Starting phenix.real_space_refine on Fri Feb 16 13:54:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz9_0315/02_2024/6hz9_0315_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz9_0315/02_2024/6hz9_0315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz9_0315/02_2024/6hz9_0315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz9_0315/02_2024/6hz9_0315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz9_0315/02_2024/6hz9_0315_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz9_0315/02_2024/6hz9_0315_trim_updated.pdb" } resolution = 4.8 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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 GLU 438": "OE1" <-> "OE2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "D GLU 181": "OE1" <-> "OE2" 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 TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 427": "OE1" <-> "OE2" Residue "M TYR 62": "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 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 GLU 438": "OE1" <-> "OE2" Residue "I GLU 439": "OE1" <-> "OE2" Residue "J GLU 181": "OE1" <-> "OE2" 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 TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 427": "OE1" <-> "OE2" Residue "N TYR 62": "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 GLU 331": "OE1" <-> "OE2" Residue "N GLU 338": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 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: 22.18, per 1000 atoms: 0.33 Number of scatterers: 67582 At special positions: 0 Unit cell: (190.05, 135.45, 127.05, 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: 47.10 Conformation dependent library (CDL) restraints added in 5.1 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: 198 helices and 30 sheets defined 44.1% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.44 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: 3.853A pdb=" N ARG A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.742A 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 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: 3.537A 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 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 344 through 349 removed outlier: 3.886A pdb=" N ARG A 348 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 3.981A 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 removed outlier: 3.544A pdb=" N GLN A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) 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 431 removed outlier: 3.546A pdb=" N ILE A 428 " --> pdb=" O TRP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'B' and resid 170 through 175 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 207 through 219 removed outlier: 4.018A pdb=" N ARG B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 219 " --> pdb=" O ALA B 215 " (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 Processing helix chain 'B' and resid 286 through 296 removed outlier: 6.612A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N MET B 295 " --> pdb=" O GLY B 291 " (cutoff:3.500A) removed outlier: 3.753A 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 Processing helix chain 'B' and resid 375 through 394 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 Processing helix chain 'C' and resid 207 through 219 removed outlier: 3.865A pdb=" N ARG C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 3.928A 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: 6.227A pdb=" N GLU C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET C 294 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET C 295 " --> pdb=" O GLY C 291 " (cutoff:3.500A) removed outlier: 3.565A 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: 3.797A 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 Processing helix chain 'C' and resid 433 through 440 Processing helix chain 'C' and resid 445 through 456 removed outlier: 3.558A pdb=" N LEU C 456 " --> pdb=" O THR C 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 207 through 219 removed outlier: 3.503A pdb=" N TYR D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) 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: 6.330A pdb=" N GLU D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N MET D 295 " --> pdb=" O GLY D 291 " (cutoff:3.500A) removed outlier: 3.597A 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: 3.590A pdb=" N LEU D 368 " --> pdb=" O PHE D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 392 Processing helix chain 'D' and resid 422 through 431 removed outlier: 3.573A 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: 3.791A 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 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: 6.928A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL E 293 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 4.444A 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: 3.678A pdb=" N ARG E 349 " --> pdb=" O ALA E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 369 Processing helix chain 'E' and resid 375 through 394 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: 3.644A pdb=" N TYR F 216 " --> pdb=" O ARG F 212 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR F 219 " --> pdb=" O ALA F 215 " (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: 3.728A pdb=" N GLN F 264 " --> pdb=" O TYR F 260 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN F 265 " --> pdb=" O ASN F 261 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU F 268 " --> pdb=" O GLN F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 295 removed outlier: 6.795A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL F 293 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET F 294 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 4.810A 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: 4.264A pdb=" N GLU F 427 " --> pdb=" O GLN F 423 " (cutoff:3.500A) removed outlier: 3.949A 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: 3.663A pdb=" N LYS F 454 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU F 455 " --> pdb=" O TRP F 451 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU F 456 " --> pdb=" O THR F 452 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 19 removed outlier: 3.819A pdb=" N TYR M 12 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR M 13 " --> pdb=" O ARG M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 56 removed outlier: 3.719A pdb=" N LEU M 51 " --> pdb=" O ASN M 47 " (cutoff:3.500A) removed outlier: 3.605A 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: 3.650A pdb=" N ILE M 109 " --> pdb=" O ALA M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 136 Processing helix chain 'M' and resid 147 through 155 removed outlier: 3.661A pdb=" N ASN M 154 " --> pdb=" O PHE M 150 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY M 155 " --> pdb=" O SER M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 174 Processing helix chain 'M' and resid 190 through 192 No H-bonds generated for 'chain 'M' and resid 190 through 192' Processing helix chain 'M' and resid 194 through 212 removed outlier: 3.534A pdb=" N ARG M 210 " --> pdb=" O TYR M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 288 removed outlier: 3.889A pdb=" N MET M 283 " --> pdb=" O TYR M 280 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN M 284 " --> pdb=" O GLN M 281 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER M 288 " --> pdb=" O TYR M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 332 through 347 removed outlier: 3.583A pdb=" N GLU M 345 " --> pdb=" O ASP M 341 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR M 346 " --> pdb=" O ILE M 342 " (cutoff:3.500A) 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: 3.854A pdb=" N ARG G 212 " --> pdb=" O THR G 208 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG G 213 " --> pdb=" O PHE G 209 " (cutoff:3.500A) removed outlier: 3.742A 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 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: 3.537A 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 338 through 340 No H-bonds generated for 'chain 'G' and resid 338 through 340' Processing helix chain 'G' and resid 344 through 349 removed outlier: 3.887A pdb=" N ARG G 348 " --> pdb=" O TYR G 344 " (cutoff:3.500A) removed outlier: 3.980A 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 removed outlier: 3.544A pdb=" N GLN G 383 " --> pdb=" O GLU G 379 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS G 384 " --> pdb=" O SER G 380 " (cutoff:3.500A) 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 431 removed outlier: 3.546A pdb=" N ILE G 428 " --> pdb=" O TRP G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 440 Processing helix chain 'G' and resid 445 through 456 Processing helix chain 'H' and resid 170 through 175 Processing helix chain 'H' and resid 181 through 194 Processing helix chain 'H' and resid 207 through 219 removed outlier: 4.018A pdb=" N ARG H 212 " --> pdb=" O THR H 208 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG H 213 " --> pdb=" O PHE H 209 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR H 216 " --> pdb=" O ARG H 212 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU H 218 " --> pdb=" O LEU H 214 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR H 219 " --> pdb=" O ALA H 215 " (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 Processing helix chain 'H' and resid 286 through 296 removed outlier: 6.613A pdb=" N GLU H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL H 293 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N MET H 294 " --> pdb=" O PHE H 290 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N MET H 295 " --> pdb=" O GLY H 291 " (cutoff:3.500A) removed outlier: 3.753A 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 Processing helix chain 'H' and resid 375 through 394 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 Processing helix chain 'I' and resid 207 through 219 removed outlier: 3.865A pdb=" N ARG I 212 " --> pdb=" O THR I 208 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG I 213 " --> pdb=" O PHE I 209 " (cutoff:3.500A) removed outlier: 3.928A 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: 6.225A pdb=" N GLU I 292 " --> pdb=" O LYS I 288 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET I 294 " --> pdb=" O PHE I 290 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET I 295 " --> pdb=" O GLY I 291 " (cutoff:3.500A) removed outlier: 3.565A 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: 3.796A 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 Processing helix chain 'I' and resid 433 through 440 Processing helix chain 'I' and resid 445 through 456 removed outlier: 3.559A pdb=" N LEU I 456 " --> pdb=" O THR I 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 194 Processing helix chain 'J' and resid 207 through 219 removed outlier: 3.503A pdb=" N TYR J 216 " --> pdb=" O ARG J 212 " (cutoff:3.500A) 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: 6.330A pdb=" N GLU J 292 " --> pdb=" O LYS J 288 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL J 293 " --> pdb=" O VAL J 289 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET J 294 " --> pdb=" O PHE J 290 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N MET J 295 " --> pdb=" O GLY J 291 " (cutoff:3.500A) removed outlier: 3.597A 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: 3.590A pdb=" N LEU J 368 " --> pdb=" O PHE J 364 " (cutoff:3.500A) Processing helix chain 'J' and resid 375 through 392 Processing helix chain 'J' and resid 422 through 431 removed outlier: 3.573A 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: 3.791A 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 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: 6.928A pdb=" N GLU K 292 " --> pdb=" O LYS K 288 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL K 293 " --> pdb=" O VAL K 289 " (cutoff:3.500A) removed outlier: 4.443A 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: 3.678A pdb=" N ARG K 349 " --> pdb=" O ALA K 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 369 Processing helix chain 'K' and resid 375 through 394 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: 3.643A pdb=" N TYR L 216 " --> pdb=" O ARG L 212 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR L 219 " --> pdb=" O ALA L 215 " (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: 3.728A pdb=" N GLN L 264 " --> pdb=" O TYR L 260 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN L 265 " --> pdb=" O ASN L 261 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA L 266 " --> pdb=" O PHE L 262 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU L 268 " --> pdb=" O GLN L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 295 removed outlier: 6.795A pdb=" N GLU L 292 " --> pdb=" O LYS L 288 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL L 293 " --> pdb=" O VAL L 289 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET L 294 " --> pdb=" O PHE L 290 " (cutoff:3.500A) removed outlier: 4.810A 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: 4.264A pdb=" N GLU L 427 " --> pdb=" O GLN L 423 " (cutoff:3.500A) removed outlier: 3.950A 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: 3.662A pdb=" N LYS L 454 " --> pdb=" O LYS L 450 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU L 455 " --> pdb=" O TRP L 451 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU L 456 " --> pdb=" O THR L 452 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 19 removed outlier: 3.817A pdb=" N TYR N 12 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR N 13 " --> pdb=" O ARG N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 56 removed outlier: 3.719A pdb=" N LEU N 51 " --> pdb=" O ASN N 47 " (cutoff:3.500A) removed outlier: 3.605A 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: 3.651A pdb=" N ILE N 109 " --> pdb=" O ALA N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 136 Processing helix chain 'N' and resid 147 through 155 removed outlier: 3.661A pdb=" N ASN N 154 " --> pdb=" O PHE N 150 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY N 155 " --> pdb=" O SER N 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 174 Processing helix chain 'N' and resid 190 through 192 No H-bonds generated for 'chain 'N' and resid 190 through 192' Processing helix chain 'N' and resid 194 through 212 removed outlier: 3.534A pdb=" N ARG N 210 " --> pdb=" O TYR N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 288 removed outlier: 3.889A pdb=" N MET N 283 " --> pdb=" O TYR N 280 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN N 284 " --> pdb=" O GLN N 281 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER N 288 " --> pdb=" O TYR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 332 through 347 removed outlier: 3.585A pdb=" N GLU N 345 " --> pdb=" O ASP N 341 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR N 346 " --> pdb=" O ILE N 342 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 351 through 354 removed outlier: 8.898A pdb=" N ILE A 197 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE A 328 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU A 199 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY A 330 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TYR A 274 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE A 329 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE A 276 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU A 331 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 6.740A 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: 8.864A pdb=" N ILE B 197 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE B 328 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LEU B 199 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY B 330 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR B 274 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE B 329 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE B 276 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N LEU B 331 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.325A 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: 6.712A pdb=" N ILE C 328 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU C 199 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY C 330 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLY C 201 " --> pdb=" O GLY C 330 " (cutoff:3.500A) removed outlier: 6.406A 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 Processing sheet with id= G, first strand: chain 'D' and resid 351 through 354 removed outlier: 6.939A pdb=" N ILE D 328 " --> pdb=" O ILE D 197 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU D 199 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY D 330 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLY D 201 " --> pdb=" O GLY D 330 " (cutoff:3.500A) removed outlier: 5.781A 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 355 removed outlier: 4.024A pdb=" N SER E 351 " --> pdb=" O ASN E 196 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE E 355 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ILE E 197 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE E 328 " --> pdb=" O ILE E 197 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU E 199 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY E 330 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N GLY E 201 " --> pdb=" O GLY E 330 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N MET E 332 " --> pdb=" O GLY E 201 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR E 274 " --> pdb=" O TYR E 327 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE E 329 " --> pdb=" O TYR E 274 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N PHE E 276 " --> pdb=" O ILE E 329 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU E 331 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE E 278 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASN E 333 " --> pdb=" O ILE E 278 " (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: 6.523A pdb=" N ILE F 328 " --> pdb=" O ILE F 197 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU F 199 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 6.599A 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: 3.824A pdb=" N ASN M 100 " --> pdb=" O ASP M 61 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'M' and resid 217 through 219 Processing sheet with id= O, first strand: chain 'M' and resid 253 through 257 removed outlier: 3.861A pdb=" N ILE M 302 " --> pdb=" O ASP M 257 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP M 320 " --> pdb=" O GLY M 299 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LEU M 301 " --> pdb=" O ASP M 320 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY M 322 " --> pdb=" O LEU M 301 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N TYR M 303 " --> pdb=" O GLY M 322 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS M 324 " --> pdb=" O TYR M 303 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N HIS M 305 " --> pdb=" O CYS M 324 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N VAL M 326 " --> pdb=" O HIS M 305 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 351 through 354 removed outlier: 8.899A pdb=" N ILE G 197 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE G 328 " --> pdb=" O ILE G 197 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU G 199 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY G 330 " --> pdb=" O LEU G 199 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TYR G 274 " --> pdb=" O TYR G 327 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE G 329 " --> pdb=" O TYR G 274 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE G 276 " --> pdb=" O ILE G 329 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU G 331 " --> pdb=" O PHE G 276 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE G 278 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 243 through 247 Processing sheet with id= R, first strand: chain 'H' and resid 351 through 354 removed outlier: 8.865A pdb=" N ILE H 197 " --> pdb=" O VAL H 326 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE H 328 " --> pdb=" O ILE H 197 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N LEU H 199 " --> pdb=" O ILE H 328 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLY H 330 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR H 274 " --> pdb=" O TYR H 327 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE H 329 " --> pdb=" O TYR H 274 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE H 276 " --> pdb=" O ILE H 329 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N LEU H 331 " --> pdb=" O PHE H 276 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ILE H 278 " --> pdb=" O LEU H 331 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 243 through 247 Processing sheet with id= T, first strand: chain 'I' and resid 351 through 354 removed outlier: 6.712A pdb=" N ILE I 328 " --> pdb=" O ILE I 197 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU I 199 " --> pdb=" O ILE I 328 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY I 330 " --> pdb=" O LEU I 199 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLY I 201 " --> pdb=" O GLY I 330 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N MET I 332 " --> pdb=" O GLY I 201 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 243 through 247 Processing sheet with id= V, first strand: chain 'J' and resid 351 through 354 removed outlier: 6.939A pdb=" N ILE J 328 " --> pdb=" O ILE J 197 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU J 199 " --> pdb=" O ILE J 328 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLY J 330 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLY J 201 " --> pdb=" O GLY J 330 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N MET J 332 " --> pdb=" O GLY J 201 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 245 through 247 Processing sheet with id= X, first strand: chain 'K' and resid 351 through 355 removed outlier: 4.024A pdb=" N SER K 351 " --> pdb=" O ASN K 196 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE K 355 " --> pdb=" O GLN K 200 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ILE K 197 " --> pdb=" O VAL K 326 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE K 328 " --> pdb=" O ILE K 197 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU K 199 " --> pdb=" O ILE K 328 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY K 330 " --> pdb=" O LEU K 199 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N GLY K 201 " --> pdb=" O GLY K 330 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N MET K 332 " --> pdb=" O GLY K 201 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TYR K 274 " --> pdb=" O TYR K 327 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE K 329 " --> pdb=" O TYR K 274 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N PHE K 276 " --> pdb=" O ILE K 329 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU K 331 " --> pdb=" O PHE K 276 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE K 278 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASN K 333 " --> pdb=" O ILE K 278 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 243 through 247 Processing sheet with id= Z, first strand: chain 'L' and resid 351 through 353 removed outlier: 6.522A pdb=" N ILE L 328 " --> pdb=" O ILE L 197 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU L 199 " --> pdb=" O ILE L 328 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY L 330 " --> pdb=" O LEU L 199 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 243 through 247 Processing sheet with id= AB, first strand: chain 'N' and resid 61 through 69 removed outlier: 3.824A pdb=" N ASN N 100 " --> pdb=" O ASP N 61 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'N' and resid 217 through 219 Processing sheet with id= AD, first strand: chain 'N' and resid 253 through 256 removed outlier: 6.338A pdb=" N ASP N 320 " --> pdb=" O GLY N 299 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LEU N 301 " --> pdb=" O ASP N 320 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLY N 322 " --> pdb=" O LEU N 301 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N TYR N 303 " --> pdb=" O GLY N 322 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS N 324 " --> pdb=" O TYR N 303 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N HIS N 305 " --> pdb=" O CYS N 324 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL N 326 " --> pdb=" O HIS N 305 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 3249 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: 25.17 Time building geometry restraints manager: 49.42 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: 62 1.22 - 1.42: 14960 1.42 - 1.62: 19805 1.62 - 1.82: 259 Bond restraints: 68392 Sorted by residual: bond pdb=" N3B GNP G1001 " pdb=" PG GNP G1001 " ideal model delta sigma weight residual 1.801 1.562 0.239 2.00e-02 2.50e+03 1.42e+02 bond pdb=" N3B GNP A1001 " pdb=" PG GNP A1001 " ideal model delta sigma weight residual 1.801 1.563 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" N3B GNP I1001 " pdb=" PG GNP I1001 " ideal model delta sigma weight residual 1.801 1.566 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" N3B GNP C1001 " pdb=" PG GNP C1001 " ideal model delta sigma weight residual 1.801 1.566 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" N3B GNP H1001 " pdb=" PG GNP H1001 " ideal model delta sigma weight residual 1.801 1.578 0.223 2.00e-02 2.50e+03 1.24e+02 ... (remaining 68387 not shown) Histogram of bond angle deviations from ideal: 57.32 - 72.64: 24 72.64 - 87.97: 23 87.97 - 103.29: 381 103.29 - 118.61: 91160 118.61 - 133.94: 31778 Bond angle restraints: 123366 Sorted by residual: angle pdb=" C GLU E 438 " pdb=" N GLU E 439 " pdb=" H GLU E 439 " ideal model delta sigma weight residual 125.01 67.94 57.07 3.00e+00 1.11e-01 3.62e+02 angle pdb=" C GLU E 391 " pdb=" N ILE E 392 " pdb=" H ILE E 392 " ideal model delta sigma weight residual 124.92 67.93 56.99 3.00e+00 1.11e-01 3.61e+02 angle pdb=" C LYS E 384 " pdb=" N MET E 385 " pdb=" H MET E 385 " ideal model delta sigma weight residual 125.00 68.02 56.99 3.00e+00 1.11e-01 3.61e+02 angle pdb=" C SER E 380 " pdb=" N LEU E 381 " pdb=" H LEU E 381 " ideal model delta sigma weight residual 125.01 68.04 56.97 3.00e+00 1.11e-01 3.61e+02 angle pdb=" CA ASP F 336 " pdb=" N ASP F 336 " pdb=" H ASP F 336 " ideal model delta sigma weight residual 114.23 57.32 56.91 3.00e+00 1.11e-01 3.60e+02 ... (remaining 123361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 31451 36.00 - 71.99: 778 71.99 - 107.99: 29 107.99 - 143.98: 2 143.98 - 179.98: 10 Dihedral angle restraints: 32270 sinusoidal: 17632 harmonic: 14638 Sorted by residual: dihedral pdb=" CD ARG G 226 " pdb=" NE ARG G 226 " pdb=" CZ ARG G 226 " pdb=" NH1 ARG G 226 " ideal model delta sinusoidal sigma weight residual 0.00 -179.98 179.98 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 -179.96 179.96 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG K 404 " pdb=" NE ARG K 404 " pdb=" CZ ARG K 404 " pdb=" NH1 ARG K 404 " ideal model delta sinusoidal sigma weight residual 0.00 -179.79 179.79 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 32267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4001 0.059 - 0.117: 875 0.117 - 0.176: 104 0.176 - 0.234: 20 0.234 - 0.293: 8 Chirality restraints: 5008 Sorted by residual: chirality pdb=" C4' GDP F1001 " pdb=" C5' GDP F1001 " pdb=" O4' GDP F1001 " pdb=" C3' GDP F1001 " both_signs ideal model delta sigma weight residual False -2.50 -2.79 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C4' GDP L1001 " pdb=" C5' GDP L1001 " pdb=" O4' GDP L1001 " pdb=" C3' GDP L1001 " both_signs ideal model delta sigma weight residual False -2.50 -2.79 0.29 2.00e-01 2.50e+01 2.12e+00 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 -2.73 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 5005 not shown) Planarity restraints: 10012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN I 243 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.82e+00 pdb=" C GLN I 243 " -0.042 2.00e-02 2.50e+03 pdb=" O GLN I 243 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY I 244 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 243 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C GLN C 243 " 0.041 2.00e-02 2.50e+03 pdb=" O GLN C 243 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY C 244 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 322 " -0.039 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO C 323 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 323 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 323 " -0.032 5.00e-02 4.00e+02 ... (remaining 10009 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 2657 2.16 - 2.77: 133377 2.77 - 3.38: 188829 3.38 - 3.99: 240945 3.99 - 4.60: 386643 Nonbonded interactions: 952451 Sorted by model distance: nonbonded pdb=" H LEU E 388 " pdb=" HA LEU E 388 " model vdw 1.548 1.816 nonbonded pdb=" H MET E 385 " pdb=" HA MET E 385 " model vdw 1.554 1.816 nonbonded pdb=" H ASP F 336 " pdb=" HA ASP F 336 " model vdw 1.558 1.816 nonbonded pdb=" H ILE E 392 " pdb=" HA ILE E 392 " model vdw 1.566 1.816 nonbonded pdb=" H LYS E 384 " pdb=" HA LYS E 384 " model vdw 1.568 1.816 ... (remaining 952446 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: 0.800 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: 0.780 Extract box with map and model: 5.820 Check model and map are aligned: 0.760 Set scattering table: 0.500 Process input model: 175.450 Find NCS groups from input model: 3.380 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 190.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.239 35024 Z= 0.610 Angle : 1.012 13.970 47382 Z= 0.517 Chirality : 0.049 0.293 5008 Planarity : 0.005 0.058 6102 Dihedral : 14.620 179.978 13368 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.51 % Allowed : 5.65 % Favored : 93.84 % 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: -0.60 (0.12), residues: 4084 helix: -0.33 (0.11), residues: 1584 sheet: 0.28 (0.22), residues: 542 loop : -0.52 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 306 HIS 0.013 0.003 HIS D 233 PHE 0.033 0.003 PHE B 377 TYR 0.034 0.003 TYR K 238 ARG 0.016 0.001 ARG M 83 *********************** 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 1318 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1299 time to evaluate : 4.333 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 200 GLN cc_start: 0.8270 (tt0) cc_final: 0.7803 (tm-30) REVERT: A 280 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8002 (mm-30) REVERT: A 295 MET cc_start: 0.7591 (ttt) cc_final: 0.6727 (ttp) REVERT: A 388 LEU cc_start: 0.9517 (tp) cc_final: 0.9258 (tt) REVERT: A 430 MET cc_start: 0.8805 (mmt) cc_final: 0.8487 (mtp) REVERT: B 185 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8488 (pt0) REVERT: B 234 GLN cc_start: 0.8896 (tt0) cc_final: 0.8341 (tp-100) REVERT: B 274 TYR cc_start: 0.7213 (m-80) cc_final: 0.6087 (m-80) REVERT: B 288 LYS cc_start: 0.9250 (tttt) cc_final: 0.8978 (tppt) REVERT: B 339 LEU cc_start: 0.8804 (mt) cc_final: 0.8330 (mt) REVERT: C 189 LYS cc_start: 0.8885 (tttt) cc_final: 0.8629 (mmmt) REVERT: C 235 SER cc_start: 0.9637 (m) cc_final: 0.9000 (t) REVERT: C 277 ILE cc_start: 0.9043 (mt) cc_final: 0.8414 (mt) REVERT: D 184 ILE cc_start: 0.9559 (tt) cc_final: 0.9334 (tt) REVERT: D 196 ASN cc_start: 0.8257 (m-40) cc_final: 0.7673 (m-40) REVERT: D 197 ILE cc_start: 0.8897 (pt) cc_final: 0.8621 (mt) REVERT: D 228 ASN cc_start: 0.8328 (t0) cc_final: 0.7421 (p0) REVERT: D 288 LYS cc_start: 0.9272 (ttpt) cc_final: 0.9025 (tttt) REVERT: D 320 PHE cc_start: 0.9005 (t80) cc_final: 0.8336 (t80) REVERT: D 336 ASP cc_start: 0.7868 (p0) cc_final: 0.7325 (p0) REVERT: D 431 THR cc_start: 0.8003 (m) cc_final: 0.6991 (m) REVERT: D 438 GLU cc_start: 0.9089 (tt0) cc_final: 0.8705 (tm-30) REVERT: D 455 LEU cc_start: 0.7995 (mt) cc_final: 0.7522 (tt) REVERT: E 246 ARG cc_start: 0.8822 (mmt180) cc_final: 0.8313 (mmt-90) REVERT: E 255 LYS cc_start: 0.8873 (tmtt) cc_final: 0.8317 (tmtt) REVERT: E 440 TYR cc_start: 0.8758 (m-10) cc_final: 0.8381 (m-10) REVERT: F 197 ILE cc_start: 0.9236 (pt) cc_final: 0.8892 (mm) REVERT: F 275 ILE cc_start: 0.8445 (mt) cc_final: 0.7563 (mt) REVERT: F 297 MET cc_start: 0.8206 (ppp) cc_final: 0.7515 (ppp) REVERT: M 52 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8498 (tp40) REVERT: M 59 GLU cc_start: 0.8951 (pt0) cc_final: 0.8361 (pt0) REVERT: M 63 ASN cc_start: 0.9180 (m110) cc_final: 0.8939 (t0) REVERT: M 67 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8448 (mp0) REVERT: M 97 ASP cc_start: 0.8822 (p0) cc_final: 0.8549 (p0) REVERT: M 134 TYR cc_start: 0.8882 (t80) cc_final: 0.8564 (t80) REVERT: M 137 LEU cc_start: 0.9629 (mt) cc_final: 0.9411 (mm) REVERT: M 167 SER cc_start: 0.9322 (m) cc_final: 0.9043 (t) REVERT: M 174 ASN cc_start: 0.8974 (m-40) cc_final: 0.8132 (t0) REVERT: M 180 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8929 (mm110) REVERT: M 280 TYR cc_start: 0.9081 (m-80) cc_final: 0.8517 (m-80) REVERT: G 200 GLN cc_start: 0.8337 (tt0) cc_final: 0.7827 (tm-30) REVERT: G 295 MET cc_start: 0.7779 (ttt) cc_final: 0.7180 (ttp) REVERT: G 388 LEU cc_start: 0.9527 (tp) cc_final: 0.9222 (tt) REVERT: G 430 MET cc_start: 0.8805 (mmt) cc_final: 0.8469 (mtm) REVERT: H 198 ILE cc_start: 0.8738 (mt) cc_final: 0.7922 (mt) REVERT: H 238 TYR cc_start: 0.8499 (t80) cc_final: 0.8258 (t80) REVERT: H 279 ASP cc_start: 0.8177 (t0) cc_final: 0.7975 (t70) REVERT: H 288 LYS cc_start: 0.9410 (tttt) cc_final: 0.9171 (tppt) REVERT: H 292 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8050 (mt-10) REVERT: H 353 ILE cc_start: 0.8558 (mt) cc_final: 0.7687 (mp) REVERT: I 189 LYS cc_start: 0.9005 (tttt) cc_final: 0.8690 (mmmt) REVERT: I 192 THR cc_start: 0.9346 (m) cc_final: 0.9024 (t) REVERT: I 235 SER cc_start: 0.9559 (m) cc_final: 0.9098 (t) REVERT: I 331 LEU cc_start: 0.7717 (mt) cc_final: 0.7110 (mt) REVERT: I 367 PHE cc_start: 0.8666 (t80) cc_final: 0.8181 (t80) REVERT: J 184 ILE cc_start: 0.9565 (tt) cc_final: 0.9338 (tt) REVERT: J 196 ASN cc_start: 0.8213 (m-40) cc_final: 0.7661 (m-40) REVERT: J 228 ASN cc_start: 0.8385 (t0) cc_final: 0.7556 (p0) REVERT: J 280 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7298 (mm-30) REVERT: J 320 PHE cc_start: 0.8999 (t80) cc_final: 0.8290 (t80) REVERT: J 336 ASP cc_start: 0.7300 (p0) cc_final: 0.6973 (p0) REVERT: J 431 THR cc_start: 0.8083 (m) cc_final: 0.6829 (m) REVERT: J 438 GLU cc_start: 0.9116 (tt0) cc_final: 0.8717 (tm-30) REVERT: J 455 LEU cc_start: 0.7962 (mt) cc_final: 0.7495 (tt) REVERT: K 229 MET cc_start: 0.7820 (ttt) cc_final: 0.7597 (ttt) REVERT: K 278 ILE cc_start: 0.8893 (mt) cc_final: 0.8625 (mp) REVERT: K 320 PHE cc_start: 0.8679 (t80) cc_final: 0.8199 (t80) REVERT: K 423 GLN cc_start: 0.8871 (tt0) cc_final: 0.8658 (mm110) REVERT: L 297 MET cc_start: 0.8407 (ppp) cc_final: 0.7933 (ppp) REVERT: L 367 PHE cc_start: 0.6599 (t80) cc_final: 0.6333 (t80) REVERT: L 392 ILE cc_start: 0.8424 (mt) cc_final: 0.8208 (mp) REVERT: N 52 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8513 (tp40) REVERT: N 167 SER cc_start: 0.9289 (m) cc_final: 0.8979 (t) REVERT: N 174 ASN cc_start: 0.9006 (m-40) cc_final: 0.8167 (t0) REVERT: N 281 GLN cc_start: 0.9047 (mt0) cc_final: 0.7890 (mp10) REVERT: N 283 MET cc_start: 0.8549 (mmt) cc_final: 0.8111 (mtp) outliers start: 19 outliers final: 9 residues processed: 1308 average time/residue: 0.9763 time to fit residues: 2026.0358 Evaluate side-chains 779 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 770 time to evaluate : 4.270 ------------------------------------------------------------------------------- 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: 8.9990 chunk 309 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 208 optimal weight: 0.9990 chunk 165 optimal weight: 9.9990 chunk 319 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 238 optimal weight: 8.9990 chunk 370 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN B 453 ASN C 264 GLN C 386 ASN F 200 GLN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 ASN G 453 ASN H 228 ASN H 299 HIS H 453 ASN I 386 ASN K 390 GLN L 299 HIS ** L 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 10 ASN N 63 ASN N 193 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 35024 Z= 0.323 Angle : 0.700 11.587 47382 Z= 0.388 Chirality : 0.042 0.347 5008 Planarity : 0.005 0.047 6102 Dihedral : 10.324 179.852 4798 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.11 % Allowed : 2.92 % Favored : 96.97 % 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: -0.27 (0.12), residues: 4084 helix: 0.10 (0.11), residues: 1772 sheet: 0.42 (0.22), residues: 550 loop : -0.52 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 332 HIS 0.012 0.001 HIS B 233 PHE 0.033 0.002 PHE D 178 TYR 0.028 0.002 TYR M 161 ARG 0.007 0.001 ARG J 190 *********************** 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 898 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 894 time to evaluate : 4.266 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 200 GLN cc_start: 0.8080 (tt0) cc_final: 0.7602 (tm-30) REVERT: A 218 LEU cc_start: 0.8657 (mt) cc_final: 0.8257 (mt) REVERT: A 276 PHE cc_start: 0.8369 (t80) cc_final: 0.8154 (t80) REVERT: A 278 ILE cc_start: 0.9261 (mp) cc_final: 0.8140 (mp) REVERT: A 387 GLU cc_start: 0.8311 (tp30) cc_final: 0.8051 (tp30) REVERT: A 388 LEU cc_start: 0.9602 (tp) cc_final: 0.9397 (tt) REVERT: A 430 MET cc_start: 0.9021 (mmt) cc_final: 0.8530 (ttp) REVERT: A 456 LEU cc_start: 0.8563 (mt) cc_final: 0.8120 (tt) REVERT: B 265 GLN cc_start: 0.9194 (mt0) cc_final: 0.8820 (mm-40) REVERT: B 274 TYR cc_start: 0.7262 (m-80) cc_final: 0.5993 (m-80) REVERT: B 288 LYS cc_start: 0.9465 (tttt) cc_final: 0.9109 (tppt) REVERT: B 292 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8207 (mp0) REVERT: B 332 MET cc_start: 0.9317 (ppp) cc_final: 0.9035 (ppp) REVERT: C 185 GLU cc_start: 0.8856 (tp30) cc_final: 0.8620 (tp30) REVERT: C 197 ILE cc_start: 0.9204 (pt) cc_final: 0.8860 (pt) REVERT: C 235 SER cc_start: 0.9478 (m) cc_final: 0.9159 (t) REVERT: D 197 ILE cc_start: 0.8884 (pt) cc_final: 0.8538 (mt) REVERT: D 234 GLN cc_start: 0.8931 (pm20) cc_final: 0.8673 (pt0) REVERT: D 320 PHE cc_start: 0.8875 (t80) cc_final: 0.8265 (t80) REVERT: D 405 ILE cc_start: 0.9473 (mt) cc_final: 0.9264 (tp) REVERT: D 412 CYS cc_start: 0.9030 (m) cc_final: 0.7598 (t) REVERT: D 431 THR cc_start: 0.7268 (m) cc_final: 0.6864 (m) REVERT: D 438 GLU cc_start: 0.9159 (tt0) cc_final: 0.8686 (tm-30) REVERT: E 255 LYS cc_start: 0.8989 (tmtt) cc_final: 0.8577 (tmtt) REVERT: E 352 PHE cc_start: 0.8689 (m-10) cc_final: 0.8447 (m-10) REVERT: E 450 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8102 (tppt) REVERT: F 197 ILE cc_start: 0.9152 (pt) cc_final: 0.8686 (mm) REVERT: F 213 ARG cc_start: 0.8317 (mmt-90) cc_final: 0.7914 (mmt90) REVERT: F 297 MET cc_start: 0.7869 (ppp) cc_final: 0.7661 (ppp) REVERT: M 42 LEU cc_start: 0.9244 (tp) cc_final: 0.9017 (mm) REVERT: M 52 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8530 (tp40) REVERT: M 67 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8563 (mp0) REVERT: M 174 ASN cc_start: 0.9014 (m-40) cc_final: 0.8191 (t0) REVERT: M 180 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8924 (mm110) REVERT: M 242 GLU cc_start: 0.6989 (tt0) cc_final: 0.6684 (pm20) REVERT: M 281 GLN cc_start: 0.9235 (mt0) cc_final: 0.8269 (mp10) REVERT: M 340 LEU cc_start: 0.9152 (mm) cc_final: 0.8907 (mm) REVERT: G 200 GLN cc_start: 0.8154 (tt0) cc_final: 0.7675 (tm-30) REVERT: G 218 LEU cc_start: 0.8724 (mt) cc_final: 0.8307 (mt) REVERT: G 236 TYR cc_start: 0.6023 (m-10) cc_final: 0.5425 (m-10) REVERT: G 276 PHE cc_start: 0.8345 (t80) cc_final: 0.8048 (t80) REVERT: G 277 ILE cc_start: 0.9090 (mt) cc_final: 0.8639 (mt) REVERT: G 278 ILE cc_start: 0.9281 (mp) cc_final: 0.8160 (mp) REVERT: G 387 GLU cc_start: 0.8251 (tp30) cc_final: 0.8029 (tp30) REVERT: G 388 LEU cc_start: 0.9629 (tp) cc_final: 0.9384 (tt) REVERT: G 430 MET cc_start: 0.9009 (mmt) cc_final: 0.8505 (ttp) REVERT: H 197 ILE cc_start: 0.9425 (pt) cc_final: 0.9126 (mt) REVERT: H 238 TYR cc_start: 0.8821 (t80) cc_final: 0.8561 (t80) REVERT: H 255 LYS cc_start: 0.9059 (tttm) cc_final: 0.8793 (tptp) REVERT: H 288 LYS cc_start: 0.9526 (tttt) cc_final: 0.9290 (tppt) REVERT: H 328 ILE cc_start: 0.9249 (mm) cc_final: 0.8889 (mm) REVERT: H 332 MET cc_start: 0.9161 (ppp) cc_final: 0.8775 (ppp) REVERT: H 350 PHE cc_start: 0.8592 (m-80) cc_final: 0.8071 (m-80) REVERT: I 176 ASP cc_start: 0.8158 (t0) cc_final: 0.7891 (t0) REVERT: I 197 ILE cc_start: 0.9436 (pt) cc_final: 0.9181 (pt) REVERT: I 200 GLN cc_start: 0.8025 (pt0) cc_final: 0.7720 (pt0) REVERT: I 331 LEU cc_start: 0.7455 (mt) cc_final: 0.7197 (mt) REVERT: I 405 ILE cc_start: 0.9631 (mp) cc_final: 0.9414 (tt) REVERT: I 437 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8893 (tp) REVERT: J 234 GLN cc_start: 0.8830 (pm20) cc_final: 0.8615 (pt0) REVERT: J 320 PHE cc_start: 0.8877 (t80) cc_final: 0.8228 (t80) REVERT: J 405 ILE cc_start: 0.9463 (mt) cc_final: 0.9245 (tp) REVERT: J 412 CYS cc_start: 0.9088 (m) cc_final: 0.7692 (t) REVERT: J 431 THR cc_start: 0.6942 (m) cc_final: 0.6331 (m) REVERT: J 438 GLU cc_start: 0.9174 (tt0) cc_final: 0.8676 (tm-30) REVERT: K 231 GLN cc_start: 0.8071 (tt0) cc_final: 0.7656 (tt0) REVERT: K 255 LYS cc_start: 0.8743 (tmtt) cc_final: 0.8066 (tmtt) REVERT: K 423 GLN cc_start: 0.8936 (tt0) cc_final: 0.8732 (mm110) REVERT: K 446 TYR cc_start: 0.8535 (t80) cc_final: 0.8315 (t80) REVERT: L 367 PHE cc_start: 0.6833 (t80) cc_final: 0.6609 (t80) REVERT: N 52 GLN cc_start: 0.9110 (mm-40) cc_final: 0.8417 (tp40) REVERT: N 174 ASN cc_start: 0.9000 (m-40) cc_final: 0.8130 (t0) REVERT: N 197 MET cc_start: 0.8834 (mmp) cc_final: 0.8606 (tpp) REVERT: N 280 TYR cc_start: 0.9229 (m-80) cc_final: 0.8734 (m-80) outliers start: 4 outliers final: 0 residues processed: 896 average time/residue: 0.9424 time to fit residues: 1341.0812 Evaluate side-chains 700 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 699 time to evaluate : 4.289 ------------------------------------------------------------------------------- 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: 7.9990 chunk 114 optimal weight: 10.0000 chunk 308 optimal weight: 10.0000 chunk 252 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 371 optimal weight: 10.0000 chunk 400 optimal weight: 8.9990 chunk 330 optimal weight: 8.9990 chunk 368 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 297 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 GLN C 366 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 ASN ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 GLN H 264 GLN I 366 ASN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 GLN ** L 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 47 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 35024 Z= 0.395 Angle : 0.725 11.179 47382 Z= 0.399 Chirality : 0.043 0.366 5008 Planarity : 0.006 0.078 6102 Dihedral : 10.398 178.773 4798 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.05 % Allowed : 3.11 % Favored : 96.84 % 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: -0.83 (0.12), residues: 4084 helix: -0.40 (0.11), residues: 1828 sheet: 0.40 (0.22), residues: 594 loop : -0.93 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 451 HIS 0.010 0.002 HIS D 233 PHE 0.043 0.002 PHE K 377 TYR 0.035 0.002 TYR N 201 ARG 0.010 0.001 ARG D 190 *********************** 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 778 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 776 time to evaluate : 4.387 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 276 PHE cc_start: 0.8382 (t80) cc_final: 0.8005 (t80) REVERT: A 387 GLU cc_start: 0.8336 (tp30) cc_final: 0.7997 (tp30) REVERT: A 430 MET cc_start: 0.8993 (mmt) cc_final: 0.8540 (ttp) REVERT: A 456 LEU cc_start: 0.8641 (mt) cc_final: 0.8275 (tt) REVERT: B 238 TYR cc_start: 0.8778 (t80) cc_final: 0.8577 (t80) REVERT: B 265 GLN cc_start: 0.9164 (mt0) cc_final: 0.8884 (mm-40) REVERT: B 288 LYS cc_start: 0.9534 (tttt) cc_final: 0.9218 (tppt) REVERT: B 294 MET cc_start: 0.8081 (tmm) cc_final: 0.7877 (tmm) REVERT: B 332 MET cc_start: 0.9406 (ppp) cc_final: 0.9005 (ppp) REVERT: C 185 GLU cc_start: 0.8980 (tp30) cc_final: 0.8652 (tp30) REVERT: C 197 ILE cc_start: 0.9374 (pt) cc_final: 0.8929 (pt) REVERT: C 200 GLN cc_start: 0.8636 (pt0) cc_final: 0.8143 (pt0) REVERT: D 197 ILE cc_start: 0.9085 (pt) cc_final: 0.8681 (mt) REVERT: D 234 GLN cc_start: 0.8999 (pm20) cc_final: 0.8325 (mt0) REVERT: D 239 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8880 (mt-10) REVERT: D 320 PHE cc_start: 0.8965 (t80) cc_final: 0.8756 (t80) REVERT: D 412 CYS cc_start: 0.9189 (m) cc_final: 0.7836 (t) REVERT: D 431 THR cc_start: 0.7404 (m) cc_final: 0.7076 (m) REVERT: D 438 GLU cc_start: 0.9172 (tt0) cc_final: 0.8707 (tm-30) REVERT: E 294 MET cc_start: 0.8976 (ttp) cc_final: 0.8345 (ttp) REVERT: E 450 LYS cc_start: 0.8543 (ttpt) cc_final: 0.8326 (tppt) REVERT: F 187 ILE cc_start: 0.9610 (mt) cc_final: 0.9349 (tp) REVERT: F 197 ILE cc_start: 0.9214 (pt) cc_final: 0.8710 (mm) REVERT: F 213 ARG cc_start: 0.8333 (mmt-90) cc_final: 0.7990 (mmt180) REVERT: F 297 MET cc_start: 0.7989 (ppp) cc_final: 0.7699 (ppp) REVERT: M 52 GLN cc_start: 0.9232 (mm-40) cc_final: 0.8696 (tp40) REVERT: M 174 ASN cc_start: 0.9112 (m-40) cc_final: 0.8196 (t0) REVERT: M 180 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8850 (mm110) REVERT: M 242 GLU cc_start: 0.6756 (tt0) cc_final: 0.6377 (pm20) REVERT: M 280 TYR cc_start: 0.9266 (m-80) cc_final: 0.8967 (m-80) REVERT: G 221 GLU cc_start: 0.6434 (tt0) cc_final: 0.5913 (mp0) REVERT: G 387 GLU cc_start: 0.8324 (tp30) cc_final: 0.7990 (tp30) REVERT: G 430 MET cc_start: 0.8984 (mmt) cc_final: 0.8457 (ttp) REVERT: H 197 ILE cc_start: 0.9507 (pt) cc_final: 0.9251 (mt) REVERT: H 242 ILE cc_start: 0.9481 (mt) cc_final: 0.8918 (mt) REVERT: H 328 ILE cc_start: 0.9242 (mm) cc_final: 0.8996 (mm) REVERT: H 332 MET cc_start: 0.9125 (ppp) cc_final: 0.8812 (ppp) REVERT: H 350 PHE cc_start: 0.8289 (m-80) cc_final: 0.7957 (m-80) REVERT: I 197 ILE cc_start: 0.9535 (pt) cc_final: 0.9314 (pt) REVERT: I 198 ILE cc_start: 0.9043 (mt) cc_final: 0.8367 (mt) REVERT: I 341 VAL cc_start: 0.8912 (t) cc_final: 0.8687 (p) REVERT: J 231 GLN cc_start: 0.8670 (mt0) cc_final: 0.8335 (tt0) REVERT: J 234 GLN cc_start: 0.8898 (pm20) cc_final: 0.8316 (mt0) REVERT: J 294 MET cc_start: 0.9154 (ttp) cc_final: 0.8803 (ttp) REVERT: J 320 PHE cc_start: 0.8944 (t80) cc_final: 0.8733 (t80) REVERT: J 405 ILE cc_start: 0.9452 (mt) cc_final: 0.9251 (tp) REVERT: J 412 CYS cc_start: 0.9228 (m) cc_final: 0.7905 (t) REVERT: J 431 THR cc_start: 0.6875 (m) cc_final: 0.6589 (m) REVERT: J 438 GLU cc_start: 0.9167 (tt0) cc_final: 0.8682 (tm-30) REVERT: K 422 THR cc_start: 0.7950 (m) cc_final: 0.7625 (m) REVERT: K 446 TYR cc_start: 0.8519 (t80) cc_final: 0.8302 (t80) REVERT: L 187 ILE cc_start: 0.9637 (mt) cc_final: 0.9382 (tp) REVERT: N 52 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8501 (tp40) REVERT: N 174 ASN cc_start: 0.9064 (m-40) cc_final: 0.8175 (t0) REVERT: N 281 GLN cc_start: 0.9180 (mp10) cc_final: 0.8445 (mp10) REVERT: N 327 ASN cc_start: 0.8654 (p0) cc_final: 0.8454 (p0) outliers start: 2 outliers final: 2 residues processed: 778 average time/residue: 0.9001 time to fit residues: 1116.5415 Evaluate side-chains 643 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 641 time to evaluate : 4.275 ------------------------------------------------------------------------------- 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: 5.9990 chunk 279 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 177 optimal weight: 0.1980 chunk 249 optimal weight: 4.9990 chunk 372 optimal weight: 0.6980 chunk 394 optimal weight: 8.9990 chunk 194 optimal weight: 0.7980 chunk 353 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 ASN ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 GLN J 200 GLN J 366 ASN ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 10 ASN N 47 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35024 Z= 0.200 Angle : 0.574 11.940 47382 Z= 0.309 Chirality : 0.041 0.352 5008 Planarity : 0.004 0.065 6102 Dihedral : 10.164 179.456 4798 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.03 % Allowed : 1.32 % Favored : 98.65 % 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: -0.34 (0.12), residues: 4084 helix: 0.03 (0.11), residues: 1810 sheet: 0.48 (0.22), residues: 594 loop : -0.63 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 332 HIS 0.019 0.002 HIS G 407 PHE 0.022 0.001 PHE K 232 TYR 0.022 0.002 TYR M 161 ARG 0.007 0.000 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 806 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 805 time to evaluate : 4.281 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 276 PHE cc_start: 0.8444 (t80) cc_final: 0.7908 (t80) REVERT: A 277 ILE cc_start: 0.9466 (mp) cc_final: 0.9117 (mp) REVERT: A 278 ILE cc_start: 0.9195 (mp) cc_final: 0.8936 (mp) REVERT: A 280 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7549 (mm-30) REVERT: A 387 GLU cc_start: 0.8203 (tp30) cc_final: 0.7869 (tp30) REVERT: A 388 LEU cc_start: 0.9539 (tt) cc_final: 0.9234 (tt) REVERT: A 430 MET cc_start: 0.8996 (mmt) cc_final: 0.8537 (ttp) REVERT: A 456 LEU cc_start: 0.8536 (mt) cc_final: 0.8202 (tt) REVERT: B 243 GLN cc_start: 0.8244 (tt0) cc_final: 0.7212 (tp-100) REVERT: B 265 GLN cc_start: 0.9131 (mt0) cc_final: 0.8770 (mm-40) REVERT: B 274 TYR cc_start: 0.7171 (m-80) cc_final: 0.5968 (m-80) REVERT: B 288 LYS cc_start: 0.9485 (tttt) cc_final: 0.9179 (tppt) REVERT: B 332 MET cc_start: 0.9400 (ppp) cc_final: 0.9091 (ppp) REVERT: B 414 LEU cc_start: 0.8711 (mt) cc_final: 0.8428 (mp) REVERT: C 185 GLU cc_start: 0.8920 (tp30) cc_final: 0.8606 (tp30) REVERT: C 197 ILE cc_start: 0.9377 (pt) cc_final: 0.9014 (pt) REVERT: C 200 GLN cc_start: 0.8580 (pt0) cc_final: 0.8171 (pt0) REVERT: D 197 ILE cc_start: 0.8956 (pt) cc_final: 0.8434 (mt) REVERT: D 234 GLN cc_start: 0.8991 (pm20) cc_final: 0.8267 (mt0) REVERT: D 239 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8859 (mt-10) REVERT: D 294 MET cc_start: 0.8855 (ttp) cc_final: 0.8545 (ttp) REVERT: D 320 PHE cc_start: 0.8839 (t80) cc_final: 0.8116 (t80) REVERT: D 412 CYS cc_start: 0.9132 (m) cc_final: 0.7743 (t) REVERT: D 431 THR cc_start: 0.6798 (m) cc_final: 0.6473 (m) REVERT: D 438 GLU cc_start: 0.9099 (tt0) cc_final: 0.8614 (tm-30) REVERT: E 450 LYS cc_start: 0.8672 (ttpt) cc_final: 0.8368 (tppt) REVERT: F 197 ILE cc_start: 0.9115 (pt) cc_final: 0.8704 (mm) REVERT: F 213 ARG cc_start: 0.8367 (mmt-90) cc_final: 0.8102 (mmt90) REVERT: F 297 MET cc_start: 0.7814 (ppp) cc_final: 0.7522 (ppp) REVERT: F 324 GLU cc_start: 0.8746 (mp0) cc_final: 0.8514 (mp0) REVERT: M 52 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8484 (tp40) REVERT: M 174 ASN cc_start: 0.9024 (m-40) cc_final: 0.8287 (t0) REVERT: M 180 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8938 (mm110) REVERT: M 242 GLU cc_start: 0.6747 (tt0) cc_final: 0.6406 (pm20) REVERT: M 280 TYR cc_start: 0.9234 (m-80) cc_final: 0.8744 (m-80) REVERT: M 281 GLN cc_start: 0.9296 (mp10) cc_final: 0.8427 (mp10) REVERT: G 276 PHE cc_start: 0.8298 (t80) cc_final: 0.7736 (t80) REVERT: G 278 ILE cc_start: 0.9263 (mp) cc_final: 0.8879 (mp) REVERT: G 280 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7755 (mm-30) REVERT: G 387 GLU cc_start: 0.8202 (tp30) cc_final: 0.7905 (tp30) REVERT: G 388 LEU cc_start: 0.9556 (tt) cc_final: 0.9240 (tt) REVERT: G 430 MET cc_start: 0.8969 (mmt) cc_final: 0.8419 (ttp) REVERT: H 197 ILE cc_start: 0.9459 (pt) cc_final: 0.9128 (mt) REVERT: H 332 MET cc_start: 0.9110 (ppp) cc_final: 0.8820 (ppp) REVERT: H 389 ASN cc_start: 0.9533 (m-40) cc_final: 0.9261 (m110) REVERT: H 397 THR cc_start: 0.8486 (p) cc_final: 0.8185 (t) REVERT: I 197 ILE cc_start: 0.9495 (pt) cc_final: 0.9274 (pt) REVERT: I 239 GLU cc_start: 0.8753 (mp0) cc_final: 0.8516 (mp0) REVERT: I 240 ASP cc_start: 0.9181 (m-30) cc_final: 0.8945 (m-30) REVERT: I 341 VAL cc_start: 0.8883 (t) cc_final: 0.8563 (p) REVERT: I 437 LEU cc_start: 0.9226 (mp) cc_final: 0.8851 (tp) REVERT: J 234 GLN cc_start: 0.8820 (pm20) cc_final: 0.8177 (mt0) REVERT: J 405 ILE cc_start: 0.9448 (mt) cc_final: 0.9241 (tp) REVERT: J 412 CYS cc_start: 0.9160 (m) cc_final: 0.7847 (t) REVERT: J 431 THR cc_start: 0.6078 (m) cc_final: 0.5776 (m) REVERT: J 438 GLU cc_start: 0.9107 (tt0) cc_final: 0.8591 (tm-30) REVERT: K 255 LYS cc_start: 0.8606 (tmtt) cc_final: 0.7963 (tmtt) REVERT: L 213 ARG cc_start: 0.8206 (mmt-90) cc_final: 0.7906 (mmt90) REVERT: L 392 ILE cc_start: 0.8365 (mt) cc_final: 0.7801 (mm) REVERT: N 52 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8373 (tp40) REVERT: N 174 ASN cc_start: 0.8981 (m-40) cc_final: 0.8223 (t0) REVERT: N 280 TYR cc_start: 0.9323 (m-80) cc_final: 0.8471 (m-80) REVERT: N 281 GLN cc_start: 0.9115 (mp10) cc_final: 0.8649 (mp10) outliers start: 1 outliers final: 0 residues processed: 805 average time/residue: 0.9563 time to fit residues: 1235.6659 Evaluate side-chains 670 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 670 time to evaluate : 4.308 ------------------------------------------------------------------------------- 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: 10.0000 chunk 223 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 293 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 336 optimal weight: 4.9990 chunk 272 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 9.9990 chunk 353 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 ASN ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 ASN ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 366 ASN ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 35024 Z= 0.313 Angle : 0.626 11.681 47382 Z= 0.343 Chirality : 0.041 0.365 5008 Planarity : 0.005 0.050 6102 Dihedral : 10.179 179.786 4798 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.03 % Allowed : 2.05 % Favored : 97.92 % 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: -0.69 (0.12), residues: 4084 helix: -0.24 (0.11), residues: 1830 sheet: 0.38 (0.22), residues: 592 loop : -0.86 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 424 HIS 0.008 0.002 HIS J 233 PHE 0.022 0.002 PHE G 410 TYR 0.025 0.002 TYR M 303 ARG 0.006 0.001 ARG B 337 *********************** 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 762 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 761 time to evaluate : 4.322 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 200 GLN cc_start: 0.6876 (tm-30) cc_final: 0.6625 (tm-30) REVERT: A 232 PHE cc_start: 0.8074 (m-10) cc_final: 0.7638 (m-10) REVERT: A 280 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7820 (mm-30) REVERT: A 387 GLU cc_start: 0.8286 (tp30) cc_final: 0.7918 (tp30) REVERT: A 388 LEU cc_start: 0.9550 (tt) cc_final: 0.9330 (tt) REVERT: A 430 MET cc_start: 0.8980 (mmt) cc_final: 0.8474 (ttp) REVERT: A 439 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8825 (mt-10) REVERT: B 265 GLN cc_start: 0.9082 (mt0) cc_final: 0.8822 (mm-40) REVERT: B 274 TYR cc_start: 0.7307 (m-80) cc_final: 0.6113 (m-80) REVERT: B 288 LYS cc_start: 0.9553 (tttt) cc_final: 0.9243 (tppt) REVERT: B 294 MET cc_start: 0.8393 (tmm) cc_final: 0.8120 (tmm) REVERT: B 332 MET cc_start: 0.9342 (ppp) cc_final: 0.9045 (ppp) REVERT: B 414 LEU cc_start: 0.8854 (mt) cc_final: 0.8567 (mp) REVERT: C 185 GLU cc_start: 0.8984 (tp30) cc_final: 0.8694 (tp30) REVERT: C 197 ILE cc_start: 0.9436 (pt) cc_final: 0.9053 (pt) REVERT: C 200 GLN cc_start: 0.8691 (pt0) cc_final: 0.8397 (pt0) REVERT: C 343 ASP cc_start: 0.9061 (t0) cc_final: 0.8800 (t0) REVERT: D 197 ILE cc_start: 0.9084 (pt) cc_final: 0.8533 (mt) REVERT: D 229 MET cc_start: 0.8124 (tmm) cc_final: 0.7855 (tmm) REVERT: D 236 TYR cc_start: 0.9321 (t80) cc_final: 0.8920 (t80) REVERT: D 239 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8733 (mt-10) REVERT: D 276 PHE cc_start: 0.8826 (t80) cc_final: 0.8407 (t80) REVERT: D 320 PHE cc_start: 0.8919 (t80) cc_final: 0.8144 (t80) REVERT: D 366 ASN cc_start: 0.8489 (m110) cc_final: 0.7992 (t0) REVERT: D 385 MET cc_start: 0.8457 (mmt) cc_final: 0.8239 (mmt) REVERT: D 412 CYS cc_start: 0.9269 (m) cc_final: 0.7938 (t) REVERT: D 431 THR cc_start: 0.6910 (m) cc_final: 0.6676 (m) REVERT: D 438 GLU cc_start: 0.9106 (tt0) cc_final: 0.8585 (tm-30) REVERT: E 213 ARG cc_start: 0.7311 (mmt90) cc_final: 0.6842 (mmm160) REVERT: E 294 MET cc_start: 0.9039 (ttp) cc_final: 0.8540 (ttp) REVERT: E 438 GLU cc_start: 0.9176 (tt0) cc_final: 0.8829 (tp30) REVERT: E 450 LYS cc_start: 0.8666 (ttpt) cc_final: 0.8259 (tppt) REVERT: F 187 ILE cc_start: 0.9599 (mt) cc_final: 0.9388 (tp) REVERT: F 197 ILE cc_start: 0.9117 (pt) cc_final: 0.8713 (mm) REVERT: F 213 ARG cc_start: 0.8351 (mmt-90) cc_final: 0.8090 (mmt90) REVERT: F 265 GLN cc_start: 0.9067 (mt0) cc_final: 0.8767 (mp10) REVERT: F 297 MET cc_start: 0.7862 (ppp) cc_final: 0.7463 (ppp) REVERT: M 52 GLN cc_start: 0.9214 (mm-40) cc_final: 0.8688 (tp40) REVERT: M 55 ARG cc_start: 0.8639 (ttm110) cc_final: 0.8000 (mmm-85) REVERT: M 174 ASN cc_start: 0.9070 (m-40) cc_final: 0.8296 (t0) REVERT: M 180 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8800 (mm110) REVERT: M 280 TYR cc_start: 0.9317 (m-80) cc_final: 0.8751 (m-80) REVERT: M 281 GLN cc_start: 0.9324 (mp10) cc_final: 0.8494 (mp10) REVERT: M 340 LEU cc_start: 0.9238 (mm) cc_final: 0.9005 (mm) REVERT: G 200 GLN cc_start: 0.7105 (tm-30) cc_final: 0.6802 (tm-30) REVERT: G 276 PHE cc_start: 0.8363 (t80) cc_final: 0.8013 (t80) REVERT: G 280 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8011 (mm-30) REVERT: G 387 GLU cc_start: 0.8290 (tp30) cc_final: 0.7922 (tp30) REVERT: G 388 LEU cc_start: 0.9556 (tt) cc_final: 0.9319 (tt) REVERT: G 430 MET cc_start: 0.8954 (mmt) cc_final: 0.8406 (ttp) REVERT: H 197 ILE cc_start: 0.9492 (pt) cc_final: 0.9207 (mt) REVERT: H 243 GLN cc_start: 0.8530 (tt0) cc_final: 0.7648 (tp-100) REVERT: H 332 MET cc_start: 0.9122 (ppp) cc_final: 0.8861 (ppp) REVERT: H 389 ASN cc_start: 0.9569 (m-40) cc_final: 0.9281 (m110) REVERT: I 197 ILE cc_start: 0.9588 (pt) cc_final: 0.9312 (pt) REVERT: I 341 VAL cc_start: 0.8932 (t) cc_final: 0.8710 (p) REVERT: J 236 TYR cc_start: 0.9320 (t80) cc_final: 0.9006 (t80) REVERT: J 276 PHE cc_start: 0.8835 (t80) cc_final: 0.8391 (t80) REVERT: J 366 ASN cc_start: 0.8516 (m110) cc_final: 0.8014 (t0) REVERT: J 412 CYS cc_start: 0.9241 (m) cc_final: 0.7896 (t) REVERT: J 431 THR cc_start: 0.6270 (m) cc_final: 0.6014 (m) REVERT: J 438 GLU cc_start: 0.9102 (tt0) cc_final: 0.8615 (tm-30) REVERT: K 438 GLU cc_start: 0.9169 (tt0) cc_final: 0.8928 (tt0) REVERT: L 265 GLN cc_start: 0.8899 (mt0) cc_final: 0.8590 (mp10) REVERT: N 52 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8539 (tp40) REVERT: N 174 ASN cc_start: 0.9044 (m-40) cc_final: 0.8253 (t0) REVERT: N 280 TYR cc_start: 0.9418 (m-80) cc_final: 0.8581 (m-80) REVERT: N 281 GLN cc_start: 0.9217 (mp10) cc_final: 0.8559 (mp10) REVERT: N 283 MET cc_start: 0.8353 (mmm) cc_final: 0.7864 (mmm) outliers start: 1 outliers final: 0 residues processed: 761 average time/residue: 0.8717 time to fit residues: 1069.7294 Evaluate side-chains 638 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 638 time to evaluate : 4.322 ------------------------------------------------------------------------------- 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: 2.9990 chunk 355 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 394 optimal weight: 4.9990 chunk 327 optimal weight: 8.9990 chunk 182 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 GLN ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35024 Z= 0.248 Angle : 0.581 12.351 47382 Z= 0.316 Chirality : 0.041 0.364 5008 Planarity : 0.005 0.115 6102 Dihedral : 9.954 179.933 4798 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -0.55 (0.12), residues: 4084 helix: -0.09 (0.12), residues: 1830 sheet: 0.51 (0.22), residues: 568 loop : -0.86 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 424 HIS 0.008 0.002 HIS M 336 PHE 0.036 0.001 PHE N 78 TYR 0.022 0.002 TYR M 161 ARG 0.006 0.001 ARG M 313 *********************** 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 730 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 730 time to evaluate : 4.445 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 232 PHE cc_start: 0.8125 (m-10) cc_final: 0.7667 (m-10) REVERT: A 276 PHE cc_start: 0.8415 (t80) cc_final: 0.8096 (t80) REVERT: A 280 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7631 (mm-30) REVERT: A 387 GLU cc_start: 0.8207 (tp30) cc_final: 0.7807 (tp30) REVERT: A 388 LEU cc_start: 0.9537 (tt) cc_final: 0.9254 (tt) REVERT: A 430 MET cc_start: 0.8988 (mmt) cc_final: 0.8494 (ttp) REVERT: B 265 GLN cc_start: 0.9052 (mt0) cc_final: 0.8803 (mm-40) REVERT: B 274 TYR cc_start: 0.7345 (m-80) cc_final: 0.6120 (m-80) REVERT: B 288 LYS cc_start: 0.9522 (tttt) cc_final: 0.9249 (tppt) REVERT: B 294 MET cc_start: 0.8498 (tmm) cc_final: 0.8203 (tmm) REVERT: B 414 LEU cc_start: 0.8852 (mt) cc_final: 0.8554 (mp) REVERT: C 197 ILE cc_start: 0.9437 (pt) cc_final: 0.9002 (pt) REVERT: C 343 ASP cc_start: 0.9007 (t0) cc_final: 0.8794 (t0) REVERT: D 197 ILE cc_start: 0.9035 (pt) cc_final: 0.8472 (mt) REVERT: D 234 GLN cc_start: 0.8973 (pm20) cc_final: 0.8334 (pt0) REVERT: D 239 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8752 (mt-10) REVERT: D 276 PHE cc_start: 0.8827 (t80) cc_final: 0.8421 (t80) REVERT: D 320 PHE cc_start: 0.8906 (t80) cc_final: 0.8119 (t80) REVERT: D 366 ASN cc_start: 0.8436 (m110) cc_final: 0.7911 (t0) REVERT: D 412 CYS cc_start: 0.9260 (m) cc_final: 0.7824 (t) REVERT: D 431 THR cc_start: 0.7164 (m) cc_final: 0.6906 (m) REVERT: D 438 GLU cc_start: 0.9088 (tt0) cc_final: 0.8563 (tm-30) REVERT: E 294 MET cc_start: 0.9006 (ttp) cc_final: 0.8504 (ttp) REVERT: E 450 LYS cc_start: 0.8651 (ttpt) cc_final: 0.8262 (tppt) REVERT: F 197 ILE cc_start: 0.9085 (pt) cc_final: 0.8663 (mm) REVERT: F 213 ARG cc_start: 0.8378 (mmt-90) cc_final: 0.8094 (mmt90) REVERT: F 265 GLN cc_start: 0.9090 (mt0) cc_final: 0.8777 (mp10) REVERT: M 52 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8761 (tp40) REVERT: M 55 ARG cc_start: 0.8576 (ttm110) cc_final: 0.8077 (mmm-85) REVERT: M 113 LEU cc_start: 0.9596 (mt) cc_final: 0.9088 (tt) REVERT: M 174 ASN cc_start: 0.9086 (m-40) cc_final: 0.8296 (t0) REVERT: M 280 TYR cc_start: 0.9311 (m-80) cc_final: 0.8715 (m-80) REVERT: M 281 GLN cc_start: 0.9307 (mp10) cc_final: 0.8511 (mp10) REVERT: M 340 LEU cc_start: 0.9290 (mm) cc_final: 0.9043 (mm) REVERT: G 276 PHE cc_start: 0.8307 (t80) cc_final: 0.8040 (t80) REVERT: G 280 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7880 (mm-30) REVERT: G 387 GLU cc_start: 0.8171 (tp30) cc_final: 0.7747 (tp30) REVERT: G 388 LEU cc_start: 0.9544 (tt) cc_final: 0.9230 (tt) REVERT: G 430 MET cc_start: 0.8937 (mmt) cc_final: 0.8428 (ttp) REVERT: H 197 ILE cc_start: 0.9497 (pt) cc_final: 0.9228 (mt) REVERT: H 231 GLN cc_start: 0.8184 (mp10) cc_final: 0.7965 (mp10) REVERT: H 316 ASP cc_start: 0.8951 (p0) cc_final: 0.8747 (p0) REVERT: H 332 MET cc_start: 0.9083 (ppp) cc_final: 0.8866 (ppp) REVERT: H 389 ASN cc_start: 0.9494 (m-40) cc_final: 0.9185 (m110) REVERT: H 414 LEU cc_start: 0.9339 (mt) cc_final: 0.9085 (mp) REVERT: I 197 ILE cc_start: 0.9563 (pt) cc_final: 0.9289 (pt) REVERT: I 341 VAL cc_start: 0.8876 (t) cc_final: 0.8644 (p) REVERT: J 234 GLN cc_start: 0.8890 (pm20) cc_final: 0.8296 (pt0) REVERT: J 276 PHE cc_start: 0.8832 (t80) cc_final: 0.8393 (t80) REVERT: J 280 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7316 (mm-30) REVERT: J 366 ASN cc_start: 0.8447 (m110) cc_final: 0.7927 (t0) REVERT: J 412 CYS cc_start: 0.9306 (m) cc_final: 0.7952 (t) REVERT: J 431 THR cc_start: 0.6391 (m) cc_final: 0.6155 (m) REVERT: J 438 GLU cc_start: 0.9096 (tt0) cc_final: 0.8558 (tm-30) REVERT: K 438 GLU cc_start: 0.9216 (tt0) cc_final: 0.8998 (tp30) REVERT: K 450 LYS cc_start: 0.8290 (ttpt) cc_final: 0.7905 (tppt) REVERT: L 265 GLN cc_start: 0.8871 (mt0) cc_final: 0.8604 (mp10) REVERT: N 52 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8529 (tp40) REVERT: N 174 ASN cc_start: 0.9041 (m-40) cc_final: 0.8235 (t0) REVERT: N 280 TYR cc_start: 0.9413 (m-80) cc_final: 0.8595 (m-80) REVERT: N 281 GLN cc_start: 0.9239 (mp10) cc_final: 0.8633 (mp10) REVERT: N 283 MET cc_start: 0.8376 (mmm) cc_final: 0.7910 (mmm) outliers start: 0 outliers final: 0 residues processed: 730 average time/residue: 0.8809 time to fit residues: 1042.7244 Evaluate side-chains 636 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 636 time to evaluate : 4.478 ------------------------------------------------------------------------------- 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: 0.9980 chunk 44 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 288 optimal weight: 4.9990 chunk 223 optimal weight: 4.9990 chunk 332 optimal weight: 8.9990 chunk 220 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 chunk 246 optimal weight: 9.9990 chunk 239 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 ASN ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 453 ASN ** M 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 453 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 336 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.6312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35024 Z= 0.267 Angle : 0.589 11.905 47382 Z= 0.320 Chirality : 0.041 0.368 5008 Planarity : 0.004 0.069 6102 Dihedral : 9.873 179.960 4798 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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 (0.12), residues: 4084 helix: -0.10 (0.12), residues: 1826 sheet: 0.60 (0.24), residues: 504 loop : -1.01 (0.13), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 287 HIS 0.015 0.002 HIS F 407 PHE 0.016 0.002 PHE D 364 TYR 0.034 0.002 TYR N 201 ARG 0.006 0.001 ARG F 349 *********************** 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 721 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 721 time to evaluate : 4.293 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 232 PHE cc_start: 0.8084 (m-10) cc_final: 0.7615 (m-10) REVERT: A 239 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8072 (mm-30) REVERT: A 276 PHE cc_start: 0.8393 (t80) cc_final: 0.8153 (t80) REVERT: A 280 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7588 (mm-30) REVERT: A 387 GLU cc_start: 0.8217 (tp30) cc_final: 0.7799 (tp30) REVERT: A 388 LEU cc_start: 0.9525 (tt) cc_final: 0.9250 (tt) REVERT: A 430 MET cc_start: 0.8981 (mmt) cc_final: 0.8508 (ttp) REVERT: A 446 TYR cc_start: 0.7031 (t80) cc_final: 0.6659 (t80) REVERT: B 232 PHE cc_start: 0.8347 (m-10) cc_final: 0.7998 (m-10) REVERT: B 283 ARG cc_start: 0.8011 (mtt90) cc_final: 0.7784 (mmt90) REVERT: B 288 LYS cc_start: 0.9548 (tttt) cc_final: 0.9165 (tppt) REVERT: B 320 PHE cc_start: 0.8127 (t80) cc_final: 0.7843 (t80) REVERT: B 414 LEU cc_start: 0.8874 (mt) cc_final: 0.8572 (mp) REVERT: C 197 ILE cc_start: 0.9454 (pt) cc_final: 0.9126 (pt) REVERT: D 229 MET cc_start: 0.8255 (tmm) cc_final: 0.7913 (tmm) REVERT: D 234 GLN cc_start: 0.9069 (pm20) cc_final: 0.8356 (pt0) REVERT: D 236 TYR cc_start: 0.9243 (t80) cc_final: 0.8817 (t80) REVERT: D 239 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8714 (mt-10) REVERT: D 276 PHE cc_start: 0.8848 (t80) cc_final: 0.8444 (t80) REVERT: D 279 ASP cc_start: 0.8268 (t0) cc_final: 0.7434 (t0) REVERT: D 320 PHE cc_start: 0.8918 (t80) cc_final: 0.8109 (t80) REVERT: D 366 ASN cc_start: 0.8450 (m110) cc_final: 0.7931 (t0) REVERT: D 412 CYS cc_start: 0.9322 (m) cc_final: 0.7921 (t) REVERT: D 431 THR cc_start: 0.7450 (m) cc_final: 0.7176 (m) REVERT: D 438 GLU cc_start: 0.9110 (tt0) cc_final: 0.8610 (tm-30) REVERT: E 213 ARG cc_start: 0.7327 (mmt90) cc_final: 0.6857 (mmm160) REVERT: E 294 MET cc_start: 0.9072 (ttp) cc_final: 0.8685 (ttp) REVERT: E 450 LYS cc_start: 0.8699 (ttpt) cc_final: 0.8296 (tppt) REVERT: F 197 ILE cc_start: 0.9118 (pt) cc_final: 0.8787 (mm) REVERT: F 213 ARG cc_start: 0.8466 (mmt-90) cc_final: 0.8149 (mmt90) REVERT: F 265 GLN cc_start: 0.9120 (mt0) cc_final: 0.8784 (mp10) REVERT: F 332 MET cc_start: 0.6312 (tmm) cc_final: 0.6050 (tmm) REVERT: M 52 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8629 (tp40) REVERT: M 280 TYR cc_start: 0.9329 (m-80) cc_final: 0.8714 (m-80) REVERT: M 281 GLN cc_start: 0.9306 (mp10) cc_final: 0.8586 (mp10) REVERT: M 340 LEU cc_start: 0.9292 (mm) cc_final: 0.9051 (mm) REVERT: G 387 GLU cc_start: 0.8144 (tp30) cc_final: 0.7715 (tp30) REVERT: G 388 LEU cc_start: 0.9523 (tt) cc_final: 0.9240 (tt) REVERT: G 430 MET cc_start: 0.8966 (mmt) cc_final: 0.8490 (ttp) REVERT: H 197 ILE cc_start: 0.9509 (pt) cc_final: 0.9262 (mt) REVERT: H 231 GLN cc_start: 0.8336 (mp10) cc_final: 0.8087 (mp10) REVERT: H 243 GLN cc_start: 0.8468 (tt0) cc_final: 0.7452 (tp-100) REVERT: H 316 ASP cc_start: 0.8965 (p0) cc_final: 0.8751 (p0) REVERT: H 332 MET cc_start: 0.9082 (ppp) cc_final: 0.8874 (ppp) REVERT: H 389 ASN cc_start: 0.9526 (m-40) cc_final: 0.9211 (m110) REVERT: H 414 LEU cc_start: 0.9333 (mt) cc_final: 0.9060 (mp) REVERT: I 197 ILE cc_start: 0.9514 (pt) cc_final: 0.9273 (pt) REVERT: J 234 GLN cc_start: 0.8960 (pm20) cc_final: 0.8288 (pt0) REVERT: J 236 TYR cc_start: 0.9267 (t80) cc_final: 0.8957 (t80) REVERT: J 276 PHE cc_start: 0.8836 (t80) cc_final: 0.8400 (t80) REVERT: J 280 GLU cc_start: 0.7782 (mm-30) cc_final: 0.6875 (mm-30) REVERT: J 412 CYS cc_start: 0.9322 (m) cc_final: 0.7943 (t) REVERT: J 431 THR cc_start: 0.6296 (m) cc_final: 0.6085 (m) REVERT: J 438 GLU cc_start: 0.9111 (tt0) cc_final: 0.8600 (tm-30) REVERT: K 450 LYS cc_start: 0.8295 (ttpt) cc_final: 0.7921 (tppt) REVERT: L 265 GLN cc_start: 0.8886 (mt0) cc_final: 0.8587 (mp10) REVERT: N 52 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8547 (tp40) REVERT: N 197 MET cc_start: 0.8930 (mmt) cc_final: 0.8610 (mmp) REVERT: N 280 TYR cc_start: 0.9437 (m-80) cc_final: 0.8646 (m-80) REVERT: N 281 GLN cc_start: 0.9295 (mp10) cc_final: 0.8755 (mp10) REVERT: N 283 MET cc_start: 0.8424 (mmm) cc_final: 0.8030 (mmm) outliers start: 0 outliers final: 0 residues processed: 721 average time/residue: 0.8684 time to fit residues: 1009.0411 Evaluate side-chains 625 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 625 time to evaluate : 4.243 ------------------------------------------------------------------------------- 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: 4.9990 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 chunk 267 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 309 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 200 GLN ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.6472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35024 Z= 0.229 Angle : 0.561 12.269 47382 Z= 0.304 Chirality : 0.041 0.369 5008 Planarity : 0.004 0.050 6102 Dihedral : 9.659 179.717 4798 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: -0.52 (0.12), residues: 4084 helix: 0.05 (0.12), residues: 1810 sheet: 0.64 (0.24), residues: 504 loop : -0.97 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 451 HIS 0.012 0.002 HIS L 407 PHE 0.016 0.001 PHE C 232 TYR 0.021 0.001 TYR G 344 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 710 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 710 time to evaluate : 4.278 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 232 PHE cc_start: 0.8107 (m-10) cc_final: 0.7651 (m-10) REVERT: A 276 PHE cc_start: 0.8384 (t80) cc_final: 0.8140 (t80) REVERT: A 280 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7366 (mm-30) REVERT: A 387 GLU cc_start: 0.8192 (tp30) cc_final: 0.7757 (tp30) REVERT: A 388 LEU cc_start: 0.9509 (tt) cc_final: 0.9226 (tt) REVERT: A 430 MET cc_start: 0.9004 (mmt) cc_final: 0.8540 (ttp) REVERT: B 232 PHE cc_start: 0.8467 (m-10) cc_final: 0.7733 (m-10) REVERT: B 237 SER cc_start: 0.8373 (t) cc_final: 0.8001 (p) REVERT: B 274 TYR cc_start: 0.7378 (m-80) cc_final: 0.6521 (m-80) REVERT: B 283 ARG cc_start: 0.7996 (mtt90) cc_final: 0.7698 (mmt90) REVERT: B 288 LYS cc_start: 0.9503 (tttt) cc_final: 0.9185 (tppt) REVERT: B 294 MET cc_start: 0.8641 (tmm) cc_final: 0.8334 (tmm) REVERT: B 320 PHE cc_start: 0.8222 (t80) cc_final: 0.7876 (t80) REVERT: B 414 LEU cc_start: 0.8898 (mt) cc_final: 0.8601 (mp) REVERT: C 197 ILE cc_start: 0.9496 (pt) cc_final: 0.9148 (pt) REVERT: D 197 ILE cc_start: 0.9069 (pt) cc_final: 0.8520 (mt) REVERT: D 229 MET cc_start: 0.7809 (tmm) cc_final: 0.7520 (tmm) REVERT: D 234 GLN cc_start: 0.9101 (pm20) cc_final: 0.8276 (pt0) REVERT: D 320 PHE cc_start: 0.8884 (t80) cc_final: 0.8119 (t80) REVERT: D 385 MET cc_start: 0.8283 (mmt) cc_final: 0.7999 (mmt) REVERT: D 412 CYS cc_start: 0.9334 (m) cc_final: 0.7863 (t) REVERT: D 431 THR cc_start: 0.7535 (m) cc_final: 0.7262 (m) REVERT: D 438 GLU cc_start: 0.9095 (tt0) cc_final: 0.8583 (tm-30) REVERT: E 213 ARG cc_start: 0.7453 (mmt90) cc_final: 0.6889 (mmm160) REVERT: E 450 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8293 (tppt) REVERT: F 197 ILE cc_start: 0.9111 (pt) cc_final: 0.8837 (mp) REVERT: F 213 ARG cc_start: 0.8452 (mmt-90) cc_final: 0.8165 (mmt90) REVERT: F 240 ASP cc_start: 0.8849 (m-30) cc_final: 0.8359 (p0) REVERT: F 265 GLN cc_start: 0.9134 (mt0) cc_final: 0.8790 (mp10) REVERT: M 52 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8796 (tp40) REVERT: M 55 ARG cc_start: 0.8643 (ttm110) cc_final: 0.8172 (mmm-85) REVERT: M 180 GLN cc_start: 0.8540 (mm-40) cc_final: 0.7942 (mp10) REVERT: M 280 TYR cc_start: 0.9327 (m-80) cc_final: 0.8740 (m-80) REVERT: M 281 GLN cc_start: 0.9323 (mp10) cc_final: 0.8669 (mp10) REVERT: M 340 LEU cc_start: 0.9265 (mm) cc_final: 0.9019 (mm) REVERT: G 239 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8082 (mm-30) REVERT: G 387 GLU cc_start: 0.8117 (tp30) cc_final: 0.7680 (tp30) REVERT: G 388 LEU cc_start: 0.9507 (tt) cc_final: 0.9210 (tt) REVERT: G 430 MET cc_start: 0.8977 (mmt) cc_final: 0.8506 (ttp) REVERT: H 197 ILE cc_start: 0.9492 (pt) cc_final: 0.9236 (mt) REVERT: H 243 GLN cc_start: 0.8467 (tt0) cc_final: 0.7402 (tp-100) REVERT: H 279 ASP cc_start: 0.8442 (t0) cc_final: 0.8101 (t0) REVERT: H 294 MET cc_start: 0.8269 (ttp) cc_final: 0.7732 (tmm) REVERT: H 320 PHE cc_start: 0.7963 (t80) cc_final: 0.7607 (t80) REVERT: H 389 ASN cc_start: 0.9481 (m-40) cc_final: 0.9173 (m110) REVERT: H 414 LEU cc_start: 0.9360 (mt) cc_final: 0.9061 (mp) REVERT: I 197 ILE cc_start: 0.9459 (pt) cc_final: 0.9233 (pt) REVERT: I 295 MET cc_start: 0.8979 (tpt) cc_final: 0.8661 (tpt) REVERT: J 229 MET cc_start: 0.8402 (tmm) cc_final: 0.8043 (tmm) REVERT: J 234 GLN cc_start: 0.8978 (pm20) cc_final: 0.8228 (pt0) REVERT: J 412 CYS cc_start: 0.9329 (m) cc_final: 0.7953 (t) REVERT: J 431 THR cc_start: 0.6160 (m) cc_final: 0.5950 (m) REVERT: J 438 GLU cc_start: 0.9096 (tt0) cc_final: 0.8584 (tm-30) REVERT: K 450 LYS cc_start: 0.8288 (ttpt) cc_final: 0.7940 (tppt) REVERT: L 240 ASP cc_start: 0.8800 (m-30) cc_final: 0.8568 (m-30) REVERT: L 265 GLN cc_start: 0.8870 (mt0) cc_final: 0.8586 (mp10) REVERT: N 52 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8527 (tp40) REVERT: N 197 MET cc_start: 0.8825 (mmt) cc_final: 0.8433 (mmp) REVERT: N 280 TYR cc_start: 0.9441 (m-80) cc_final: 0.8679 (m-80) REVERT: N 281 GLN cc_start: 0.9300 (mp10) cc_final: 0.8773 (mp10) REVERT: N 283 MET cc_start: 0.8409 (mmm) cc_final: 0.8050 (mmm) outliers start: 0 outliers final: 0 residues processed: 710 average time/residue: 0.8734 time to fit residues: 1000.1300 Evaluate side-chains 615 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 615 time to evaluate : 4.472 ------------------------------------------------------------------------------- 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: 9.9990 chunk 366 optimal weight: 2.9990 chunk 220 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 287 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 331 optimal weight: 9.9990 chunk 346 optimal weight: 0.0370 chunk 365 optimal weight: 6.9990 overall best weight: 3.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 ASN ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 366 ASN ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.6609 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= 0.203 Angle : 0.551 11.895 47382 Z= 0.297 Chirality : 0.041 0.369 5008 Planarity : 0.004 0.068 6102 Dihedral : 9.328 179.562 4798 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -0.35 (0.13), residues: 4084 helix: 0.16 (0.12), residues: 1820 sheet: 0.66 (0.24), residues: 504 loop : -0.83 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP N 332 HIS 0.013 0.002 HIS L 407 PHE 0.034 0.001 PHE L 178 TYR 0.022 0.001 TYR A 344 ARG 0.010 0.001 ARG D 349 *********************** 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 711 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 711 time to evaluate : 4.428 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 232 PHE cc_start: 0.8160 (m-10) cc_final: 0.7844 (m-10) REVERT: A 280 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7265 (mm-30) REVERT: A 387 GLU cc_start: 0.8142 (tp30) cc_final: 0.7706 (tp30) REVERT: A 388 LEU cc_start: 0.9479 (tt) cc_final: 0.9169 (tt) REVERT: A 430 MET cc_start: 0.9048 (mmt) cc_final: 0.8566 (ttp) REVERT: B 231 GLN cc_start: 0.7904 (mp10) cc_final: 0.7462 (mp10) REVERT: B 237 SER cc_start: 0.8772 (t) cc_final: 0.8475 (p) REVERT: B 288 LYS cc_start: 0.9507 (tttt) cc_final: 0.9184 (tppt) REVERT: B 294 MET cc_start: 0.8688 (tmm) cc_final: 0.8384 (tmm) REVERT: B 320 PHE cc_start: 0.8342 (t80) cc_final: 0.7949 (t80) REVERT: B 346 LEU cc_start: 0.8899 (tp) cc_final: 0.8635 (tp) REVERT: B 414 LEU cc_start: 0.8945 (mt) cc_final: 0.8647 (mp) REVERT: C 197 ILE cc_start: 0.9437 (pt) cc_final: 0.9044 (pt) REVERT: D 197 ILE cc_start: 0.9048 (pt) cc_final: 0.8462 (mt) REVERT: D 229 MET cc_start: 0.7844 (tmm) cc_final: 0.7572 (tmm) REVERT: D 234 GLN cc_start: 0.9035 (pm20) cc_final: 0.8230 (pt0) REVERT: D 276 PHE cc_start: 0.8769 (t80) cc_final: 0.8388 (t80) REVERT: D 294 MET cc_start: 0.8623 (ttp) cc_final: 0.8396 (ttp) REVERT: D 320 PHE cc_start: 0.8900 (t80) cc_final: 0.8161 (t80) REVERT: D 366 ASN cc_start: 0.8464 (m110) cc_final: 0.8037 (t0) REVERT: D 385 MET cc_start: 0.8336 (mmt) cc_final: 0.8088 (mmt) REVERT: D 412 CYS cc_start: 0.9331 (m) cc_final: 0.7840 (t) REVERT: D 438 GLU cc_start: 0.9106 (tt0) cc_final: 0.8593 (tm-30) REVERT: E 213 ARG cc_start: 0.7586 (mmt90) cc_final: 0.6983 (mmm160) REVERT: E 438 GLU cc_start: 0.9202 (tt0) cc_final: 0.8795 (tp30) REVERT: E 450 LYS cc_start: 0.8726 (ttpt) cc_final: 0.8298 (tppt) REVERT: F 197 ILE cc_start: 0.9111 (pt) cc_final: 0.8872 (mp) REVERT: F 213 ARG cc_start: 0.8474 (mmt-90) cc_final: 0.8185 (mmt90) REVERT: F 240 ASP cc_start: 0.8807 (m-30) cc_final: 0.8300 (p0) REVERT: F 332 MET cc_start: 0.6232 (tmm) cc_final: 0.5813 (tmm) REVERT: M 52 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8601 (tp40) REVERT: M 280 TYR cc_start: 0.9265 (m-80) cc_final: 0.8659 (m-80) REVERT: M 281 GLN cc_start: 0.9306 (mp10) cc_final: 0.8648 (mp10) REVERT: M 300 LEU cc_start: 0.9290 (tt) cc_final: 0.8357 (mm) REVERT: G 239 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8109 (mm-30) REVERT: G 280 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7520 (mm-30) REVERT: G 356 GLU cc_start: 0.8154 (pt0) cc_final: 0.7895 (pm20) REVERT: G 387 GLU cc_start: 0.8097 (tp30) cc_final: 0.7689 (tp30) REVERT: G 388 LEU cc_start: 0.9480 (tt) cc_final: 0.9161 (tt) REVERT: G 430 MET cc_start: 0.8978 (mmt) cc_final: 0.8463 (ttp) REVERT: H 197 ILE cc_start: 0.9525 (pt) cc_final: 0.9165 (mt) REVERT: H 243 GLN cc_start: 0.8404 (tt0) cc_final: 0.7368 (tp-100) REVERT: H 320 PHE cc_start: 0.7975 (t80) cc_final: 0.7643 (t80) REVERT: H 332 MET cc_start: 0.9094 (ppp) cc_final: 0.8862 (ppp) REVERT: H 350 PHE cc_start: 0.8561 (m-80) cc_final: 0.8253 (m-80) REVERT: H 389 ASN cc_start: 0.9464 (m-40) cc_final: 0.9153 (m110) REVERT: H 414 LEU cc_start: 0.9354 (mt) cc_final: 0.9048 (mp) REVERT: I 197 ILE cc_start: 0.9430 (pt) cc_final: 0.8870 (pt) REVERT: I 346 LEU cc_start: 0.9678 (tp) cc_final: 0.9442 (tp) REVERT: J 229 MET cc_start: 0.8380 (tmm) cc_final: 0.8064 (tmm) REVERT: J 234 GLN cc_start: 0.8942 (pm20) cc_final: 0.8192 (pt0) REVERT: J 276 PHE cc_start: 0.8758 (t80) cc_final: 0.8394 (t80) REVERT: J 366 ASN cc_start: 0.8445 (m110) cc_final: 0.7986 (t0) REVERT: J 412 CYS cc_start: 0.9323 (m) cc_final: 0.7924 (t) REVERT: J 431 THR cc_start: 0.6085 (m) cc_final: 0.5875 (m) REVERT: J 438 GLU cc_start: 0.9093 (tt0) cc_final: 0.8580 (tm-30) REVERT: K 450 LYS cc_start: 0.8258 (ttpt) cc_final: 0.7895 (tppt) REVERT: N 52 GLN cc_start: 0.8988 (mm-40) cc_final: 0.8497 (tp40) REVERT: N 197 MET cc_start: 0.8879 (mmt) cc_final: 0.8457 (mmp) REVERT: N 280 TYR cc_start: 0.9439 (m-80) cc_final: 0.8672 (m-80) REVERT: N 281 GLN cc_start: 0.9282 (mp10) cc_final: 0.8755 (mp10) REVERT: N 283 MET cc_start: 0.8401 (mmm) cc_final: 0.8073 (mmm) outliers start: 0 outliers final: 0 residues processed: 711 average time/residue: 0.8804 time to fit residues: 1009.2587 Evaluate side-chains 626 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 626 time to evaluate : 4.286 ------------------------------------------------------------------------------- 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: 9.9990 chunk 387 optimal weight: 8.9990 chunk 236 optimal weight: 0.6980 chunk 183 optimal weight: 10.0000 chunk 269 optimal weight: 1.9990 chunk 406 optimal weight: 9.9990 chunk 374 optimal weight: 7.9990 chunk 323 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 250 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.6743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35024 Z= 0.224 Angle : 0.556 11.971 47382 Z= 0.300 Chirality : 0.041 0.371 5008 Planarity : 0.004 0.059 6102 Dihedral : 9.306 179.462 4798 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % 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: -0.37 (0.13), residues: 4084 helix: 0.18 (0.12), residues: 1816 sheet: 0.61 (0.24), residues: 504 loop : -0.86 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 451 HIS 0.011 0.002 HIS L 407 PHE 0.027 0.001 PHE H 352 TYR 0.020 0.001 TYR M 161 ARG 0.015 0.001 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 717 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 717 time to evaluate : 4.315 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 280 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7130 (mm-30) REVERT: A 387 GLU cc_start: 0.8182 (tp30) cc_final: 0.7746 (tp30) REVERT: A 388 LEU cc_start: 0.9486 (tt) cc_final: 0.9188 (tt) REVERT: A 430 MET cc_start: 0.9050 (mmt) cc_final: 0.8561 (ttp) REVERT: B 231 GLN cc_start: 0.8017 (mp10) cc_final: 0.7657 (mp10) REVERT: B 232 PHE cc_start: 0.8062 (m-10) cc_final: 0.7601 (m-10) REVERT: B 237 SER cc_start: 0.8888 (t) cc_final: 0.8621 (p) REVERT: B 274 TYR cc_start: 0.7352 (m-80) cc_final: 0.6476 (m-80) REVERT: B 288 LYS cc_start: 0.9542 (tttt) cc_final: 0.9180 (tppt) REVERT: B 294 MET cc_start: 0.8763 (tmm) cc_final: 0.8460 (tmm) REVERT: B 320 PHE cc_start: 0.8437 (t80) cc_final: 0.8009 (t80) REVERT: B 332 MET cc_start: 0.9339 (ppp) cc_final: 0.9123 (ppp) REVERT: B 414 LEU cc_start: 0.8997 (mt) cc_final: 0.8705 (mp) REVERT: C 197 ILE cc_start: 0.9438 (pt) cc_final: 0.9090 (pt) REVERT: D 229 MET cc_start: 0.7890 (tmm) cc_final: 0.7573 (tmm) REVERT: D 234 GLN cc_start: 0.9065 (pm20) cc_final: 0.8213 (pt0) REVERT: D 276 PHE cc_start: 0.8827 (t80) cc_final: 0.8439 (t80) REVERT: D 320 PHE cc_start: 0.8905 (t80) cc_final: 0.8168 (t80) REVERT: D 366 ASN cc_start: 0.8406 (m110) cc_final: 0.7960 (t0) REVERT: D 385 MET cc_start: 0.8320 (mmt) cc_final: 0.8071 (mmt) REVERT: D 412 CYS cc_start: 0.9348 (m) cc_final: 0.7894 (t) REVERT: D 431 THR cc_start: 0.7626 (m) cc_final: 0.7360 (m) REVERT: D 438 GLU cc_start: 0.9100 (tt0) cc_final: 0.8600 (tm-30) REVERT: E 213 ARG cc_start: 0.7616 (mmt90) cc_final: 0.7057 (mmm160) REVERT: E 438 GLU cc_start: 0.9199 (tt0) cc_final: 0.8938 (tp30) REVERT: E 450 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8305 (tppt) REVERT: F 197 ILE cc_start: 0.9119 (pt) cc_final: 0.8862 (mp) REVERT: F 213 ARG cc_start: 0.8640 (mmt-90) cc_final: 0.8314 (mmt90) REVERT: F 240 ASP cc_start: 0.8792 (m-30) cc_final: 0.8338 (p0) REVERT: F 332 MET cc_start: 0.6182 (tmm) cc_final: 0.5792 (tmm) REVERT: M 67 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8555 (tt0) REVERT: M 280 TYR cc_start: 0.9268 (m-80) cc_final: 0.8657 (m-80) REVERT: M 281 GLN cc_start: 0.9318 (mp10) cc_final: 0.8669 (mp10) REVERT: G 239 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8153 (mm-30) REVERT: G 280 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7474 (mm-30) REVERT: G 387 GLU cc_start: 0.8134 (tp30) cc_final: 0.7738 (tp30) REVERT: G 388 LEU cc_start: 0.9478 (tt) cc_final: 0.9202 (tt) REVERT: G 430 MET cc_start: 0.8995 (mmt) cc_final: 0.8517 (ttp) REVERT: H 197 ILE cc_start: 0.9500 (pt) cc_final: 0.9171 (mt) REVERT: H 243 GLN cc_start: 0.8405 (tt0) cc_final: 0.7339 (tp-100) REVERT: H 320 PHE cc_start: 0.8036 (t80) cc_final: 0.7689 (t80) REVERT: H 332 MET cc_start: 0.9070 (ppp) cc_final: 0.8848 (ppp) REVERT: H 333 ASN cc_start: 0.9078 (p0) cc_final: 0.8353 (p0) REVERT: H 389 ASN cc_start: 0.9477 (m-40) cc_final: 0.9154 (m110) REVERT: H 414 LEU cc_start: 0.9361 (mt) cc_final: 0.9058 (mp) REVERT: I 197 ILE cc_start: 0.9368 (pt) cc_final: 0.8960 (pt) REVERT: I 346 LEU cc_start: 0.9684 (tp) cc_final: 0.9458 (tp) REVERT: I 385 MET cc_start: 0.8232 (mmt) cc_final: 0.7992 (mmt) REVERT: J 229 MET cc_start: 0.8395 (tmm) cc_final: 0.8059 (tmm) REVERT: J 234 GLN cc_start: 0.8954 (pm20) cc_final: 0.8210 (pt0) REVERT: J 276 PHE cc_start: 0.8780 (t80) cc_final: 0.8417 (t80) REVERT: J 366 ASN cc_start: 0.8439 (m110) cc_final: 0.7964 (t0) REVERT: J 412 CYS cc_start: 0.9352 (m) cc_final: 0.7974 (t) REVERT: J 438 GLU cc_start: 0.9097 (tt0) cc_final: 0.8577 (tm-30) REVERT: K 450 LYS cc_start: 0.8258 (ttpt) cc_final: 0.7882 (tppt) REVERT: L 213 ARG cc_start: 0.8207 (mmt90) cc_final: 0.7950 (mmt90) REVERT: N 52 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8492 (tp40) REVERT: N 197 MET cc_start: 0.8912 (mmt) cc_final: 0.8501 (mmp) REVERT: N 280 TYR cc_start: 0.9453 (m-80) cc_final: 0.8673 (m-80) REVERT: N 281 GLN cc_start: 0.9295 (mp10) cc_final: 0.8772 (mp10) REVERT: N 283 MET cc_start: 0.8425 (mmm) cc_final: 0.8119 (mmm) outliers start: 0 outliers final: 0 residues processed: 717 average time/residue: 0.9133 time to fit residues: 1057.5067 Evaluate side-chains 629 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 629 time to evaluate : 4.286 ------------------------------------------------------------------------------- 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: 8.9990 chunk 99 optimal weight: 7.9990 chunk 298 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 324 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 332 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.085653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.070286 restraints weight = 372735.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.074035 restraints weight = 179784.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.076498 restraints weight = 103835.923| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.6925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35024 Z= 0.242 Angle : 0.571 11.985 47382 Z= 0.309 Chirality : 0.041 0.372 5008 Planarity : 0.004 0.042 6102 Dihedral : 9.328 179.304 4798 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % 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: -0.44 (0.13), residues: 4084 helix: 0.13 (0.12), residues: 1816 sheet: 0.41 (0.24), residues: 512 loop : -0.86 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP N 332 HIS 0.010 0.002 HIS L 407 PHE 0.032 0.002 PHE H 352 TYR 0.022 0.002 TYR B 238 ARG 0.005 0.001 ARG B 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17003.75 seconds wall clock time: 295 minutes 4.63 seconds (17704.63 seconds total)