330 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR B 274 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE B 329 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE B 276 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N LEU B 331 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ILE B 278 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 243 through 247 Processing sheet with id= E, first strand: chain 'C' and resid 351 through 354 removed outlier: 6.585A pdb=" N ILE C 328 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU C 199 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY C 330 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLY C 201 " --> pdb=" O GLY C 330 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N MET C 332 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 243 through 247 removed outlier: 3.601A pdb=" N GLY C 244 " --> pdb=" O LYS C 255 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 351 through 354 removed outlier: 3.623A pdb=" N SER D 351 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE D 328 " --> pdb=" O ILE D 197 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU D 199 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLY D 330 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLY D 201 " --> pdb=" O GLY D 330 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N MET D 332 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 245 through 247 Processing sheet with id= I, first strand: chain 'E' and resid 351 through 354 removed outlier: 3.799A pdb=" N SER E 351 " --> pdb=" O ASN E 196 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N ILE E 197 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE E 328 " --> pdb=" O ILE E 197 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU E 199 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY E 330 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N GLY E 201 " --> pdb=" O GLY E 330 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET E 332 " --> pdb=" O GLY E 201 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR E 274 " --> pdb=" O TYR E 327 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE E 329 " --> pdb=" O TYR E 274 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE E 276 " --> pdb=" O ILE E 329 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU E 331 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE E 278 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ASN E 333 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN E 228 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASP E 279 " --> pdb=" O ASN E 228 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL E 230 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 243 through 247 Processing sheet with id= K, first strand: chain 'F' and resid 351 through 353 removed outlier: 6.811A pdb=" N ILE F 328 " --> pdb=" O ILE F 197 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LEU F 199 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY F 330 " --> pdb=" O LEU F 199 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 243 through 247 Processing sheet with id= M, first strand: chain 'M' and resid 61 through 69 removed outlier: 3.517A pdb=" N ASP M 61 " --> pdb=" O ASN M 100 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN M 100 " --> pdb=" O ASP M 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET M 98 " --> pdb=" O ASN M 63 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'M' and resid 176 through 178 Processing sheet with id= O, first strand: chain 'M' and resid 217 through 219 Processing sheet with id= P, first strand: chain 'M' and resid 253 through 257 removed outlier: 3.917A pdb=" N ILE M 302 " --> pdb=" O ASP M 257 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASP M 320 " --> pdb=" O GLY M 299 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU M 301 " --> pdb=" O ASP M 320 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLY M 322 " --> pdb=" O LEU M 301 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N TYR M 303 " --> pdb=" O GLY M 322 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS M 324 " --> pdb=" O TYR M 303 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N HIS M 305 " --> pdb=" O CYS M 324 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL M 326 " --> pdb=" O HIS M 305 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 351 through 354 removed outlier: 8.780A pdb=" N ILE G 197 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE G 328 " --> pdb=" O ILE G 197 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU G 199 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY G 330 " --> pdb=" O LEU G 199 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR G 274 " --> pdb=" O TYR G 327 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE G 329 " --> pdb=" O TYR G 274 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE G 276 " --> pdb=" O ILE G 329 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU G 331 " --> pdb=" O PHE G 276 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE G 278 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 243 through 247 Processing sheet with id= S, first strand: chain 'H' and resid 351 through 354 removed outlier: 8.699A pdb=" N ILE H 197 " --> pdb=" O VAL H 326 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE H 328 " --> pdb=" O ILE H 197 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU H 199 " --> pdb=" O ILE H 328 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY H 330 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR H 274 " --> pdb=" O TYR H 327 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE H 329 " --> pdb=" O TYR H 274 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE H 276 " --> pdb=" O ILE H 329 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N LEU H 331 " --> pdb=" O PHE H 276 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE H 278 " --> pdb=" O LEU H 331 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 243 through 247 Processing sheet with id= U, first strand: chain 'I' and resid 351 through 354 removed outlier: 6.584A pdb=" N ILE I 328 " --> pdb=" O ILE I 197 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU I 199 " --> pdb=" O ILE I 328 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY I 330 " --> pdb=" O LEU I 199 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLY I 201 " --> pdb=" O GLY I 330 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N MET I 332 " --> pdb=" O GLY I 201 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 243 through 247 removed outlier: 3.600A pdb=" N GLY I 244 " --> pdb=" O LYS I 255 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 351 through 354 removed outlier: 3.622A pdb=" N SER J 351 " --> pdb=" O ASN J 196 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE J 328 " --> pdb=" O ILE J 197 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU J 199 " --> pdb=" O ILE J 328 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLY J 330 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLY J 201 " --> pdb=" O GLY J 330 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N MET J 332 " --> pdb=" O GLY J 201 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 245 through 247 Processing sheet with id= Y, first strand: chain 'K' and resid 351 through 354 removed outlier: 3.799A pdb=" N SER K 351 " --> pdb=" O ASN K 196 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N ILE K 197 " --> pdb=" O VAL K 326 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE K 328 " --> pdb=" O ILE K 197 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU K 199 " --> pdb=" O ILE K 328 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY K 330 " --> pdb=" O LEU K 199 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N GLY K 201 " --> pdb=" O GLY K 330 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET K 332 " --> pdb=" O GLY K 201 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR K 274 " --> pdb=" O TYR K 327 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE K 329 " --> pdb=" O TYR K 274 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE K 276 " --> pdb=" O ILE K 329 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU K 331 " --> pdb=" O PHE K 276 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE K 278 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ASN K 333 " --> pdb=" O ILE K 278 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN K 228 " --> pdb=" O ILE K 277 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASP K 279 " --> pdb=" O ASN K 228 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL K 230 " --> pdb=" O ASP K 279 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 243 through 247 Processing sheet with id= AA, first strand: chain 'L' and resid 351 through 353 removed outlier: 6.812A pdb=" N ILE L 328 " --> pdb=" O ILE L 197 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU L 199 " --> pdb=" O ILE L 328 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY L 330 " --> pdb=" O LEU L 199 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 243 through 247 Processing sheet with id= AC, first strand: chain 'N' and resid 61 through 69 removed outlier: 3.516A pdb=" N ASP N 61 " --> pdb=" O ASN N 100 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN N 100 " --> pdb=" O ASP N 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET N 98 " --> pdb=" O ASN N 63 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'N' and resid 176 through 178 Processing sheet with id= AE, first strand: chain 'N' and resid 217 through 219 Processing sheet with id= AF, first strand: chain 'N' and resid 253 through 257 removed outlier: 3.917A pdb=" N ILE N 302 " --> pdb=" O ASP N 257 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASP N 320 " --> pdb=" O GLY N 299 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU N 301 " --> pdb=" O ASP N 320 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLY N 322 " --> pdb=" O LEU N 301 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N TYR N 303 " --> pdb=" O GLY N 322 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N CYS N 324 " --> pdb=" O TYR N 303 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N HIS N 305 " --> pdb=" O CYS N 324 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL N 326 " --> pdb=" O HIS N 305 " (cutoff:3.500A) 1102 hydrogen bonds defined for protein. 3192 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: 23.85 Time building geometry restraints manager: 46.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 33306 1.03 - 1.22: 68 1.22 - 1.42: 14947 1.42 - 1.62: 19817 1.62 - 1.81: 254 Bond restraints: 68392 Sorted by residual: bond pdb=" N3B GNP A1001 " pdb=" PG GNP A1001 " ideal model delta sigma weight residual 1.801 1.532 0.269 2.00e-02 2.50e+03 1.80e+02 bond pdb=" N3B GNP G1001 " pdb=" PG GNP G1001 " ideal model delta sigma weight residual 1.801 1.532 0.269 2.00e-02 2.50e+03 1.80e+02 bond pdb=" N3B GNP I1001 " pdb=" PG GNP I1001 " ideal model delta sigma weight residual 1.801 1.543 0.258 2.00e-02 2.50e+03 1.66e+02 bond pdb=" N3B GNP C1001 " pdb=" PG GNP C1001 " ideal model delta sigma weight residual 1.801 1.544 0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" N3B GNP H1001 " pdb=" PG GNP H1001 " ideal model delta sigma weight residual 1.801 1.565 0.236 2.00e-02 2.50e+03 1.39e+02 ... (remaining 68387 not shown) Histogram of bond angle deviations from ideal: 97.45 - 104.76: 737 104.76 - 112.07: 75538 112.07 - 119.38: 17854 119.38 - 126.68: 28793 126.68 - 133.99: 444 Bond angle restraints: 123366 Sorted by residual: angle pdb=" O1A GNP H1001 " pdb=" PA GNP H1001 " pdb=" O2A GNP H1001 " ideal model delta sigma weight residual 121.48 107.24 14.24 3.00e+00 1.11e-01 2.25e+01 angle pdb=" O1A GNP B1001 " pdb=" PA GNP B1001 " pdb=" O2A GNP B1001 " ideal model delta sigma weight residual 121.48 107.25 14.23 3.00e+00 1.11e-01 2.25e+01 angle pdb=" O1A GNP C1001 " pdb=" PA GNP C1001 " pdb=" O2A GNP C1001 " ideal model delta sigma weight residual 121.48 108.08 13.40 3.00e+00 1.11e-01 2.00e+01 angle pdb=" O1A GNP I1001 " pdb=" PA GNP I1001 " pdb=" O2A GNP I1001 " ideal model delta sigma weight residual 121.48 108.16 13.32 3.00e+00 1.11e-01 1.97e+01 angle pdb=" O1A GNP A1001 " pdb=" PA GNP A1001 " pdb=" O2A GNP A1001 " ideal model delta sigma weight residual 121.48 108.38 13.10 3.00e+00 1.11e-01 1.91e+01 ... (remaining 123361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 31452 35.97 - 71.95: 778 71.95 - 107.92: 28 107.92 - 143.90: 2 143.90 - 179.87: 10 Dihedral angle restraints: 32270 sinusoidal: 17632 harmonic: 14638 Sorted by residual: dihedral pdb=" CD ARG E 226 " pdb=" NE ARG E 226 " pdb=" CZ ARG E 226 " pdb=" NH1 ARG E 226 " ideal model delta sinusoidal sigma weight residual 0.00 179.87 -179.87 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG K 226 " pdb=" NE ARG K 226 " pdb=" CZ ARG K 226 " pdb=" NH1 ARG K 226 " ideal model delta sinusoidal sigma weight residual 0.00 179.87 -179.87 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG A 226 " pdb=" NE ARG A 226 " pdb=" CZ ARG A 226 " pdb=" NH1 ARG A 226 " ideal model delta sinusoidal sigma weight residual 0.00 179.82 -179.82 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 32267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3828 0.054 - 0.108: 1023 0.108 - 0.162: 139 0.162 - 0.216: 6 0.216 - 0.270: 12 Chirality restraints: 5008 Sorted by residual: chirality pdb=" C4' GNP A1001 " pdb=" C3' GNP A1001 " pdb=" C5' GNP A1001 " pdb=" O4' GNP A1001 " both_signs ideal model delta sigma weight residual False -2.44 -2.71 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C4' GNP G1001 " pdb=" C3' GNP G1001 " pdb=" C5' GNP G1001 " pdb=" O4' GNP G1001 " both_signs ideal model delta sigma weight residual False -2.44 -2.71 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C3' GDP F1001 " pdb=" C4' GDP F1001 " pdb=" O3' GDP F1001 " pdb=" C2' GDP F1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 5005 not shown) Planarity restraints: 10012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL I 322 " 0.047 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO I 323 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO I 323 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO I 323 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 322 " -0.047 5.00e-02 4.00e+02 7.00e-02 7.84e+00 pdb=" N PRO C 323 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 323 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 323 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 322 " 0.035 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO J 323 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO J 323 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 323 " 0.029 5.00e-02 4.00e+02 ... (remaining 10009 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 5821 2.22 - 2.82: 149633 2.82 - 3.41: 175652 3.41 - 4.01: 237465 4.01 - 4.60: 376535 Nonbonded interactions: 945106 Sorted by model distance: nonbonded pdb=" O LEU L 310 " pdb=" HG SER L 313 " model vdw 1.626 1.850 nonbonded pdb=" O LEU F 310 " pdb=" HG SER F 313 " model vdw 1.626 1.850 nonbonded pdb=" HG SER L 408 " pdb=" O4' GDP L1001 " model vdw 1.634 1.850 nonbonded pdb=" HG SER F 408 " pdb=" O4' GDP F1001 " model vdw 1.634 1.850 nonbonded pdb=" H ASN G 248 " pdb=" O GLY G 251 " model vdw 1.635 1.850 ... (remaining 945101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 174 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 175 through 271 or (resid 272 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ 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 \ HE2 or name HE3 or name HZ3)) or resid 273 through 383 or (resid 384 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 n \ ame NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HD2 or name HD3 or name HE2 or name HE3)) or resid 385 or (resid 386 and (na \ me N or name CA or name C or name O or name CB or name CG or name OD1 or name ND \ 2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 387 throu \ gh 403 or (resid 404 and (name N or name CA or name C or name O or name CB or na \ me 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 n \ ame HE )) or resid 405 through 406 or (resid 407 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resi \ d 408 through 453 or (resid 454 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name CE or name NZ 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 HE2 or na \ me HE3 or name HZ2)) or resid 455 through 457)) selection = (chain 'B' and ((resid 174 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 175 through 225 or (resid 226 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name N \ H2 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 resid 227 through 271 \ or (resid 272 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name CE or name NZ 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 HE2 or name HE3 or name HZ3 \ )) or resid 273 through 383 or (resid 384 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD or name CE or name NZ 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 \ HE2 or name HE3)) or resid 385 or (resid 386 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or n \ ame HB2 or name HB3 or name HD21)) or resid 387 through 403 or (resid 404 and (n \ ame 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 resid 405 thro \ ugh 406 or (resid 407 and (name N or name CA or name C or name O or name CB or n \ ame CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or n \ ame HB2 or name HB3 or name HD2 or name HE1)) or resid 408 through 453 or (resid \ 454 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 H 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 HZ2)) or res \ id 455 through 457)) selection = (chain 'C' and ((resid 174 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 175 through 225 or (resid 226 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name N \ H2 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 resid 227 through 271 \ or (resid 272 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name CE or name NZ 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 HE2 or name HE3 or name HZ3 \ )) or resid 273 through 383 or (resid 384 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD or name CE or name NZ 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 \ HE2 or name HE3)) or resid 385 or (resid 386 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or n \ ame HB2 or name HB3 or name HD21)) or resid 387 through 403 or (resid 404 and (n \ ame 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 resid 405 thro \ ugh 406 or (resid 407 and (name N or name CA or name C or name O or name CB or n \ ame CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or n \ ame HB2 or name HB3 or name HD2 or name HE1)) or resid 408 through 457)) selection = (chain 'D' and (resid 174 through 207 or (resid 208 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 209 through 225 or (resid 22 \ 6 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 resid 227 through 383 or (resid 384 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 \ H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or nam \ e HD3 or name HE2 or name HE3)) or resid 385 or (resid 386 and (name N or name C \ A or name C or name O or name CB or name CG or name OD1 or name ND2 or name H or \ name HA or name HB2 or name HB3 or name HD21)) or resid 387 through 403 or (res \ id 404 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 HB \ 2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE )) or r \ esid 405 through 406 or (resid 407 and (name N or name CA or name C or name O or \ name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or \ name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 408 through \ 453 or (resid 454 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 H 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 \ HZ2)) or resid 455 through 457)) selection = (chain 'E' and ((resid 174 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 175 through 207 or (resid 208 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name H \ G21 or name HG22 or name HG23)) or resid 209 through 271 or (resid 272 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 H 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 HZ3)) or resid 273 through \ 403 or (resid 404 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 H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or nam \ e HE )) or resid 405 through 406 or (resid 407 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 408 through 453 or (resid 454 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 H 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 HZ2)) or resid 455 through 457)) selection = (chain 'F' and ((resid 174 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 175 through 207 or (resid 208 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name H \ G21 or name HG22 or name HG23)) or resid 209 through 225 or (resid 226 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 HH \ 12)) or resid 227 through 271 or (resid 272 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 H or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or na \ me HE2 or name HE3 or name HZ3)) or resid 273 through 383 or (resid 384 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name CE o \ r name NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 o \ r name HD2 or name HD3 or name HE2 or name HE3)) or resid 385 or (resid 386 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 387 th \ rough 403 or (resid 404 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 n \ ame HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 o \ r name HE )) or resid 405 through 406 or (resid 407 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 408 through 453 or (resid 454 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 H or name HA or nam \ e HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or \ name HE3 or name HZ2)) or resid 455 through 457)) selection = (chain 'G' and ((resid 174 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 175 through 271 or (resid 272 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ 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 \ HE2 or name HE3 or name HZ3)) or resid 273 through 383 or (resid 384 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 n \ ame NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HD2 or name HD3 or name HE2 or name HE3)) or resid 385 or (resid 386 and (na \ me N or name CA or name C or name O or name CB or name CG or name OD1 or name ND \ 2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 387 throu \ gh 403 or (resid 404 and (name N or name CA or name C or name O or name CB or na \ me 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 n \ ame HE )) or resid 405 through 406 or (resid 407 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resi \ d 408 through 453 or (resid 454 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name CE or name NZ 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 HE2 or na \ me HE3 or name HZ2)) or resid 455 through 457)) selection = (chain 'H' and ((resid 174 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 175 through 225 or (resid 226 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name N \ H2 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 resid 227 through 271 \ or (resid 272 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name CE or name NZ 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 HE2 or name HE3 or name HZ3 \ )) or resid 273 through 383 or (resid 384 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD or name CE or name NZ 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 \ HE2 or name HE3)) or resid 385 or (resid 386 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or n \ ame HB2 or name HB3 or name HD21)) or resid 387 through 403 or (resid 404 and (n \ ame 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 resid 405 thro \ ugh 406 or (resid 407 and (name N or name CA or name C or name O or name CB or n \ ame CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or n \ ame HB2 or name HB3 or name HD2 or name HE1)) or resid 408 through 453 or (resid \ 454 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 H 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 HZ2)) or res \ id 455 through 457)) selection = (chain 'I' and ((resid 174 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 175 through 225 or (resid 226 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name N \ H2 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 resid 227 through 271 \ or (resid 272 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name CE or name NZ 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 HE2 or name HE3 or name HZ3 \ )) or resid 273 through 383 or (resid 384 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD or name CE or name NZ 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 \ HE2 or name HE3)) or resid 385 or (resid 386 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or n \ ame HB2 or name HB3 or name HD21)) or resid 387 through 403 or (resid 404 and (n \ ame 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 resid 405 thro \ ugh 406 or (resid 407 and (name N or name CA or name C or name O or name CB or n \ ame CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or n \ ame HB2 or name HB3 or name HD2 or name HE1)) or resid 408 through 457)) selection = (chain 'J' and (resid 174 through 207 or (resid 208 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 209 through 225 or (resid 22 \ 6 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 resid 227 through 383 or (resid 384 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 \ H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or nam \ e HD3 or name HE2 or name HE3)) or resid 385 or (resid 386 and (name N or name C \ A or name C or name O or name CB or name CG or name OD1 or name ND2 or name H or \ name HA or name HB2 or name HB3 or name HD21)) or resid 387 through 403 or (res \ id 404 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 HB \ 2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE )) or r \ esid 405 through 406 or (resid 407 and (name N or name CA or name C or name O or \ name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or \ name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 408 through \ 453 or (resid 454 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 H 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 \ HZ2)) or resid 455 through 457)) selection = (chain 'K' and ((resid 174 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 175 through 207 or (resid 208 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name H \ G21 or name HG22 or name HG23)) or resid 209 through 271 or (resid 272 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 H 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 HZ3)) or resid 273 through \ 403 or (resid 404 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 H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or nam \ e HE )) or resid 405 through 406 or (resid 407 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 408 through 453 or (resid 454 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 H 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 HZ2)) or resid 455 through 457)) selection = (chain 'L' and ((resid 174 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 175 through 207 or (resid 208 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name H \ G21 or name HG22 or name HG23)) or resid 209 through 225 or (resid 226 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 HH \ 12)) or resid 227 through 271 or (resid 272 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 H or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or na \ me HE2 or name HE3 or name HZ3)) or resid 273 through 383 or (resid 384 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name CE o \ r name NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 o \ r name HD2 or name HD3 or name HE2 or name HE3)) or resid 385 or (resid 386 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 387 th \ rough 403 or (resid 404 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 n \ ame HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 o \ r name HE )) or resid 405 through 406 or (resid 407 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 408 through 453 or (resid 454 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 H or name HA or nam \ e HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or \ name HE3 or name HZ2)) or resid 455 through 457)) } ncs_group { reference = chain 'M' selection = chain 'N' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.710 Extract box with map and model: 5.520 Check model and map are aligned: 0.730 Set scattering table: 0.460 Process input model: 168.950 Find NCS groups from input model: 2.890 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 182.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.269 35024 Z= 0.651 Angle : 1.004 14.244 47382 Z= 0.505 Chirality : 0.048 0.270 5008 Planarity : 0.005 0.070 6102 Dihedral : 14.641 179.875 13368 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.59 % Allowed : 6.22 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.12), residues: 4084 helix: -0.45 (0.11), residues: 1688 sheet: 0.06 (0.21), residues: 578 loop : -0.49 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 306 HIS 0.008 0.002 HIS D 407 PHE 0.034 0.003 PHE H 209 TYR 0.030 0.003 TYR F 238 ARG 0.012 0.001 ARG E 404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 1213 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1191 time to evaluate : 4.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 GLN cc_start: 0.8490 (tt0) cc_final: 0.7905 (tt0) REVERT: A 278 ILE cc_start: 0.9221 (mt) cc_final: 0.8988 (mt) REVERT: B 233 HIS cc_start: 0.8065 (p90) cc_final: 0.7617 (p90) REVERT: C 175 ASN cc_start: 0.7560 (p0) cc_final: 0.7186 (m-40) REVERT: C 176 ASP cc_start: 0.7701 (t0) cc_final: 0.7356 (p0) REVERT: C 235 SER cc_start: 0.9421 (m) cc_final: 0.9084 (p) REVERT: C 239 GLU cc_start: 0.8584 (mp0) cc_final: 0.8327 (mm-30) REVERT: C 254 ARG cc_start: 0.8384 (ttp-170) cc_final: 0.7688 (ttp-170) REVERT: C 263 CYS cc_start: 0.8722 (m) cc_final: 0.8463 (p) REVERT: C 280 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8656 (mt-10) REVERT: C 455 LEU cc_start: 0.7557 (mt) cc_final: 0.7044 (tt) REVERT: D 274 TYR cc_start: 0.7238 (m-80) cc_final: 0.6657 (m-80) REVERT: D 276 PHE cc_start: 0.8325 (t80) cc_final: 0.8071 (t80) REVERT: D 294 MET cc_start: 0.7822 (ttp) cc_final: 0.7477 (ttp) REVERT: D 311 THR cc_start: 0.9174 (m) cc_final: 0.8881 (m) REVERT: D 352 PHE cc_start: 0.8546 (m-80) cc_final: 0.7895 (m-10) REVERT: D 387 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7651 (mt-10) REVERT: E 255 LYS cc_start: 0.9046 (tmtt) cc_final: 0.8827 (tppp) REVERT: E 295 MET cc_start: 0.8153 (ptt) cc_final: 0.7733 (tmm) REVERT: F 308 VAL cc_start: 0.8899 (m) cc_final: 0.8520 (m) REVERT: M 52 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8268 (mm-40) REVERT: M 62 TYR cc_start: 0.8238 (m-80) cc_final: 0.7929 (m-80) REVERT: M 102 ASP cc_start: 0.6976 (t0) cc_final: 0.5596 (t0) REVERT: M 107 ARG cc_start: 0.8437 (mtm180) cc_final: 0.7951 (mtm180) REVERT: M 197 MET cc_start: 0.8747 (mmm) cc_final: 0.8445 (tpp) REVERT: M 240 ARG cc_start: 0.8577 (mtp85) cc_final: 0.8150 (ttm-80) REVERT: G 278 ILE cc_start: 0.9215 (mt) cc_final: 0.8975 (mt) REVERT: H 275 ILE cc_start: 0.9058 (mm) cc_final: 0.8667 (tt) REVERT: H 344 TYR cc_start: 0.8719 (m-80) cc_final: 0.8454 (m-80) REVERT: H 346 LEU cc_start: 0.9323 (tp) cc_final: 0.9024 (tt) REVERT: H 430 MET cc_start: 0.8501 (mmt) cc_final: 0.7902 (mmt) REVERT: I 176 ASP cc_start: 0.7646 (t0) cc_final: 0.7219 (p0) REVERT: I 235 SER cc_start: 0.9490 (m) cc_final: 0.9253 (p) REVERT: I 254 ARG cc_start: 0.8603 (ttp-170) cc_final: 0.7639 (ptm160) REVERT: I 263 CYS cc_start: 0.8894 (m) cc_final: 0.8559 (p) REVERT: I 280 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8637 (mt-10) REVERT: I 383 GLN cc_start: 0.8660 (tt0) cc_final: 0.8394 (tm-30) REVERT: I 455 LEU cc_start: 0.7543 (mt) cc_final: 0.7037 (tt) REVERT: J 274 TYR cc_start: 0.7408 (m-80) cc_final: 0.6733 (m-80) REVERT: J 294 MET cc_start: 0.7576 (ttp) cc_final: 0.7319 (ttp) REVERT: J 352 PHE cc_start: 0.8482 (m-80) cc_final: 0.7817 (m-10) REVERT: J 387 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7728 (mt-10) REVERT: J 427 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8500 (mt-10) REVERT: J 444 ASP cc_start: 0.7314 (t0) cc_final: 0.6091 (m-30) REVERT: K 255 LYS cc_start: 0.9044 (tmtt) cc_final: 0.8810 (tppp) REVERT: K 295 MET cc_start: 0.8189 (ptt) cc_final: 0.7720 (tmm) REVERT: L 308 VAL cc_start: 0.8958 (m) cc_final: 0.8707 (m) REVERT: N 52 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8293 (mm-40) REVERT: N 62 TYR cc_start: 0.8202 (m-80) cc_final: 0.7851 (m-80) REVERT: N 102 ASP cc_start: 0.6981 (t0) cc_final: 0.5611 (t0) REVERT: N 107 ARG cc_start: 0.8443 (mtm180) cc_final: 0.7955 (mtm180) REVERT: N 197 MET cc_start: 0.8760 (mmm) cc_final: 0.8459 (tpp) REVERT: N 240 ARG cc_start: 0.8580 (mtp85) cc_final: 0.8139 (ttm-80) outliers start: 22 outliers final: 9 residues processed: 1211 average time/residue: 1.0093 time to fit residues: 1902.6073 Evaluate side-chains 720 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 711 time to evaluate : 4.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 9.9990 chunk 309 optimal weight: 0.3980 chunk 171 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 208 optimal weight: 0.8980 chunk 165 optimal weight: 10.0000 chunk 319 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 238 optimal weight: 9.9990 chunk 370 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS B 453 ASN C 383 GLN D 285 ASN M 3 GLN M 312 HIS ** G 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN J 285 ASN N 3 GLN N 312 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35024 Z= 0.229 Angle : 0.596 6.974 47382 Z= 0.314 Chirality : 0.039 0.160 5008 Planarity : 0.005 0.054 6102 Dihedral : 10.026 178.896 4798 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.05 % Allowed : 2.54 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.12), residues: 4084 helix: 0.45 (0.12), residues: 1762 sheet: 0.17 (0.22), residues: 548 loop : -0.25 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP N 332 HIS 0.006 0.001 HIS B 233 PHE 0.023 0.002 PHE J 442 TYR 0.017 0.002 TYR N 161 ARG 0.008 0.001 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 873 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 871 time to evaluate : 4.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ARG cc_start: 0.8071 (mtm180) cc_final: 0.7716 (mtm-85) REVERT: A 231 GLN cc_start: 0.8170 (tt0) cc_final: 0.7832 (tt0) REVERT: A 280 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7700 (mm-30) REVERT: A 288 LYS cc_start: 0.8721 (mttt) cc_final: 0.8478 (mtpp) REVERT: A 387 GLU cc_start: 0.8474 (tt0) cc_final: 0.8248 (tt0) REVERT: A 437 LEU cc_start: 0.9415 (mt) cc_final: 0.9167 (mt) REVERT: B 233 HIS cc_start: 0.8048 (p90) cc_final: 0.6931 (p90) REVERT: B 274 TYR cc_start: 0.7836 (m-80) cc_final: 0.7630 (m-10) REVERT: B 346 LEU cc_start: 0.9292 (tp) cc_final: 0.9075 (tt) REVERT: C 200 GLN cc_start: 0.8771 (pt0) cc_final: 0.8422 (pt0) REVERT: C 235 SER cc_start: 0.9430 (m) cc_final: 0.9100 (p) REVERT: C 239 GLU cc_start: 0.8646 (mp0) cc_final: 0.8264 (mm-30) REVERT: C 280 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8648 (mm-30) REVERT: D 191 LEU cc_start: 0.9430 (tp) cc_final: 0.9209 (tp) REVERT: D 200 GLN cc_start: 0.8532 (pt0) cc_final: 0.8307 (pt0) REVERT: D 306 TRP cc_start: 0.7719 (m100) cc_final: 0.7208 (m100) REVERT: D 352 PHE cc_start: 0.8646 (m-80) cc_final: 0.7834 (m-10) REVERT: D 387 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7892 (mt-10) REVERT: E 430 MET cc_start: 0.8553 (mmt) cc_final: 0.8183 (mtt) REVERT: F 213 ARG cc_start: 0.8268 (mmt-90) cc_final: 0.7796 (mmm160) REVERT: M 62 TYR cc_start: 0.8090 (m-80) cc_final: 0.7836 (m-80) REVERT: M 83 ARG cc_start: 0.7492 (ttp-170) cc_final: 0.7193 (ttm-80) REVERT: M 93 VAL cc_start: 0.9581 (t) cc_final: 0.9167 (m) REVERT: M 102 ASP cc_start: 0.7116 (t0) cc_final: 0.5585 (t0) REVERT: M 107 ARG cc_start: 0.8601 (mtm180) cc_final: 0.7956 (mtm180) REVERT: M 189 ASP cc_start: 0.7493 (t0) cc_final: 0.6985 (t0) REVERT: M 197 MET cc_start: 0.8572 (mmm) cc_final: 0.8166 (tpp) REVERT: M 244 ASP cc_start: 0.7819 (t0) cc_final: 0.7609 (t0) REVERT: M 257 ASP cc_start: 0.8149 (t0) cc_final: 0.7665 (t70) REVERT: M 281 GLN cc_start: 0.9261 (tt0) cc_final: 0.8839 (tt0) REVERT: G 226 ARG cc_start: 0.8052 (mtm180) cc_final: 0.7661 (mtm-85) REVERT: G 280 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7759 (mm-30) REVERT: G 288 LYS cc_start: 0.8723 (mttt) cc_final: 0.8468 (mtpp) REVERT: G 387 GLU cc_start: 0.8477 (tt0) cc_final: 0.8233 (tt0) REVERT: G 437 LEU cc_start: 0.9413 (mt) cc_final: 0.9171 (mt) REVERT: H 274 TYR cc_start: 0.7922 (m-80) cc_final: 0.7396 (m-10) REVERT: H 275 ILE cc_start: 0.9072 (mm) cc_final: 0.8690 (tt) REVERT: H 346 LEU cc_start: 0.9260 (tp) cc_final: 0.8998 (tt) REVERT: I 235 SER cc_start: 0.9505 (m) cc_final: 0.9287 (p) REVERT: I 280 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8445 (mm-30) REVERT: J 191 LEU cc_start: 0.9429 (tp) cc_final: 0.9214 (tp) REVERT: J 200 GLN cc_start: 0.8460 (pt0) cc_final: 0.8166 (pt0) REVERT: J 352 PHE cc_start: 0.8687 (m-80) cc_final: 0.7827 (m-10) REVERT: J 387 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7869 (mt-10) REVERT: J 437 LEU cc_start: 0.9424 (mm) cc_final: 0.9212 (mt) REVERT: K 430 MET cc_start: 0.8589 (mmt) cc_final: 0.8225 (mtt) REVERT: L 213 ARG cc_start: 0.8294 (mmt-90) cc_final: 0.7788 (mmm160) REVERT: N 62 TYR cc_start: 0.8048 (m-80) cc_final: 0.7736 (m-80) REVERT: N 83 ARG cc_start: 0.7522 (ttp-170) cc_final: 0.7222 (ttm-80) REVERT: N 93 VAL cc_start: 0.9566 (t) cc_final: 0.9149 (m) REVERT: N 102 ASP cc_start: 0.7168 (t0) cc_final: 0.5617 (t0) REVERT: N 107 ARG cc_start: 0.8605 (mtm180) cc_final: 0.7953 (mtm180) REVERT: N 189 ASP cc_start: 0.7508 (t0) cc_final: 0.6982 (t0) REVERT: N 197 MET cc_start: 0.8593 (mmm) cc_final: 0.8213 (tpp) REVERT: N 257 ASP cc_start: 0.8153 (t0) cc_final: 0.7660 (t70) REVERT: N 281 GLN cc_start: 0.9290 (tt0) cc_final: 0.8861 (tt0) outliers start: 2 outliers final: 2 residues processed: 873 average time/residue: 0.9982 time to fit residues: 1372.3510 Evaluate side-chains 654 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 652 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 308 optimal weight: 7.9990 chunk 252 optimal weight: 0.0980 chunk 102 optimal weight: 0.7980 chunk 371 optimal weight: 8.9990 chunk 400 optimal weight: 7.9990 chunk 330 optimal weight: 5.9990 chunk 368 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 297 optimal weight: 2.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 312 HIS H 228 ASN H 285 ASN H 299 HIS ** K 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 426 ASN N 281 GLN N 312 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35024 Z= 0.222 Angle : 0.545 6.563 47382 Z= 0.284 Chirality : 0.039 0.160 5008 Planarity : 0.004 0.061 6102 Dihedral : 9.721 179.849 4798 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.03 % Allowed : 2.03 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.13), residues: 4084 helix: 0.60 (0.12), residues: 1768 sheet: 0.13 (0.22), residues: 548 loop : -0.25 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 451 HIS 0.011 0.001 HIS K 407 PHE 0.016 0.001 PHE L 178 TYR 0.013 0.001 TYR N 134 ARG 0.014 0.001 ARG E 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 782 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 781 time to evaluate : 4.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ILE cc_start: 0.7785 (mm) cc_final: 0.7456 (mm) REVERT: A 226 ARG cc_start: 0.8273 (mtm180) cc_final: 0.7744 (mtm-85) REVERT: A 280 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7857 (mm-30) REVERT: A 288 LYS cc_start: 0.8894 (mttt) cc_final: 0.8620 (mtpp) REVERT: A 423 GLN cc_start: 0.8431 (tt0) cc_final: 0.8211 (tp40) REVERT: B 205 VAL cc_start: 0.9204 (m) cc_final: 0.8737 (t) REVERT: B 237 SER cc_start: 0.9456 (t) cc_final: 0.8966 (p) REVERT: B 243 GLN cc_start: 0.7553 (tt0) cc_final: 0.7285 (tt0) REVERT: B 346 LEU cc_start: 0.9317 (tp) cc_final: 0.9089 (tt) REVERT: C 235 SER cc_start: 0.9415 (m) cc_final: 0.9077 (p) REVERT: C 239 GLU cc_start: 0.8709 (mp0) cc_final: 0.8304 (mm-30) REVERT: C 280 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8504 (mm-30) REVERT: D 189 LYS cc_start: 0.9174 (tppt) cc_final: 0.8875 (tptm) REVERT: D 200 GLN cc_start: 0.8513 (pt0) cc_final: 0.8162 (pt0) REVERT: D 263 CYS cc_start: 0.8867 (m) cc_final: 0.8618 (m) REVERT: D 306 TRP cc_start: 0.7818 (m100) cc_final: 0.7199 (m100) REVERT: D 352 PHE cc_start: 0.8554 (m-80) cc_final: 0.7884 (m-10) REVERT: E 430 MET cc_start: 0.8523 (mmt) cc_final: 0.8282 (mtt) REVERT: F 213 ARG cc_start: 0.8183 (mmt-90) cc_final: 0.7734 (mmm160) REVERT: M 62 TYR cc_start: 0.8210 (m-80) cc_final: 0.7946 (m-80) REVERT: M 93 VAL cc_start: 0.9588 (t) cc_final: 0.9170 (m) REVERT: M 102 ASP cc_start: 0.7326 (t0) cc_final: 0.5729 (t0) REVERT: M 107 ARG cc_start: 0.8720 (mtm180) cc_final: 0.8074 (mtm180) REVERT: M 189 ASP cc_start: 0.7394 (t0) cc_final: 0.6757 (t0) REVERT: M 197 MET cc_start: 0.8667 (mmm) cc_final: 0.8430 (tpp) REVERT: M 209 CYS cc_start: 0.7698 (m) cc_final: 0.6873 (t) REVERT: M 257 ASP cc_start: 0.8130 (t0) cc_final: 0.7813 (t70) REVERT: M 281 GLN cc_start: 0.9041 (tt0) cc_final: 0.8389 (tt0) REVERT: M 283 MET cc_start: 0.8508 (mmp) cc_final: 0.8238 (mmp) REVERT: M 312 HIS cc_start: 0.7161 (m-70) cc_final: 0.6953 (m90) REVERT: M 341 ASP cc_start: 0.8707 (m-30) cc_final: 0.8464 (m-30) REVERT: G 187 ILE cc_start: 0.7804 (mm) cc_final: 0.7488 (mm) REVERT: G 226 ARG cc_start: 0.8232 (mtm180) cc_final: 0.7698 (mtm-85) REVERT: G 288 LYS cc_start: 0.8892 (mttt) cc_final: 0.8609 (mtpp) REVERT: G 387 GLU cc_start: 0.8382 (tt0) cc_final: 0.8179 (tt0) REVERT: G 423 GLN cc_start: 0.8461 (tt0) cc_final: 0.8248 (tp40) REVERT: H 205 VAL cc_start: 0.9226 (m) cc_final: 0.8789 (t) REVERT: H 237 SER cc_start: 0.9451 (t) cc_final: 0.8701 (p) REVERT: H 243 GLN cc_start: 0.7490 (tt0) cc_final: 0.7244 (tt0) REVERT: H 346 LEU cc_start: 0.9205 (tp) cc_final: 0.8898 (tt) REVERT: I 176 ASP cc_start: 0.6752 (p0) cc_final: 0.6177 (p0) REVERT: I 235 SER cc_start: 0.9488 (m) cc_final: 0.9260 (p) REVERT: I 280 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8458 (mm-30) REVERT: J 189 LYS cc_start: 0.9168 (tppt) cc_final: 0.8868 (tptm) REVERT: J 200 GLN cc_start: 0.8528 (pt0) cc_final: 0.8184 (pt0) REVERT: J 352 PHE cc_start: 0.8580 (m-80) cc_final: 0.7818 (m-10) REVERT: K 430 MET cc_start: 0.8563 (mmt) cc_final: 0.8297 (mtt) REVERT: L 213 ARG cc_start: 0.8217 (mmt-90) cc_final: 0.7752 (mmm160) REVERT: L 274 TYR cc_start: 0.5939 (m-80) cc_final: 0.5313 (m-80) REVERT: L 283 ARG cc_start: 0.7809 (tpp-160) cc_final: 0.7504 (mmp-170) REVERT: N 62 TYR cc_start: 0.8182 (m-80) cc_final: 0.7855 (m-80) REVERT: N 93 VAL cc_start: 0.9578 (t) cc_final: 0.9153 (m) REVERT: N 102 ASP cc_start: 0.7367 (t0) cc_final: 0.5750 (t0) REVERT: N 107 ARG cc_start: 0.8734 (mtm180) cc_final: 0.8071 (mtm180) REVERT: N 189 ASP cc_start: 0.7401 (t0) cc_final: 0.6762 (t0) REVERT: N 197 MET cc_start: 0.8682 (mmm) cc_final: 0.8438 (tpp) REVERT: N 209 CYS cc_start: 0.7775 (m) cc_final: 0.6910 (t) REVERT: N 257 ASP cc_start: 0.8085 (t0) cc_final: 0.7797 (t70) REVERT: N 283 MET cc_start: 0.8521 (mmp) cc_final: 0.8256 (mmp) REVERT: N 312 HIS cc_start: 0.7172 (m-70) cc_final: 0.6967 (m90) REVERT: N 341 ASP cc_start: 0.8689 (m-30) cc_final: 0.8462 (m-30) outliers start: 1 outliers final: 0 residues processed: 782 average time/residue: 0.9686 time to fit residues: 1201.3251 Evaluate side-chains 592 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 592 time to evaluate : 4.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 0.8980 chunk 279 optimal weight: 8.9990 chunk 192 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 249 optimal weight: 8.9990 chunk 372 optimal weight: 10.0000 chunk 394 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 353 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 ASN C 386 ASN F 299 HIS ** M 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 233 HIS I 261 ASN I 386 ASN N 277 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 35024 Z= 0.303 Angle : 0.584 6.916 47382 Z= 0.307 Chirality : 0.039 0.143 5008 Planarity : 0.005 0.062 6102 Dihedral : 9.663 179.860 4798 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.13), residues: 4084 helix: 0.41 (0.12), residues: 1776 sheet: -0.10 (0.22), residues: 556 loop : -0.49 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 424 HIS 0.010 0.002 HIS K 407 PHE 0.017 0.002 PHE A 209 TYR 0.020 0.002 TYR E 344 ARG 0.008 0.001 ARG N 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 729 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 729 time to evaluate : 4.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ILE cc_start: 0.7714 (mm) cc_final: 0.7419 (mm) REVERT: A 226 ARG cc_start: 0.8270 (mtm180) cc_final: 0.7592 (mtm-85) REVERT: A 231 GLN cc_start: 0.8309 (tt0) cc_final: 0.7902 (tt0) REVERT: A 280 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7678 (mm-30) REVERT: A 288 LYS cc_start: 0.9064 (mttt) cc_final: 0.8813 (mtpp) REVERT: B 205 VAL cc_start: 0.9301 (m) cc_final: 0.8927 (t) REVERT: B 237 SER cc_start: 0.9590 (t) cc_final: 0.9012 (p) REVERT: B 297 MET cc_start: 0.8707 (ptp) cc_final: 0.8423 (ptp) REVERT: B 346 LEU cc_start: 0.9373 (tp) cc_final: 0.9076 (tt) REVERT: B 399 LEU cc_start: 0.8602 (mt) cc_final: 0.8338 (mp) REVERT: C 235 SER cc_start: 0.9430 (m) cc_final: 0.9193 (p) REVERT: C 239 GLU cc_start: 0.8888 (mp0) cc_final: 0.8431 (mm-30) REVERT: C 280 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8622 (mm-30) REVERT: D 189 LYS cc_start: 0.9230 (tppt) cc_final: 0.8940 (tptm) REVERT: D 200 GLN cc_start: 0.8511 (pt0) cc_final: 0.8169 (pt0) REVERT: D 306 TRP cc_start: 0.7973 (m100) cc_final: 0.7471 (m100) REVERT: D 352 PHE cc_start: 0.8484 (m-80) cc_final: 0.7994 (m-10) REVERT: D 424 TRP cc_start: 0.7648 (t60) cc_final: 0.7421 (t60) REVERT: E 213 ARG cc_start: 0.7902 (mmt90) cc_final: 0.7193 (mmp-170) REVERT: F 213 ARG cc_start: 0.8151 (mmt-90) cc_final: 0.7813 (mmm160) REVERT: M 11 ILE cc_start: 0.9351 (mt) cc_final: 0.9127 (tt) REVERT: M 93 VAL cc_start: 0.9575 (t) cc_final: 0.9195 (m) REVERT: M 129 GLU cc_start: 0.8564 (tp30) cc_final: 0.8283 (tp30) REVERT: M 136 LYS cc_start: 0.8937 (mttt) cc_final: 0.8692 (mttt) REVERT: M 197 MET cc_start: 0.8794 (mmm) cc_final: 0.8505 (tpp) REVERT: M 209 CYS cc_start: 0.7906 (m) cc_final: 0.7206 (t) REVERT: M 283 MET cc_start: 0.8732 (mmp) cc_final: 0.8501 (mmp) REVERT: G 187 ILE cc_start: 0.7754 (mm) cc_final: 0.7465 (mm) REVERT: G 226 ARG cc_start: 0.8238 (mtm180) cc_final: 0.7547 (mtm-85) REVERT: G 280 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7199 (mp0) REVERT: G 288 LYS cc_start: 0.9081 (mttt) cc_final: 0.8829 (mtpp) REVERT: H 205 VAL cc_start: 0.9318 (m) cc_final: 0.8963 (t) REVERT: H 346 LEU cc_start: 0.9279 (tp) cc_final: 0.8960 (tt) REVERT: H 426 ASN cc_start: 0.7992 (m-40) cc_final: 0.7766 (m-40) REVERT: I 383 GLN cc_start: 0.8616 (tt0) cc_final: 0.8397 (tm-30) REVERT: J 189 LYS cc_start: 0.9215 (tppt) cc_final: 0.8947 (tptm) REVERT: J 200 GLN cc_start: 0.8608 (pt0) cc_final: 0.8304 (pt0) REVERT: J 352 PHE cc_start: 0.8633 (m-80) cc_final: 0.7964 (m-10) REVERT: K 213 ARG cc_start: 0.7933 (mmt90) cc_final: 0.7206 (mmp-170) REVERT: L 274 TYR cc_start: 0.5844 (m-80) cc_final: 0.5438 (m-80) REVERT: N 11 ILE cc_start: 0.9359 (mt) cc_final: 0.9134 (tt) REVERT: N 93 VAL cc_start: 0.9563 (t) cc_final: 0.9162 (m) REVERT: N 197 MET cc_start: 0.8834 (mmm) cc_final: 0.8563 (tpp) REVERT: N 209 CYS cc_start: 0.7923 (m) cc_final: 0.7194 (t) REVERT: N 283 MET cc_start: 0.8736 (mmp) cc_final: 0.8501 (mmp) outliers start: 0 outliers final: 0 residues processed: 729 average time/residue: 0.9461 time to fit residues: 1091.3905 Evaluate side-chains 552 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 552 time to evaluate : 4.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 293 optimal weight: 0.7980 chunk 162 optimal weight: 9.9990 chunk 336 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 7.9990 chunk 353 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 281 GLN M 312 HIS I 305 ASN ** J 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 312 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35024 Z= 0.244 Angle : 0.534 6.274 47382 Z= 0.279 Chirality : 0.039 0.139 5008 Planarity : 0.004 0.046 6102 Dihedral : 9.151 179.385 4798 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.13), residues: 4084 helix: 0.49 (0.12), residues: 1776 sheet: -0.18 (0.22), residues: 576 loop : -0.47 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 451 HIS 0.008 0.001 HIS K 407 PHE 0.019 0.001 PHE F 232 TYR 0.020 0.001 TYR B 274 ARG 0.006 0.000 ARG C 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 701 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 701 time to evaluate : 4.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ILE cc_start: 0.7723 (mm) cc_final: 0.7461 (mm) REVERT: A 226 ARG cc_start: 0.8375 (mtm180) cc_final: 0.7663 (mtm-85) REVERT: A 280 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7662 (mm-30) REVERT: B 205 VAL cc_start: 0.9305 (m) cc_final: 0.8979 (t) REVERT: B 237 SER cc_start: 0.9378 (t) cc_final: 0.8793 (p) REVERT: B 243 GLN cc_start: 0.7629 (tt0) cc_final: 0.7412 (tt0) REVERT: B 297 MET cc_start: 0.8824 (ptp) cc_final: 0.8555 (ptp) REVERT: B 346 LEU cc_start: 0.9335 (tp) cc_final: 0.9103 (tt) REVERT: C 235 SER cc_start: 0.9493 (m) cc_final: 0.9204 (p) REVERT: C 280 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8590 (mm-30) REVERT: D 189 LYS cc_start: 0.9297 (tppt) cc_final: 0.8960 (tptm) REVERT: D 200 GLN cc_start: 0.8444 (pt0) cc_final: 0.8092 (pt0) REVERT: D 352 PHE cc_start: 0.8489 (m-80) cc_final: 0.8019 (m-10) REVERT: D 424 TRP cc_start: 0.7763 (t60) cc_final: 0.7563 (t60) REVERT: E 213 ARG cc_start: 0.7912 (mmt90) cc_final: 0.7245 (mmp-170) REVERT: F 283 ARG cc_start: 0.8074 (tpp-160) cc_final: 0.7835 (mmp-170) REVERT: M 93 VAL cc_start: 0.9585 (t) cc_final: 0.9176 (m) REVERT: M 129 GLU cc_start: 0.8556 (tp30) cc_final: 0.8177 (tp30) REVERT: M 197 MET cc_start: 0.8845 (mmm) cc_final: 0.8563 (tpp) REVERT: M 209 CYS cc_start: 0.7987 (m) cc_final: 0.7433 (t) REVERT: M 324 CYS cc_start: 0.7881 (p) cc_final: 0.7657 (p) REVERT: G 187 ILE cc_start: 0.7720 (mm) cc_final: 0.7460 (mm) REVERT: G 226 ARG cc_start: 0.8336 (mtm180) cc_final: 0.7609 (mtm-85) REVERT: G 280 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7452 (mm-30) REVERT: G 288 LYS cc_start: 0.9131 (mttt) cc_final: 0.8908 (mtpp) REVERT: H 205 VAL cc_start: 0.9304 (m) cc_final: 0.9012 (t) REVERT: H 297 MET cc_start: 0.9041 (ptp) cc_final: 0.8818 (ptp) REVERT: H 385 MET cc_start: 0.8438 (mmt) cc_final: 0.8158 (mmp) REVERT: H 426 ASN cc_start: 0.7991 (m-40) cc_final: 0.7735 (m-40) REVERT: I 280 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8521 (mm-30) REVERT: J 189 LYS cc_start: 0.9286 (tppt) cc_final: 0.8941 (tptm) REVERT: J 200 GLN cc_start: 0.8520 (pt0) cc_final: 0.8177 (pt0) REVERT: J 263 CYS cc_start: 0.9214 (m) cc_final: 0.8934 (m) REVERT: J 352 PHE cc_start: 0.8569 (m-80) cc_final: 0.7938 (m-10) REVERT: K 213 ARG cc_start: 0.7949 (mmt90) cc_final: 0.7257 (mmp-170) REVERT: L 213 ARG cc_start: 0.8179 (mmt-90) cc_final: 0.7601 (mmt90) REVERT: L 274 TYR cc_start: 0.6345 (m-80) cc_final: 0.5430 (m-80) REVERT: N 93 VAL cc_start: 0.9563 (t) cc_final: 0.9163 (m) REVERT: N 197 MET cc_start: 0.8875 (mmm) cc_final: 0.8546 (tpp) REVERT: N 209 CYS cc_start: 0.7999 (m) cc_final: 0.7440 (t) REVERT: N 222 TYR cc_start: 0.7508 (t80) cc_final: 0.6617 (t80) REVERT: N 324 CYS cc_start: 0.7881 (p) cc_final: 0.7629 (p) outliers start: 0 outliers final: 0 residues processed: 701 average time/residue: 0.9173 time to fit residues: 1022.3483 Evaluate side-chains 545 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 545 time to evaluate : 4.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.5980 chunk 355 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 231 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 394 optimal weight: 6.9990 chunk 327 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 180 GLN M 312 HIS ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 305 ASN ** J 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 180 GLN N 312 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 35024 Z= 0.236 Angle : 0.527 6.248 47382 Z= 0.275 Chirality : 0.039 0.139 5008 Planarity : 0.004 0.050 6102 Dihedral : 8.956 179.806 4798 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.13), residues: 4084 helix: 0.58 (0.12), residues: 1770 sheet: -0.14 (0.22), residues: 560 loop : -0.47 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 332 HIS 0.010 0.001 HIS N 89 PHE 0.022 0.001 PHE L 252 TYR 0.018 0.001 TYR B 274 ARG 0.006 0.000 ARG L 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 673 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 673 time to evaluate : 4.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ILE cc_start: 0.7677 (mm) cc_final: 0.7398 (mm) REVERT: A 196 ASN cc_start: 0.7784 (m-40) cc_final: 0.7010 (m-40) REVERT: A 226 ARG cc_start: 0.8428 (mtm180) cc_final: 0.7743 (mtm-85) REVERT: A 280 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7566 (mm-30) REVERT: B 205 VAL cc_start: 0.9322 (m) cc_final: 0.9075 (t) REVERT: B 297 MET cc_start: 0.8809 (ptp) cc_final: 0.8591 (ptp) REVERT: B 346 LEU cc_start: 0.9342 (tp) cc_final: 0.9114 (tt) REVERT: B 451 TRP cc_start: 0.8385 (m100) cc_final: 0.7362 (m100) REVERT: C 235 SER cc_start: 0.9454 (m) cc_final: 0.9207 (p) REVERT: C 280 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8518 (mm-30) REVERT: D 189 LYS cc_start: 0.9306 (tppt) cc_final: 0.8946 (tptm) REVERT: D 200 GLN cc_start: 0.8441 (pt0) cc_final: 0.8089 (pt0) REVERT: D 352 PHE cc_start: 0.8390 (m-80) cc_final: 0.7937 (m-10) REVERT: E 213 ARG cc_start: 0.7923 (mmt90) cc_final: 0.7296 (mmp-170) REVERT: E 439 GLU cc_start: 0.7851 (mp0) cc_final: 0.7416 (mp0) REVERT: M 93 VAL cc_start: 0.9571 (t) cc_final: 0.9190 (m) REVERT: M 107 ARG cc_start: 0.8570 (mtm180) cc_final: 0.8130 (mtm180) REVERT: M 136 LYS cc_start: 0.8902 (mttt) cc_final: 0.8680 (mttt) REVERT: M 197 MET cc_start: 0.8886 (mmm) cc_final: 0.8640 (tpp) REVERT: M 209 CYS cc_start: 0.8075 (m) cc_final: 0.7637 (t) REVERT: G 187 ILE cc_start: 0.7672 (mm) cc_final: 0.7383 (mm) REVERT: G 226 ARG cc_start: 0.8408 (mtm180) cc_final: 0.7716 (mtm-85) REVERT: G 288 LYS cc_start: 0.9163 (mttt) cc_final: 0.8917 (mtpp) REVERT: H 205 VAL cc_start: 0.9312 (m) cc_final: 0.9087 (t) REVERT: H 426 ASN cc_start: 0.7972 (m-40) cc_final: 0.7768 (m-40) REVERT: I 280 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8528 (mm-30) REVERT: J 189 LYS cc_start: 0.9284 (tppt) cc_final: 0.8944 (tptm) REVERT: J 200 GLN cc_start: 0.8514 (pt0) cc_final: 0.8201 (pt0) REVERT: J 352 PHE cc_start: 0.8572 (m-80) cc_final: 0.7973 (m-10) REVERT: K 213 ARG cc_start: 0.7953 (mmt90) cc_final: 0.7292 (mmp-170) REVERT: K 297 MET cc_start: 0.8040 (ptm) cc_final: 0.7823 (ptp) REVERT: K 439 GLU cc_start: 0.7836 (mp0) cc_final: 0.7410 (mp0) REVERT: L 213 ARG cc_start: 0.8199 (mmt-90) cc_final: 0.7830 (mmm160) REVERT: L 274 TYR cc_start: 0.6453 (m-80) cc_final: 0.5500 (m-80) REVERT: N 93 VAL cc_start: 0.9545 (t) cc_final: 0.9151 (m) REVERT: N 107 ARG cc_start: 0.8588 (mtm180) cc_final: 0.8138 (mtm180) REVERT: N 197 MET cc_start: 0.8899 (mmm) cc_final: 0.8650 (tpp) REVERT: N 209 CYS cc_start: 0.8018 (m) cc_final: 0.7532 (t) REVERT: N 348 LYS cc_start: 0.7643 (mttt) cc_final: 0.7442 (mmmt) outliers start: 0 outliers final: 0 residues processed: 673 average time/residue: 0.8873 time to fit residues: 948.0970 Evaluate side-chains 562 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 562 time to evaluate : 4.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 224 optimal weight: 0.7980 chunk 288 optimal weight: 6.9990 chunk 223 optimal weight: 0.0670 chunk 332 optimal weight: 7.9990 chunk 220 optimal weight: 10.0000 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 181 optimal weight: 0.8980 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN ** M 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 180 GLN M 312 HIS ** I 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 180 GLN N 277 GLN N 312 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 35024 Z= 0.136 Angle : 0.480 5.894 47382 Z= 0.244 Chirality : 0.039 0.148 5008 Planarity : 0.004 0.047 6102 Dihedral : 8.578 179.977 4798 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.13), residues: 4084 helix: 1.07 (0.12), residues: 1732 sheet: 0.13 (0.22), residues: 572 loop : -0.17 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 306 HIS 0.009 0.001 HIS G 407 PHE 0.027 0.001 PHE J 290 TYR 0.018 0.001 TYR B 274 ARG 0.006 0.000 ARG L 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 716 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 716 time to evaluate : 4.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ILE cc_start: 0.7545 (mm) cc_final: 0.7303 (mm) REVERT: A 226 ARG cc_start: 0.8396 (mtm180) cc_final: 0.7833 (mtm-85) REVERT: B 218 LEU cc_start: 0.8897 (mm) cc_final: 0.8632 (tp) REVERT: B 346 LEU cc_start: 0.9355 (tp) cc_final: 0.9121 (tt) REVERT: C 235 SER cc_start: 0.9475 (m) cc_final: 0.9099 (p) REVERT: D 189 LYS cc_start: 0.9276 (tppt) cc_final: 0.8886 (tptm) REVERT: D 200 GLN cc_start: 0.8477 (pt0) cc_final: 0.8064 (pt0) REVERT: D 263 CYS cc_start: 0.9053 (m) cc_final: 0.8597 (m) REVERT: D 352 PHE cc_start: 0.8238 (m-80) cc_final: 0.7774 (m-10) REVERT: E 213 ARG cc_start: 0.7923 (mmt90) cc_final: 0.7299 (mmp-170) REVERT: E 439 GLU cc_start: 0.7803 (mp0) cc_final: 0.7354 (mp0) REVERT: F 403 PHE cc_start: 0.7967 (m-10) cc_final: 0.7702 (m-10) REVERT: M 40 ASP cc_start: 0.8459 (m-30) cc_final: 0.8007 (m-30) REVERT: M 75 ARG cc_start: 0.8621 (ttp80) cc_final: 0.8144 (tmm-80) REVERT: M 93 VAL cc_start: 0.9577 (t) cc_final: 0.9186 (m) REVERT: M 129 GLU cc_start: 0.8419 (tp30) cc_final: 0.8021 (tp30) REVERT: M 197 MET cc_start: 0.8785 (mmm) cc_final: 0.8544 (tpp) REVERT: M 209 CYS cc_start: 0.8162 (m) cc_final: 0.7663 (t) REVERT: M 241 MET cc_start: 0.6982 (ptm) cc_final: 0.6726 (ptm) REVERT: M 257 ASP cc_start: 0.8179 (t0) cc_final: 0.7832 (t0) REVERT: G 187 ILE cc_start: 0.7536 (mm) cc_final: 0.7283 (mm) REVERT: G 226 ARG cc_start: 0.8391 (mtm180) cc_final: 0.7823 (mtm-85) REVERT: G 288 LYS cc_start: 0.9054 (mttt) cc_final: 0.8796 (mtpp) REVERT: H 185 GLU cc_start: 0.7788 (pm20) cc_final: 0.7454 (pm20) REVERT: H 295 MET cc_start: 0.8602 (ttp) cc_final: 0.8105 (ttm) REVERT: H 426 ASN cc_start: 0.7985 (m-40) cc_final: 0.7779 (m-40) REVERT: I 280 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8466 (mm-30) REVERT: J 189 LYS cc_start: 0.9271 (tppt) cc_final: 0.8906 (tptm) REVERT: J 200 GLN cc_start: 0.8496 (pt0) cc_final: 0.8151 (pt0) REVERT: J 263 CYS cc_start: 0.9063 (m) cc_final: 0.8672 (m) REVERT: J 352 PHE cc_start: 0.8439 (m-80) cc_final: 0.7776 (m-10) REVERT: K 213 ARG cc_start: 0.7950 (mmt90) cc_final: 0.7295 (mmp-170) REVERT: K 439 GLU cc_start: 0.7785 (mp0) cc_final: 0.7353 (mp0) REVERT: L 213 ARG cc_start: 0.8136 (mmt-90) cc_final: 0.7515 (mmt90) REVERT: L 274 TYR cc_start: 0.6160 (m-80) cc_final: 0.5114 (m-80) REVERT: L 296 LEU cc_start: 0.8243 (mp) cc_final: 0.7621 (tp) REVERT: N 40 ASP cc_start: 0.8444 (m-30) cc_final: 0.7982 (m-30) REVERT: N 93 VAL cc_start: 0.9530 (t) cc_final: 0.9125 (m) REVERT: N 197 MET cc_start: 0.8820 (mmm) cc_final: 0.8553 (tpp) REVERT: N 209 CYS cc_start: 0.8128 (m) cc_final: 0.7669 (t) REVERT: N 257 ASP cc_start: 0.8239 (t0) cc_final: 0.7821 (t0) REVERT: N 283 MET cc_start: 0.8847 (mmp) cc_final: 0.8635 (mmp) outliers start: 0 outliers final: 0 residues processed: 716 average time/residue: 0.9308 time to fit residues: 1066.7555 Evaluate side-chains 577 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 577 time to evaluate : 4.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 118 optimal weight: 0.4980 chunk 77 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 250 optimal weight: 0.7980 chunk 267 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 309 optimal weight: 0.5980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 275 HIS M 312 HIS ** I 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 312 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.6373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 35024 Z= 0.150 Angle : 0.474 6.167 47382 Z= 0.240 Chirality : 0.038 0.141 5008 Planarity : 0.004 0.046 6102 Dihedral : 8.523 179.904 4798 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.13), residues: 4084 helix: 1.18 (0.12), residues: 1750 sheet: 0.31 (0.23), residues: 544 loop : -0.16 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 306 HIS 0.006 0.001 HIS G 407 PHE 0.012 0.001 PHE B 252 TYR 0.019 0.001 TYR N 201 ARG 0.004 0.000 ARG L 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 686 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 686 time to evaluate : 4.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ILE cc_start: 0.7592 (mm) cc_final: 0.7317 (mm) REVERT: A 226 ARG cc_start: 0.8413 (mtm180) cc_final: 0.7840 (mtm-85) REVERT: A 280 GLU cc_start: 0.6295 (mp0) cc_final: 0.6024 (mp0) REVERT: B 185 GLU cc_start: 0.7756 (pm20) cc_final: 0.7523 (pm20) REVERT: B 218 LEU cc_start: 0.8875 (mm) cc_final: 0.8657 (tp) REVERT: B 346 LEU cc_start: 0.9276 (tp) cc_final: 0.9073 (tt) REVERT: C 235 SER cc_start: 0.9533 (m) cc_final: 0.9198 (p) REVERT: C 280 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8379 (mm-30) REVERT: D 189 LYS cc_start: 0.9279 (tppt) cc_final: 0.8881 (tptm) REVERT: D 200 GLN cc_start: 0.8484 (pt0) cc_final: 0.8094 (pt0) REVERT: D 263 CYS cc_start: 0.9072 (m) cc_final: 0.8608 (m) REVERT: D 352 PHE cc_start: 0.8255 (m-80) cc_final: 0.7799 (m-10) REVERT: E 439 GLU cc_start: 0.7821 (mp0) cc_final: 0.7395 (mp0) REVERT: F 403 PHE cc_start: 0.7946 (m-10) cc_final: 0.7655 (m-10) REVERT: M 40 ASP cc_start: 0.8477 (m-30) cc_final: 0.8102 (m-30) REVERT: M 93 VAL cc_start: 0.9529 (t) cc_final: 0.9171 (m) REVERT: M 129 GLU cc_start: 0.8413 (tp30) cc_final: 0.8103 (tp30) REVERT: M 197 MET cc_start: 0.8815 (mmm) cc_final: 0.8610 (tpp) REVERT: M 209 CYS cc_start: 0.8061 (m) cc_final: 0.7700 (t) REVERT: M 257 ASP cc_start: 0.8222 (t0) cc_final: 0.7773 (t0) REVERT: M 312 HIS cc_start: 0.7214 (m-70) cc_final: 0.6986 (m-70) REVERT: G 187 ILE cc_start: 0.7567 (mm) cc_final: 0.7288 (mm) REVERT: G 196 ASN cc_start: 0.8331 (t0) cc_final: 0.7668 (t0) REVERT: G 226 ARG cc_start: 0.8412 (mtm180) cc_final: 0.7823 (mtm-85) REVERT: G 288 LYS cc_start: 0.9091 (mttt) cc_final: 0.8845 (mtpp) REVERT: H 426 ASN cc_start: 0.8013 (m-40) cc_final: 0.7793 (m-40) REVERT: J 189 LYS cc_start: 0.9271 (tppt) cc_final: 0.8861 (tptm) REVERT: J 200 GLN cc_start: 0.8519 (pt0) cc_final: 0.8150 (pt0) REVERT: J 263 CYS cc_start: 0.9062 (m) cc_final: 0.8674 (m) REVERT: J 352 PHE cc_start: 0.8440 (m-80) cc_final: 0.7756 (m-10) REVERT: K 439 GLU cc_start: 0.7795 (mp0) cc_final: 0.7373 (mp0) REVERT: L 213 ARG cc_start: 0.8094 (mmt-90) cc_final: 0.7598 (mmm-85) REVERT: L 274 TYR cc_start: 0.6194 (m-80) cc_final: 0.5088 (m-80) REVERT: L 296 LEU cc_start: 0.8210 (mp) cc_final: 0.7700 (tp) REVERT: L 382 CYS cc_start: 0.7426 (m) cc_final: 0.6403 (t) REVERT: N 40 ASP cc_start: 0.8474 (m-30) cc_final: 0.8045 (m-30) REVERT: N 93 VAL cc_start: 0.9530 (t) cc_final: 0.9151 (m) REVERT: N 197 MET cc_start: 0.8848 (mmm) cc_final: 0.8601 (tpp) REVERT: N 209 CYS cc_start: 0.8108 (m) cc_final: 0.7683 (t) REVERT: N 257 ASP cc_start: 0.8167 (t0) cc_final: 0.7779 (t0) REVERT: N 312 HIS cc_start: 0.7202 (m-70) cc_final: 0.6961 (m-70) outliers start: 0 outliers final: 0 residues processed: 686 average time/residue: 0.8929 time to fit residues: 979.2779 Evaluate side-chains 565 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 565 time to evaluate : 4.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 6.9990 chunk 376 optimal weight: 8.9990 chunk 343 optimal weight: 8.9990 chunk 366 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 287 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 331 optimal weight: 7.9990 chunk 346 optimal weight: 10.0000 chunk 365 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN ** I 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 305 ASN J 370 ASN ** K 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.6601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 35024 Z= 0.287 Angle : 0.553 6.572 47382 Z= 0.290 Chirality : 0.039 0.135 5008 Planarity : 0.004 0.047 6102 Dihedral : 8.862 179.389 4798 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.13), residues: 4084 helix: 0.84 (0.12), residues: 1752 sheet: -0.08 (0.22), residues: 592 loop : -0.44 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 424 HIS 0.008 0.002 HIS M 89 PHE 0.020 0.002 PHE B 350 TYR 0.025 0.002 TYR H 236 ARG 0.007 0.001 ARG J 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 644 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 644 time to evaluate : 4.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ILE cc_start: 0.7632 (mm) cc_final: 0.7388 (mm) REVERT: A 226 ARG cc_start: 0.8456 (mtm180) cc_final: 0.7777 (mtm-85) REVERT: A 280 GLU cc_start: 0.6707 (mp0) cc_final: 0.6338 (mp0) REVERT: B 185 GLU cc_start: 0.7944 (pm20) cc_final: 0.7724 (pm20) REVERT: B 295 MET cc_start: 0.8713 (ttp) cc_final: 0.8212 (ttm) REVERT: B 320 PHE cc_start: 0.7965 (t80) cc_final: 0.7699 (t80) REVERT: B 346 LEU cc_start: 0.9286 (tp) cc_final: 0.9021 (tt) REVERT: C 280 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8528 (mm-30) REVERT: D 189 LYS cc_start: 0.9305 (tppt) cc_final: 0.8900 (tptm) REVERT: D 200 GLN cc_start: 0.8522 (pt0) cc_final: 0.8192 (pt0) REVERT: D 352 PHE cc_start: 0.8441 (m-80) cc_final: 0.8017 (m-10) REVERT: F 403 PHE cc_start: 0.8021 (m-10) cc_final: 0.7605 (m-10) REVERT: M 40 ASP cc_start: 0.8517 (m-30) cc_final: 0.8119 (m-30) REVERT: M 93 VAL cc_start: 0.9592 (t) cc_final: 0.9255 (m) REVERT: M 136 LYS cc_start: 0.8937 (mttt) cc_final: 0.8724 (mttt) REVERT: M 197 MET cc_start: 0.8956 (mmm) cc_final: 0.8744 (tpp) REVERT: M 209 CYS cc_start: 0.8143 (m) cc_final: 0.7840 (t) REVERT: G 187 ILE cc_start: 0.7648 (mm) cc_final: 0.7386 (mm) REVERT: G 226 ARG cc_start: 0.8469 (mtm180) cc_final: 0.7769 (mtm-85) REVERT: G 288 LYS cc_start: 0.9180 (mttt) cc_final: 0.8918 (mtpp) REVERT: H 295 MET cc_start: 0.8675 (ttp) cc_final: 0.8165 (ttm) REVERT: H 297 MET cc_start: 0.8935 (ptp) cc_final: 0.8556 (ptp) REVERT: H 320 PHE cc_start: 0.8030 (t80) cc_final: 0.7785 (t80) REVERT: H 426 ASN cc_start: 0.8083 (m-40) cc_final: 0.7847 (m-40) REVERT: I 280 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8517 (mm-30) REVERT: J 189 LYS cc_start: 0.9269 (tppt) cc_final: 0.8866 (tptm) REVERT: J 200 GLN cc_start: 0.8534 (pt0) cc_final: 0.8208 (pt0) REVERT: J 352 PHE cc_start: 0.8564 (m-80) cc_final: 0.7978 (m-10) REVERT: L 213 ARG cc_start: 0.8176 (mmt-90) cc_final: 0.7476 (mmt90) REVERT: L 274 TYR cc_start: 0.6602 (m-80) cc_final: 0.5639 (m-80) REVERT: N 40 ASP cc_start: 0.8526 (m-30) cc_final: 0.8107 (m-30) REVERT: N 93 VAL cc_start: 0.9555 (t) cc_final: 0.9195 (m) REVERT: N 197 MET cc_start: 0.8971 (mmm) cc_final: 0.8739 (tpp) REVERT: N 209 CYS cc_start: 0.8132 (m) cc_final: 0.7814 (t) outliers start: 0 outliers final: 0 residues processed: 644 average time/residue: 0.8824 time to fit residues: 909.1228 Evaluate side-chains 514 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 514 time to evaluate : 4.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 0.6980 chunk 387 optimal weight: 0.5980 chunk 236 optimal weight: 0.8980 chunk 183 optimal weight: 7.9990 chunk 269 optimal weight: 5.9990 chunk 406 optimal weight: 0.7980 chunk 374 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 250 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 312 HIS ** I 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 312 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.6648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 35024 Z= 0.140 Angle : 0.487 7.371 47382 Z= 0.247 Chirality : 0.039 0.159 5008 Planarity : 0.003 0.045 6102 Dihedral : 8.488 179.607 4798 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.13), residues: 4084 helix: 1.18 (0.12), residues: 1754 sheet: 0.30 (0.23), residues: 544 loop : -0.20 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 306 HIS 0.011 0.001 HIS N 312 PHE 0.031 0.001 PHE D 290 TYR 0.020 0.001 TYR G 440 ARG 0.008 0.000 ARG B 347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 666 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 666 time to evaluate : 4.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ILE cc_start: 0.7709 (mm) cc_final: 0.7487 (mm) REVERT: A 226 ARG cc_start: 0.8438 (mtm180) cc_final: 0.7964 (mtm-85) REVERT: A 280 GLU cc_start: 0.6609 (mp0) cc_final: 0.6406 (mp0) REVERT: B 295 MET cc_start: 0.8666 (ttp) cc_final: 0.8143 (ttm) REVERT: B 346 LEU cc_start: 0.9256 (tp) cc_final: 0.8988 (tt) REVERT: C 280 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8383 (mm-30) REVERT: C 370 ASN cc_start: 0.8622 (t0) cc_final: 0.8222 (m110) REVERT: D 189 LYS cc_start: 0.9262 (tppt) cc_final: 0.8848 (tptm) REVERT: D 200 GLN cc_start: 0.8465 (pt0) cc_final: 0.8072 (pt0) REVERT: D 352 PHE cc_start: 0.8144 (m-80) cc_final: 0.7798 (m-80) REVERT: E 297 MET cc_start: 0.7794 (ptp) cc_final: 0.7544 (ptp) REVERT: M 40 ASP cc_start: 0.8443 (m-30) cc_final: 0.8062 (m-30) REVERT: M 93 VAL cc_start: 0.9567 (t) cc_final: 0.9221 (m) REVERT: M 197 MET cc_start: 0.8846 (mmm) cc_final: 0.8467 (tpp) REVERT: M 209 CYS cc_start: 0.8102 (m) cc_final: 0.7794 (t) REVERT: M 257 ASP cc_start: 0.8236 (t0) cc_final: 0.7876 (t0) REVERT: G 187 ILE cc_start: 0.7597 (mm) cc_final: 0.7351 (mm) REVERT: G 196 ASN cc_start: 0.8515 (t0) cc_final: 0.7748 (t0) REVERT: G 226 ARG cc_start: 0.8462 (mtm180) cc_final: 0.7756 (mtm-85) REVERT: G 237 SER cc_start: 0.7876 (t) cc_final: 0.7271 (p) REVERT: G 239 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7591 (mt-10) REVERT: G 288 LYS cc_start: 0.9061 (mttt) cc_final: 0.8825 (mtpp) REVERT: H 295 MET cc_start: 0.8570 (ttp) cc_final: 0.8038 (ttm) REVERT: H 426 ASN cc_start: 0.8015 (m-40) cc_final: 0.7799 (m-40) REVERT: I 280 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8354 (mm-30) REVERT: J 189 LYS cc_start: 0.9239 (tppt) cc_final: 0.8838 (tptm) REVERT: J 200 GLN cc_start: 0.8533 (pt0) cc_final: 0.8171 (pt0) REVERT: J 263 CYS cc_start: 0.9082 (m) cc_final: 0.8712 (m) REVERT: J 352 PHE cc_start: 0.8414 (m-80) cc_final: 0.7808 (m-10) REVERT: L 213 ARG cc_start: 0.8114 (mmt-90) cc_final: 0.7434 (mmt90) REVERT: L 274 TYR cc_start: 0.6223 (m-80) cc_final: 0.5067 (m-80) REVERT: L 296 LEU cc_start: 0.8436 (mp) cc_final: 0.7701 (tp) REVERT: L 382 CYS cc_start: 0.7521 (m) cc_final: 0.6501 (t) REVERT: N 40 ASP cc_start: 0.8486 (m-30) cc_final: 0.8083 (m-30) REVERT: N 93 VAL cc_start: 0.9558 (t) cc_final: 0.9176 (m) REVERT: N 197 MET cc_start: 0.8886 (mmm) cc_final: 0.8480 (tpp) REVERT: N 209 CYS cc_start: 0.8090 (m) cc_final: 0.7771 (t) REVERT: N 257 ASP cc_start: 0.8275 (t0) cc_final: 0.7909 (t0) outliers start: 0 outliers final: 0 residues processed: 666 average time/residue: 0.8973 time to fit residues: 958.7787 Evaluate side-chains 558 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 558 time to evaluate : 4.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 8.9990 chunk 344 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 298 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 324 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 332 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 ASN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN ** I 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 305 ASN ** K 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.101552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.083580 restraints weight = 267981.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.087269 restraints weight = 118490.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.089683 restraints weight = 68393.785| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.6822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35024 Z= 0.270 Angle : 0.542 6.786 47382 Z= 0.285 Chirality : 0.039 0.176 5008 Planarity : 0.004 0.045 6102 Dihedral : 8.780 179.387 4798 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.13), residues: 4084 helix: 0.90 (0.12), residues: 1762 sheet: 0.02 (0.23), residues: 552 loop : -0.45 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 306 HIS 0.008 0.002 HIS M 89 PHE 0.031 0.002 PHE B 359 TYR 0.019 0.002 TYR G 236 ARG 0.006 0.001 ARG H 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16567.41 seconds wall clock time: 286 minutes 59.51 seconds (17219.51 seconds total)