Starting phenix.real_space_refine (version: dev) on Sun Feb 26 09:59:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz8_0314/02_2023/6hz8_0314_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz8_0314/02_2023/6hz8_0314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz8_0314/02_2023/6hz8_0314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz8_0314/02_2023/6hz8_0314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz8_0314/02_2023/6hz8_0314_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz8_0314/02_2023/6hz8_0314_trim_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned 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 PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 280": "OE1" <-> "OE2" Residue "C ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D 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 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 TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 348": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 374": "OE1" <-> "OE2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F GLU 427": "OE1" <-> "OE2" Residue "M ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 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 "M TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 171": "OE1" <-> "OE2" Residue "I GLU 181": "OE1" <-> "OE2" Residue "I GLU 185": "OE1" <-> "OE2" Residue "I ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 280": "OE1" <-> "OE2" Residue "I ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 292": "OE1" <-> "OE2" Residue "I ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 304": "OE1" <-> "OE2" Residue "I GLU 317": "OE1" <-> "OE2" Residue "I ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 324": "OE1" <-> "OE2" Residue "I ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 438": "OE1" <-> "OE2" Residue "I GLU 439": "OE1" <-> "OE2" Residue "J GLU 181": "OE1" <-> "OE2" Residue "J 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 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 TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 348": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 374": "OE1" <-> "OE2" Residue "L GLU 379": "OE1" <-> "OE2" Residue "L GLU 427": "OE1" <-> "OE2" Residue "N ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 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" Residue "N TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 24.61, per 1000 atoms: 0.36 Number of scatterers: 67582 At special positions: 0 Unit cell: (190.05, 133.35, 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: 42.17 Conformation dependent library (CDL) restraints added in 4.0 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: 196 helices and 32 sheets defined 44.0% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 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: 3.616A pdb=" N ALA A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 258 through 268 removed outlier: 3.671A pdb=" N GLU A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 286 through 289 No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 291 through 294 Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 337 through 340 Processing helix chain 'A' and resid 344 through 349 removed outlier: 3.810A pdb=" N ARG A 348 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 344 through 349' Processing helix chain 'A' and resid 362 through 370 Processing helix chain 'A' and resid 375 through 394 Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 408 through 411 No H-bonds generated for 'chain 'A' and resid 408 through 411' Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 445 through 456 removed outlier: 3.526A pdb=" N LYS A 454 " --> pdb=" O LYS A 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 removed outlier: 3.626A pdb=" N ASN B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.853A pdb=" N ILE B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 219 removed outlier: 3.858A pdb=" N ARG B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 No H-bonds generated for 'chain 'B' and resid 238 through 241' Processing helix chain 'B' and resid 258 through 268 Processing helix chain 'B' and resid 286 through 296 removed outlier: 6.839A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N MET B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N MET B 295 " --> pdb=" O GLY B 291 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 344 through 347 No H-bonds generated for 'chain 'B' and resid 344 through 347' Processing helix chain 'B' and resid 362 through 370 removed outlier: 3.827A pdb=" N PHE B 367 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 368 " --> pdb=" O PHE B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 394 removed outlier: 3.538A pdb=" N LYS B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) 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 removed outlier: 3.568A pdb=" N TRP B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 174 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.525A pdb=" N ILE C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 219 removed outlier: 3.910A pdb=" N ARG C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 3.752A 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: 6.477A pdb=" N GLU C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N MET C 294 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N MET C 295 " --> pdb=" O GLY C 291 " (cutoff:3.500A) removed outlier: 3.668A 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: 3.802A 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 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.541A pdb=" N LYS D 189 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 219 Processing helix chain 'D' and resid 238 through 241 No H-bonds generated for 'chain 'D' and resid 238 through 241' Processing helix chain 'D' and resid 258 through 268 Processing helix chain 'D' and resid 286 through 296 removed outlier: 6.474A pdb=" N GLU D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N MET D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N MET D 295 " --> pdb=" O GLY D 291 " (cutoff:3.500A) removed outlier: 3.916A 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 344 through 349 Processing helix chain 'D' and resid 362 through 371 Processing helix chain 'D' and resid 375 through 392 Processing helix chain 'D' and resid 422 through 431 Processing helix chain 'D' and resid 433 through 440 Processing helix chain 'D' and resid 445 through 456 removed outlier: 3.582A pdb=" N LEU D 456 " --> pdb=" O THR D 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.905A pdb=" N LEU E 188 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS E 189 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 3.840A 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: 7.206A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL E 293 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 4.877A 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: 3.625A pdb=" N ARG E 348 " --> pdb=" O TYR E 344 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG E 349 " --> pdb=" O ALA E 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 344 through 349' Processing helix chain 'E' and resid 362 through 369 Processing helix chain 'E' and resid 375 through 394 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 removed outlier: 3.595A pdb=" N LEU E 456 " --> pdb=" O THR E 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 194 removed outlier: 3.574A pdb=" N ILE F 193 " --> pdb=" O LYS F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 219 removed outlier: 3.508A pdb=" N ALA F 211 " --> pdb=" O LYS F 207 " (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: 3.694A pdb=" N GLN F 264 " --> pdb=" O TYR F 260 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN F 265 " --> pdb=" O ASN F 261 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU F 268 " --> pdb=" O GLN F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 295 removed outlier: 6.992A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL F 293 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N MET F 294 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 4.989A 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: 4.372A pdb=" N GLU F 427 " --> pdb=" O GLN F 423 " (cutoff:3.500A) removed outlier: 4.023A 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: 3.916A pdb=" N LYS F 454 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 455 " --> pdb=" O TRP F 451 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU F 456 " --> pdb=" O THR F 452 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 19 removed outlier: 3.514A pdb=" N TYR M 17 " --> pdb=" O MET M 14 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP M 19 " --> pdb=" O THR M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 56 removed outlier: 4.030A pdb=" N LEU M 51 " --> pdb=" O ASN M 47 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN M 52 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU M 53 " --> pdb=" O GLY M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 84 Processing helix chain 'M' and resid 104 through 118 removed outlier: 3.535A pdb=" N ILE M 109 " --> pdb=" O ALA M 105 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE M 115 " --> pdb=" O SER M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 135 removed outlier: 3.618A pdb=" N SER M 132 " --> pdb=" O ASP M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 155 removed outlier: 3.581A pdb=" N LEU M 153 " --> pdb=" O HIS M 149 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN M 154 " --> pdb=" O PHE M 150 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLY M 155 " --> pdb=" O SER M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 174 removed outlier: 3.582A pdb=" N PHE M 164 " --> pdb=" O ARG M 160 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL M 165 " --> pdb=" O TYR M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 212 removed outlier: 3.801A pdb=" N ARG M 210 " --> pdb=" O TYR M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 288 removed outlier: 4.018A pdb=" N MET M 283 " --> pdb=" O TYR M 280 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER M 288 " --> pdb=" O TYR M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 332 through 347 removed outlier: 3.540A pdb=" N LEU M 340 " --> pdb=" O HIS M 336 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU M 345 " --> pdb=" O ASP M 341 " (cutoff:3.500A) removed outlier: 3.628A 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: 3.615A pdb=" N ALA G 211 " --> pdb=" O LYS G 207 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG G 212 " --> pdb=" O THR G 208 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG G 213 " --> pdb=" O PHE G 209 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR G 216 " --> pdb=" O ARG G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 241 No H-bonds generated for 'chain 'G' and resid 238 through 241' Processing helix chain 'G' and resid 258 through 268 removed outlier: 3.671A pdb=" N GLU G 268 " --> pdb=" O GLN G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 283 No H-bonds generated for 'chain 'G' and resid 281 through 283' Processing helix chain 'G' and resid 286 through 289 No H-bonds generated for 'chain 'G' and resid 286 through 289' Processing helix chain 'G' and resid 291 through 294 Processing helix chain 'G' and resid 304 through 306 No H-bonds generated for 'chain 'G' and resid 304 through 306' Processing helix chain 'G' and resid 337 through 340 Processing helix chain 'G' and resid 344 through 349 removed outlier: 3.810A pdb=" N ARG G 348 " --> pdb=" O TYR G 344 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG G 349 " --> pdb=" O ALA G 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 344 through 349' Processing helix chain 'G' and resid 362 through 370 Processing helix chain 'G' and resid 375 through 394 Processing helix chain 'G' and resid 401 through 403 No H-bonds generated for 'chain 'G' and resid 401 through 403' Processing helix chain 'G' and resid 408 through 411 No H-bonds generated for 'chain 'G' and resid 408 through 411' Processing helix chain 'G' and resid 422 through 431 Processing helix chain 'G' and resid 433 through 440 Processing helix chain 'G' and resid 445 through 456 removed outlier: 3.526A pdb=" N LYS G 454 " --> pdb=" O LYS G 450 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 175 removed outlier: 3.626A pdb=" N ASN H 175 " --> pdb=" O GLU H 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 194 removed outlier: 3.853A pdb=" N ILE H 193 " --> pdb=" O LYS H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 219 removed outlier: 3.857A pdb=" N ARG H 212 " --> pdb=" O THR H 208 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG H 213 " --> pdb=" O PHE H 209 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA H 215 " --> pdb=" O ALA H 211 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR H 216 " --> pdb=" O ARG H 212 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU H 217 " --> pdb=" O ARG H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 241 No H-bonds generated for 'chain 'H' and resid 238 through 241' Processing helix chain 'H' and resid 258 through 268 Processing helix chain 'H' and resid 286 through 296 removed outlier: 6.839A pdb=" N GLU H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL H 293 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N MET H 294 " --> pdb=" O PHE H 290 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N MET H 295 " --> pdb=" O GLY H 291 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU H 296 " --> pdb=" O GLU H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 306 No H-bonds generated for 'chain 'H' and resid 304 through 306' Processing helix chain 'H' and resid 344 through 347 No H-bonds generated for 'chain 'H' and resid 344 through 347' Processing helix chain 'H' and resid 362 through 370 removed outlier: 3.827A pdb=" N PHE H 367 " --> pdb=" O GLN H 363 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU H 368 " --> pdb=" O PHE H 364 " (cutoff:3.500A) Processing helix chain 'H' and resid 375 through 394 removed outlier: 3.538A pdb=" N LYS H 384 " --> pdb=" O SER H 380 " (cutoff:3.500A) 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 removed outlier: 3.568A pdb=" N TRP H 451 " --> pdb=" O LYS H 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 174 Processing helix chain 'I' and resid 181 through 194 removed outlier: 3.525A pdb=" N ILE I 193 " --> pdb=" O LYS I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 219 removed outlier: 3.910A pdb=" N ARG I 212 " --> pdb=" O THR I 208 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG I 213 " --> pdb=" O PHE I 209 " (cutoff:3.500A) removed outlier: 3.751A 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: 6.478A pdb=" N GLU I 292 " --> pdb=" O LYS I 288 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N MET I 294 " --> pdb=" O PHE I 290 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N MET I 295 " --> pdb=" O GLY I 291 " (cutoff:3.500A) removed outlier: 3.668A 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: 3.801A 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 Processing helix chain 'J' and resid 181 through 194 removed outlier: 3.541A pdb=" N LYS J 189 " --> pdb=" O GLU J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 207 through 219 Processing helix chain 'J' and resid 238 through 241 No H-bonds generated for 'chain 'J' and resid 238 through 241' Processing helix chain 'J' and resid 258 through 268 Processing helix chain 'J' and resid 286 through 296 removed outlier: 6.475A pdb=" N GLU J 292 " --> pdb=" O LYS J 288 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL J 293 " --> pdb=" O VAL J 289 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N MET J 294 " --> pdb=" O PHE J 290 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N MET J 295 " --> pdb=" O GLY J 291 " (cutoff:3.500A) removed outlier: 3.916A 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 344 through 349 Processing helix chain 'J' and resid 362 through 371 Processing helix chain 'J' and resid 375 through 392 Processing helix chain 'J' and resid 422 through 431 Processing helix chain 'J' and resid 433 through 440 Processing helix chain 'J' and resid 445 through 456 removed outlier: 3.582A pdb=" N LEU J 456 " --> pdb=" O THR J 452 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 194 removed outlier: 3.906A pdb=" N LEU K 188 " --> pdb=" O ILE K 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS K 189 " --> pdb=" O GLU K 185 " (cutoff:3.500A) removed outlier: 3.839A 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: 7.205A pdb=" N GLU K 292 " --> pdb=" O LYS K 288 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL K 293 " --> pdb=" O VAL K 289 " (cutoff:3.500A) removed outlier: 4.877A 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: 3.625A pdb=" N ARG K 348 " --> pdb=" O TYR K 344 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG K 349 " --> pdb=" O ALA K 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 344 through 349' Processing helix chain 'K' and resid 362 through 369 Processing helix chain 'K' and resid 375 through 394 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 removed outlier: 3.595A pdb=" N LEU K 456 " --> pdb=" O THR K 452 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 194 removed outlier: 3.574A pdb=" N ILE L 193 " --> pdb=" O LYS L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 207 through 219 removed outlier: 3.508A pdb=" N ALA L 211 " --> pdb=" O LYS L 207 " (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: 3.694A pdb=" N GLN L 264 " --> pdb=" O TYR L 260 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN L 265 " --> pdb=" O ASN L 261 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA L 266 " --> pdb=" O PHE L 262 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU L 268 " --> pdb=" O GLN L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 295 removed outlier: 6.991A pdb=" N GLU L 292 " --> pdb=" O LYS L 288 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL L 293 " --> pdb=" O VAL L 289 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N MET L 294 " --> pdb=" O PHE L 290 " (cutoff:3.500A) removed outlier: 4.989A 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: 4.374A pdb=" N GLU L 427 " --> pdb=" O GLN L 423 " (cutoff:3.500A) removed outlier: 4.022A 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: 3.916A pdb=" N LYS L 454 " --> pdb=" O LYS L 450 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU L 455 " --> pdb=" O TRP L 451 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU L 456 " --> pdb=" O THR L 452 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 19 removed outlier: 3.514A pdb=" N TYR N 17 " --> pdb=" O MET N 14 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP N 19 " --> pdb=" O THR N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 56 removed outlier: 4.030A pdb=" N LEU N 51 " --> pdb=" O ASN N 47 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN N 52 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU N 53 " --> pdb=" O GLY N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 84 Processing helix chain 'N' and resid 104 through 118 removed outlier: 3.535A pdb=" N ILE N 109 " --> pdb=" O ALA N 105 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE N 115 " --> pdb=" O SER N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 135 removed outlier: 3.618A pdb=" N SER N 132 " --> pdb=" O ASP N 128 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 155 removed outlier: 3.582A pdb=" N LEU N 153 " --> pdb=" O HIS N 149 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN N 154 " --> pdb=" O PHE N 150 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLY N 155 " --> pdb=" O SER N 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 174 removed outlier: 3.581A pdb=" N PHE N 164 " --> pdb=" O ARG N 160 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL N 165 " --> pdb=" O TYR N 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 212 removed outlier: 3.800A pdb=" N ARG N 210 " --> pdb=" O TYR N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 288 removed outlier: 4.018A pdb=" N MET N 283 " --> pdb=" O TYR N 280 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER N 288 " --> pdb=" O TYR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 332 through 347 removed outlier: 3.540A pdb=" N LEU N 340 " --> pdb=" O HIS N 336 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU N 345 " --> pdb=" O ASP N 341 " (cutoff:3.500A) removed outlier: 3.627A 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: 8.810A pdb=" N ILE A 197 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 328 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU A 199 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY A 330 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N TYR A 274 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE A 329 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE A 276 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU A 331 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 6.890A 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: 8.826A pdb=" N ILE B 197 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE B 328 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU B 199 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY B 330 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR B 274 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ILE B 329 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE B 276 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N LEU B 331 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.458A 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: 6.377A pdb=" N ILE C 328 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU C 199 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY C 330 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLY C 201 " --> pdb=" O GLY C 330 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N MET C 332 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 245 through 247 Processing sheet with id= G, first strand: chain 'D' and resid 351 through 354 removed outlier: 6.531A pdb=" N ILE D 328 " --> pdb=" O ILE D 197 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU D 199 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLY D 330 " --> pdb=" O LEU D 199 " (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 353 removed outlier: 3.822A pdb=" N SER E 351 " --> pdb=" O ASN E 196 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N ILE E 197 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE E 328 " --> pdb=" O ILE E 197 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU E 199 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY E 330 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY E 201 " --> pdb=" O GLY E 330 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N MET E 332 " --> pdb=" O GLY E 201 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR E 274 " --> pdb=" O TYR E 327 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE E 329 " --> pdb=" O TYR E 274 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE E 276 " --> pdb=" O ILE E 329 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU E 331 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE E 278 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN E 333 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASN E 228 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASP E 279 " --> pdb=" O ASN E 228 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL E 230 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 243 through 247 Processing sheet with id= K, first strand: chain 'F' and resid 351 through 353 removed outlier: 6.674A pdb=" N ILE F 328 " --> pdb=" O ILE F 197 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU F 199 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY F 330 " --> pdb=" O LEU F 199 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 243 through 247 Processing sheet with id= M, first strand: chain 'M' and resid 61 through 69 removed outlier: 3.551A pdb=" N ASP M 61 " --> pdb=" O ASN M 100 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN M 100 " --> pdb=" O ASP M 61 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'M' and resid 176 through 178 Processing sheet with id= O, first strand: chain 'M' and resid 217 through 219 Processing sheet with id= P, first strand: chain 'M' and resid 253 through 259 removed outlier: 3.736A pdb=" N ILE M 302 " --> pdb=" O ASP M 257 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS M 259 " --> pdb=" O ILE M 302 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP M 320 " --> pdb=" O GLY M 299 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N LEU M 301 " --> pdb=" O ASP M 320 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLY M 322 " --> pdb=" O LEU M 301 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N TYR M 303 " --> pdb=" O GLY M 322 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N CYS M 324 " --> pdb=" O TYR M 303 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N HIS M 305 " --> pdb=" O CYS M 324 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL M 326 " --> pdb=" O HIS M 305 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 351 through 354 removed outlier: 8.810A pdb=" N ILE G 197 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE G 328 " --> pdb=" O ILE G 197 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU G 199 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY G 330 " --> pdb=" O LEU G 199 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N TYR G 274 " --> pdb=" O TYR G 327 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE G 329 " --> pdb=" O TYR G 274 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE G 276 " --> pdb=" O ILE G 329 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU G 331 " --> pdb=" O PHE G 276 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE G 278 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 243 through 247 Processing sheet with id= S, first strand: chain 'H' and resid 351 through 354 removed outlier: 8.826A pdb=" N ILE H 197 " --> pdb=" O VAL H 326 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE H 328 " --> pdb=" O ILE H 197 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU H 199 " --> pdb=" O ILE H 328 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY H 330 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR H 274 " --> pdb=" O TYR H 327 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILE H 329 " --> pdb=" O TYR H 274 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE H 276 " --> pdb=" O ILE H 329 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU H 331 " --> pdb=" O PHE H 276 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILE H 278 " --> pdb=" O LEU H 331 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 243 through 247 Processing sheet with id= U, first strand: chain 'I' and resid 351 through 354 removed outlier: 6.377A pdb=" N ILE I 328 " --> pdb=" O ILE I 197 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU I 199 " --> pdb=" O ILE I 328 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY I 330 " --> pdb=" O LEU I 199 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLY I 201 " --> pdb=" O GLY I 330 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N MET I 332 " --> pdb=" O GLY I 201 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 245 through 247 Processing sheet with id= W, first strand: chain 'J' and resid 351 through 354 removed outlier: 6.531A pdb=" N ILE J 328 " --> pdb=" O ILE J 197 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU J 199 " --> pdb=" O ILE J 328 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY J 330 " --> pdb=" O LEU J 199 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 245 through 247 Processing sheet with id= Y, first strand: chain 'K' and resid 351 through 353 removed outlier: 3.822A pdb=" N SER K 351 " --> pdb=" O ASN K 196 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N ILE K 197 " --> pdb=" O VAL K 326 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE K 328 " --> pdb=" O ILE K 197 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LEU K 199 " --> pdb=" O ILE K 328 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY K 330 " --> pdb=" O LEU K 199 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY K 201 " --> pdb=" O GLY K 330 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET K 332 " --> pdb=" O GLY K 201 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TYR K 274 " --> pdb=" O TYR K 327 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE K 329 " --> pdb=" O TYR K 274 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE K 276 " --> pdb=" O ILE K 329 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU K 331 " --> pdb=" O PHE K 276 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE K 278 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ASN K 333 " --> pdb=" O ILE K 278 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN K 228 " --> pdb=" O ILE K 277 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASP K 279 " --> pdb=" O ASN K 228 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL K 230 " --> pdb=" O ASP K 279 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 243 through 247 Processing sheet with id= AA, first strand: chain 'L' and resid 351 through 353 removed outlier: 6.674A pdb=" N ILE L 328 " --> pdb=" O ILE L 197 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU L 199 " --> pdb=" O ILE L 328 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY L 330 " --> pdb=" O LEU L 199 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 243 through 247 Processing sheet with id= AC, first strand: chain 'N' and resid 61 through 69 removed outlier: 3.551A pdb=" N ASP N 61 " --> pdb=" O ASN N 100 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN N 100 " --> pdb=" O ASP N 61 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'N' and resid 176 through 178 Processing sheet with id= AE, first strand: chain 'N' and resid 217 through 219 Processing sheet with id= AF, first strand: chain 'N' and resid 253 through 259 removed outlier: 3.736A pdb=" N ILE N 302 " --> pdb=" O ASP N 257 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS N 259 " --> pdb=" O ILE N 302 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP N 320 " --> pdb=" O GLY N 299 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N LEU N 301 " --> pdb=" O ASP N 320 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLY N 322 " --> pdb=" O LEU N 301 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N TYR N 303 " --> pdb=" O GLY N 322 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N CYS N 324 " --> pdb=" O TYR N 303 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N HIS N 305 " --> pdb=" O CYS N 324 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL N 326 " --> pdb=" O HIS N 305 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 3114 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 23.74 Time building geometry restraints manager: 44.46 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: 14949 1.42 - 1.61: 19821 1.61 - 1.81: 254 Bond restraints: 68392 Sorted by residual: bond pdb=" N3B GNP C1001 " pdb=" PG GNP C1001 " ideal model delta sigma weight residual 1.801 1.545 0.256 2.00e-02 2.50e+03 1.64e+02 bond pdb=" N3B GNP I1001 " pdb=" PG GNP I1001 " ideal model delta sigma weight residual 1.801 1.546 0.255 2.00e-02 2.50e+03 1.63e+02 bond pdb=" N3B GNP G1001 " pdb=" PG GNP G1001 " ideal model delta sigma weight residual 1.801 1.548 0.253 2.00e-02 2.50e+03 1.60e+02 bond pdb=" N3B GNP A1001 " pdb=" PG GNP A1001 " ideal model delta sigma weight residual 1.801 1.548 0.253 2.00e-02 2.50e+03 1.60e+02 bond pdb=" N3B GNP H1001 " pdb=" PG GNP H1001 " ideal model delta sigma weight residual 1.801 1.592 0.209 2.00e-02 2.50e+03 1.09e+02 ... (remaining 68387 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.14: 791 105.14 - 112.35: 76094 112.35 - 119.55: 18259 119.55 - 126.76: 27791 126.76 - 133.97: 431 Bond angle restraints: 123366 Sorted by residual: angle pdb=" O1A GNP B1001 " pdb=" PA GNP B1001 " pdb=" O2A GNP B1001 " ideal model delta sigma weight residual 121.48 108.13 13.35 3.00e+00 1.11e-01 1.98e+01 angle pdb=" O1A GNP H1001 " pdb=" PA GNP H1001 " pdb=" O2A GNP H1001 " ideal model delta sigma weight residual 121.48 108.16 13.32 3.00e+00 1.11e-01 1.97e+01 angle pdb=" O3A GNP G1001 " pdb=" PA GNP G1001 " pdb=" O5' GNP G1001 " ideal model delta sigma weight residual 97.31 110.44 -13.13 3.00e+00 1.11e-01 1.92e+01 angle pdb=" O3A GNP A1001 " pdb=" PA GNP A1001 " pdb=" O5' GNP A1001 " ideal model delta sigma weight residual 97.31 110.44 -13.13 3.00e+00 1.11e-01 1.92e+01 angle pdb=" O1A GNP A1001 " pdb=" PA GNP A1001 " pdb=" O2A GNP A1001 " ideal model delta sigma weight residual 121.48 108.53 12.95 3.00e+00 1.11e-01 1.86e+01 ... (remaining 123361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 27097 36.00 - 71.99: 453 71.99 - 107.99: 28 107.99 - 143.98: 2 143.98 - 179.98: 10 Dihedral angle restraints: 27590 sinusoidal: 12952 harmonic: 14638 Sorted by residual: dihedral pdb=" CD ARG E 404 " pdb=" NE ARG E 404 " pdb=" CZ ARG E 404 " pdb=" NH1 ARG E 404 " 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 -179.93 179.93 1 1.00e+01 1.00e-02 1.92e+02 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 -179.93 179.93 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 27587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4123 0.061 - 0.122: 790 0.122 - 0.183: 79 0.183 - 0.244: 12 0.244 - 0.305: 4 Chirality restraints: 5008 Sorted by residual: chirality pdb=" C4' GNP A1001 " pdb=" C3' GNP A1001 " pdb=" C5' GNP A1001 " pdb=" O4' GNP A1001 " both_signs ideal model delta sigma weight residual False -2.44 -2.74 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C4' GNP G1001 " pdb=" C3' GNP G1001 " pdb=" C5' GNP G1001 " pdb=" O4' GNP G1001 " both_signs ideal model delta sigma weight residual False -2.44 -2.74 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C3' GDP E1001 " pdb=" C4' GDP E1001 " pdb=" O3' GDP E1001 " pdb=" C2' GDP E1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 5005 not shown) Planarity restraints: 10012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 209 " 0.020 2.00e-02 2.50e+03 1.24e-02 4.65e+00 pdb=" CG PHE B 209 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 209 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 209 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 209 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 209 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 209 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE B 209 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE B 209 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE B 209 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE B 209 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE B 209 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 209 " -0.020 2.00e-02 2.50e+03 1.24e-02 4.59e+00 pdb=" CG PHE H 209 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE H 209 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE H 209 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE H 209 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE H 209 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 209 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE H 209 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE H 209 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE H 209 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE H 209 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE H 209 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL I 322 " 0.035 5.00e-02 4.00e+02 5.21e-02 4.35e+00 pdb=" N PRO I 323 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO I 323 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 323 " 0.029 5.00e-02 4.00e+02 ... (remaining 10009 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 4952 2.21 - 2.81: 145290 2.81 - 3.41: 178400 3.41 - 4.00: 236183 4.00 - 4.60: 375571 Nonbonded interactions: 940396 Sorted by model distance: nonbonded pdb="HH12 ARG I 246 " pdb=" O GLY N 74 " model vdw 1.615 1.850 nonbonded pdb=" O PHE C 441 " pdb="HE21 GLN C 448 " model vdw 1.637 1.850 nonbonded pdb=" OE1 GLN J 231 " pdb="HH21 ARG K 349 " model vdw 1.638 1.850 nonbonded pdb=" O PHE I 441 " pdb="HE21 GLN I 448 " model vdw 1.639 1.850 nonbonded pdb=" O GLY E 206 " pdb=" H VAL E 210 " model vdw 1.654 1.850 ... (remaining 940391 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 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. 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: 0.610 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: 0.970 Extract box with map and model: 7.450 Check model and map are aligned: 0.740 Process input model: 158.620 Find NCS groups from input model: 2.950 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.470 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 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 0.256 35024 Z= 0.596 Angle : 0.988 13.349 47382 Z= 0.494 Chirality : 0.048 0.305 5008 Planarity : 0.005 0.052 6102 Dihedral : 14.593 179.976 13200 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 0.59 % 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: -0.48 (0.12), residues: 4084 helix: -0.20 (0.11), residues: 1550 sheet: 0.10 (0.21), residues: 572 loop : -0.41 (0.14), residues: 1962 *********************** 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 1347 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1325 time to evaluate : 4.218 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 outliers start: 22 outliers final: 6 residues processed: 1339 average time/residue: 1.0048 time to fit residues: 2096.1307 Evaluate side-chains 766 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 760 time to evaluate : 4.122 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 6 average time/residue: 0.9341 time to fit residues: 14.3291 ------------------------------------------------------------------------------- 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: 7.9990 chunk 309 optimal weight: 7.9990 chunk 171 optimal weight: 6.9990 chunk 105 optimal weight: 0.5980 chunk 208 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 319 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 238 optimal weight: 7.9990 chunk 370 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN A 453 ASN B 453 ASN C 386 ASN E 333 ASN E 453 ASN F 299 HIS M 37 ASN M 119 HIS G 423 GLN G 453 ASN H 228 ASN H 453 ASN I 386 ASN L 299 HIS N 37 ASN N 119 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 35024 Z= 0.205 Angle : 0.600 6.948 47382 Z= 0.314 Chirality : 0.040 0.171 5008 Planarity : 0.005 0.047 6102 Dihedral : 9.986 179.817 4630 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.12), residues: 4084 helix: 0.33 (0.12), residues: 1666 sheet: 0.51 (0.22), residues: 538 loop : -0.31 (0.14), residues: 1880 *********************** 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 937 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 935 time to evaluate : 4.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 937 average time/residue: 0.9797 time to fit residues: 1437.1246 Evaluate side-chains 706 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 704 time to evaluate : 4.187 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.6480 time to fit residues: 7.8853 ------------------------------------------------------------------------------- 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: 6.9990 chunk 114 optimal weight: 10.0000 chunk 308 optimal weight: 8.9990 chunk 252 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 371 optimal weight: 9.9990 chunk 400 optimal weight: 5.9990 chunk 330 optimal weight: 5.9990 chunk 368 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 chunk 297 optimal weight: 4.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 ASN F 264 GLN ** M 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 449 GLN ** H 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 264 GLN ** N 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 35024 Z= 0.350 Angle : 0.658 9.169 47382 Z= 0.348 Chirality : 0.040 0.221 5008 Planarity : 0.005 0.053 6102 Dihedral : 9.883 179.780 4630 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 0.00 % 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: -0.29 (0.12), residues: 4084 helix: 0.09 (0.12), residues: 1702 sheet: 0.36 (0.21), residues: 596 loop : -0.53 (0.14), residues: 1786 *********************** 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 798 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 798 time to evaluate : 4.251 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 outliers start: 0 outliers final: 0 residues processed: 798 average time/residue: 0.9152 time to fit residues: 1155.1011 Evaluate side-chains 647 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 647 time to evaluate : 4.204 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2372 ------------------------------------------------------------------------------- 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: 9.9990 chunk 279 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 372 optimal weight: 10.0000 chunk 394 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 353 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN B 234 GLN ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN F 196 ASN ** M 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 423 GLN ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 GLN H 363 GLN ** I 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 196 ASN N 88 ASN ** N 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 284 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 35024 Z= 0.315 Angle : 0.612 8.201 47382 Z= 0.326 Chirality : 0.040 0.195 5008 Planarity : 0.005 0.063 6102 Dihedral : 9.312 179.498 4630 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 0.00 % 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: -0.51 (0.12), residues: 4084 helix: -0.01 (0.12), residues: 1704 sheet: 0.21 (0.21), residues: 572 loop : -0.72 (0.14), residues: 1808 *********************** 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 764 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 764 time to evaluate : 4.234 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 outliers start: 0 outliers final: 0 residues processed: 764 average time/residue: 0.9276 time to fit residues: 1139.8392 Evaluate side-chains 626 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 626 time to evaluate : 4.182 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 293 optimal weight: 5.9990 chunk 162 optimal weight: 0.0870 chunk 336 optimal weight: 8.9990 chunk 272 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 201 optimal weight: 7.9990 chunk 353 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 4.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 HIS ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 GLN F 196 ASN M 88 ASN M 106 ASN M 119 HIS ** M 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 449 GLN ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 363 GLN I 370 ASN ** K 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 196 ASN N 119 HIS ** N 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.5850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 35024 Z= 0.286 Angle : 0.583 7.431 47382 Z= 0.308 Chirality : 0.039 0.134 5008 Planarity : 0.005 0.077 6102 Dihedral : 8.893 179.561 4630 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.08 % 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: -0.48 (0.13), residues: 4084 helix: 0.08 (0.12), residues: 1698 sheet: 0.06 (0.21), residues: 574 loop : -0.71 (0.14), residues: 1812 *********************** 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 744 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 741 time to evaluate : 4.424 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 outliers start: 3 outliers final: 0 residues processed: 744 average time/residue: 0.9032 time to fit residues: 1094.8631 Evaluate side-chains 612 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 612 time to evaluate : 4.145 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.7980 chunk 355 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 231 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 394 optimal weight: 4.9990 chunk 327 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 GLN F 196 ASN M 119 HIS ** M 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 196 ASN N 119 HIS N 193 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 35024 Z= 0.237 Angle : 0.551 6.094 47382 Z= 0.288 Chirality : 0.039 0.140 5008 Planarity : 0.004 0.055 6102 Dihedral : 8.737 179.705 4630 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.03 % 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: -0.36 (0.13), residues: 4084 helix: 0.22 (0.12), residues: 1700 sheet: 0.05 (0.21), residues: 574 loop : -0.67 (0.14), residues: 1810 *********************** 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 738 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 737 time to evaluate : 5.263 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 outliers start: 1 outliers final: 0 residues processed: 738 average time/residue: 0.8826 time to fit residues: 1046.8300 Evaluate side-chains 611 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 611 time to evaluate : 4.139 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3281 ------------------------------------------------------------------------------- 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: 4.9990 chunk 44 optimal weight: 0.5980 chunk 224 optimal weight: 7.9990 chunk 288 optimal weight: 0.2980 chunk 223 optimal weight: 2.9990 chunk 332 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 393 optimal weight: 3.9990 chunk 246 optimal weight: 7.9990 chunk 239 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 ASN M 119 HIS M 193 ASN ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 196 ASN N 119 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.6306 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= 0.204 Angle : 0.525 5.582 47382 Z= 0.273 Chirality : 0.039 0.143 5008 Planarity : 0.004 0.065 6102 Dihedral : 8.655 179.902 4630 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 0.03 % 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: -0.21 (0.13), residues: 4084 helix: 0.41 (0.12), residues: 1700 sheet: 0.06 (0.21), residues: 572 loop : -0.62 (0.14), residues: 1812 *********************** 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 726 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 725 time to evaluate : 4.277 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 outliers start: 1 outliers final: 0 residues processed: 726 average time/residue: 0.8787 time to fit residues: 1037.7954 Evaluate side-chains 606 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 606 time to evaluate : 4.207 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3353 ------------------------------------------------------------------------------- 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: 10.0000 chunk 234 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 250 optimal weight: 7.9990 chunk 267 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 309 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN M 119 HIS ** K 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 196 ASN N 119 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.6487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 35024 Z= 0.240 Angle : 0.547 7.057 47382 Z= 0.286 Chirality : 0.039 0.218 5008 Planarity : 0.004 0.067 6102 Dihedral : 8.663 179.920 4630 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 0.00 % 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: -0.28 (0.13), residues: 4084 helix: 0.37 (0.12), residues: 1706 sheet: 0.02 (0.21), residues: 572 loop : -0.70 (0.14), residues: 1806 *********************** 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 705 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 705 time to evaluate : 4.176 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 outliers start: 0 outliers final: 0 residues processed: 705 average time/residue: 0.8796 time to fit residues: 1017.8396 Evaluate side-chains 589 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 589 time to evaluate : 4.255 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4482 ------------------------------------------------------------------------------- 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: 3.9990 chunk 376 optimal weight: 7.9990 chunk 343 optimal weight: 0.8980 chunk 366 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 chunk 287 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 chunk 331 optimal weight: 0.9990 chunk 346 optimal weight: 9.9990 chunk 365 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 ASN M 119 HIS ** I 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 ASN ** K 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 196 ASN N 119 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.6547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 35024 Z= 0.150 Angle : 0.496 6.308 47382 Z= 0.253 Chirality : 0.039 0.211 5008 Planarity : 0.004 0.050 6102 Dihedral : 8.377 179.943 4630 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.00 % 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: 0.16 (0.13), residues: 4084 helix: 0.77 (0.12), residues: 1706 sheet: 0.23 (0.21), residues: 564 loop : -0.49 (0.15), residues: 1814 *********************** 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 731 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 731 time to evaluate : 4.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 731 average time/residue: 0.8539 time to fit residues: 1021.0082 Evaluate side-chains 601 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 601 time to evaluate : 4.183 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3067 ------------------------------------------------------------------------------- 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: 8.9990 chunk 387 optimal weight: 7.9990 chunk 236 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 269 optimal weight: 7.9990 chunk 406 optimal weight: 1.9990 chunk 374 optimal weight: 0.5980 chunk 323 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 198 optimal weight: 0.8980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 ASN M 119 HIS ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 196 ASN N 119 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.6714 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= 0.188 Angle : 0.511 5.570 47382 Z= 0.263 Chirality : 0.039 0.187 5008 Planarity : 0.004 0.045 6102 Dihedral : 8.345 179.772 4630 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.00 % 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: 0.12 (0.13), residues: 4084 helix: 0.76 (0.12), residues: 1716 sheet: 0.07 (0.20), residues: 604 loop : -0.49 (0.15), residues: 1764 ********************** 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 705 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 705 time to evaluate : 4.244 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 outliers start: 0 outliers final: 0 residues processed: 705 average time/residue: 0.8602 time to fit residues: 997.4354 Evaluate side-chains 598 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 598 time to evaluate : 4.248 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3841 ------------------------------------------------------------------------------- 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: 10.0000 chunk 344 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 324 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 332 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 ASN M 119 HIS ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 196 ASN N 119 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.123393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.103671 restraints weight = 261834.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.108005 restraints weight = 119117.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.110829 restraints weight = 69270.307| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.6924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 35024 Z= 0.317 Angle : 0.602 7.441 47382 Z= 0.319 Chirality : 0.040 0.240 5008 Planarity : 0.005 0.131 6102 Dihedral : 8.561 179.754 4630 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.00 % 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: -0.46 (0.13), residues: 4084 helix: 0.30 (0.12), residues: 1718 sheet: -0.33 (0.20), residues: 616 loop : -0.80 (0.14), residues: 1750 =============================================================================== Job complete usr+sys time: 16838.98 seconds wall clock time: 291 minutes 30.83 seconds (17490.83 seconds total)