Starting phenix.real_space_refine (version: dev) on Sun Feb 26 09:55:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz5_0311/02_2023/6hz5_0311_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz5_0311/02_2023/6hz5_0311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz5_0311/02_2023/6hz5_0311.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz5_0311/02_2023/6hz5_0311.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz5_0311/02_2023/6hz5_0311_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz5_0311/02_2023/6hz5_0311_trim_updated.pdb" } resolution = 4.2 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 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 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 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 TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 191": "OE1" <-> "OE2" Residue "M GLU 194": "OE1" <-> "OE2" Residue "M GLU 196": "OE1" <-> "OE2" Residue "M ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 242": "OE1" <-> "OE2" Residue "M GLU 251": "OE1" <-> "OE2" Residue "M TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 331": "OE1" <-> "OE2" Residue "M GLU 338": "OE1" <-> "OE2" Residue "G GLU 185": "OE1" <-> "OE2" Residue "G ARG 226": not complete - not flipped Residue "G GLU 280": "OE1" <-> "OE2" Residue "G GLU 292": "OE1" <-> "OE2" Residue "G ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 317": "OE1" <-> "OE2" Residue "G ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 387": "OE1" <-> "OE2" Residue "H GLU 185": "OE1" <-> "OE2" Residue "H ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 221": "OE1" <-> "OE2" Residue "H ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 239": "OE1" <-> "OE2" Residue "H GLU 271": "OE1" <-> "OE2" Residue "H GLU 280": "OE1" <-> "OE2" Residue "H ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 314": "OE1" <-> "OE2" Residue "H ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 348": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 395": "OE1" <-> "OE2" Residue "H GLU 427": "OE1" <-> "OE2" Residue "H GLU 438": "OE1" <-> "OE2" Residue "H GLU 439": "OE1" <-> "OE2" Residue "I 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 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 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 TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 191": "OE1" <-> "OE2" Residue "N GLU 194": "OE1" <-> "OE2" Residue "N GLU 196": "OE1" <-> "OE2" Residue "N ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 242": "OE1" <-> "OE2" Residue "N GLU 251": "OE1" <-> "OE2" Residue "N TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 331": "OE1" <-> "OE2" Residue "N GLU 338": "OE1" <-> "OE2" Time to flip residues: 0.09s 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: 23.22, per 1000 atoms: 0.34 Number of scatterers: 67582 At special positions: 0 Unit cell: (183.75, 135.45, 120.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 156 16.00 P 30 15.00 Mg 6 11.99 O 6402 8.00 N 5748 7.00 C 21872 6.00 H 33368 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 43.74 Conformation dependent library (CDL) restraints added in 4.9 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: 202 helices and 30 sheets defined 44.6% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 207 through 219 removed outlier: 3.677A pdb=" N ARG A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.666A 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: 3.522A pdb=" N GLN A 265 " --> pdb=" O ASN A 261 " (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: 3.757A pdb=" N ARG A 348 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 344 through 349' Processing helix chain 'A' and resid 362 through 370 Processing helix chain 'A' and resid 375 through 394 Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'B' and resid 170 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.744A pdb=" N ILE B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 219 removed outlier: 3.879A pdb=" N ARG B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 No H-bonds generated for 'chain 'B' and resid 238 through 241' Processing helix chain 'B' and resid 258 through 268 Processing helix chain 'B' and resid 286 through 296 removed outlier: 6.974A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N MET B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N MET B 295 " --> pdb=" O GLY B 291 " (cutoff:3.500A) removed outlier: 3.810A 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: 3.578A pdb=" N LEU B 368 " --> pdb=" O PHE B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 394 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 408 through 411 No H-bonds generated for 'chain 'B' and resid 408 through 411' Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 433 through 441 Processing helix chain 'B' and resid 445 through 456 Processing helix chain 'C' and resid 170 through 174 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 207 through 219 removed outlier: 3.876A pdb=" N ARG C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 3.594A 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 removed outlier: 3.557A pdb=" N GLU C 268 " --> pdb=" O GLN C 264 " (cutoff:3.500A) 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: 6.349A pdb=" N VAL C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET C 294 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N MET C 295 " --> pdb=" O GLY C 291 " (cutoff:3.500A) removed outlier: 3.596A 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: 3.928A pdb=" N ARG C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 371 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: 3.551A 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: 6.606A pdb=" N GLU D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N MET D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N MET D 295 " --> pdb=" O GLY D 291 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 346 through 349 No H-bonds generated for 'chain 'D' and resid 346 through 349' Processing helix chain 'D' and resid 362 through 371 Processing helix chain 'D' and resid 375 through 394 removed outlier: 3.569A pdb=" N GLN D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 388 " --> pdb=" O LYS D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 411 No H-bonds generated for 'chain 'D' and resid 408 through 411' Processing helix chain 'D' and resid 422 through 431 removed outlier: 3.611A pdb=" N MET D 430 " --> pdb=" O ASN D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 440 Processing helix chain 'D' and resid 445 through 456 removed outlier: 3.627A pdb=" N LEU D 456 " --> pdb=" O THR D 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.555A pdb=" N LEU E 188 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 3.813A 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 268 removed outlier: 3.610A pdb=" N GLU E 268 " --> pdb=" O GLN E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 283 No H-bonds generated for 'chain 'E' and resid 281 through 283' Processing helix chain 'E' and resid 286 through 294 removed outlier: 6.869A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL E 293 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 4.829A 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: 3.537A pdb=" N ARG E 348 " --> pdb=" O TYR E 344 " (cutoff:3.500A) removed outlier: 3.755A 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 Processing helix chain 'F' and resid 181 through 194 removed outlier: 3.595A pdb=" N LEU F 188 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 193 " --> pdb=" O LYS F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 219 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 269 removed outlier: 3.517A pdb=" N GLU F 268 " --> pdb=" O GLN F 264 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN F 269 " --> pdb=" O GLN F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 295 removed outlier: 7.046A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL F 293 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N MET F 294 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 5.106A 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: 4.165A pdb=" N GLU F 427 " --> pdb=" O GLN F 423 " (cutoff:3.500A) removed outlier: 3.864A 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: 3.599A pdb=" N TRP F 451 " --> pdb=" O LYS F 447 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS F 454 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU F 455 " --> pdb=" O TRP F 451 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU F 456 " --> pdb=" O THR F 452 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 19 removed outlier: 3.648A pdb=" N TYR M 12 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR M 13 " --> pdb=" O ARG M 9 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET M 14 " --> pdb=" O ASN M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 56 removed outlier: 3.808A pdb=" N LEU M 51 " --> pdb=" O ASN M 47 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG M 55 " --> pdb=" O LEU M 51 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG M 56 " --> pdb=" O GLN M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 83 Processing helix chain 'M' and resid 104 through 118 removed outlier: 3.695A pdb=" N ILE M 109 " --> pdb=" O ALA M 105 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS M 110 " --> pdb=" O ASN M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 135 Processing helix chain 'M' and resid 147 through 155 removed outlier: 3.574A pdb=" N LEU M 153 " --> pdb=" O HIS M 149 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN M 154 " --> pdb=" O PHE M 150 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY M 155 " --> pdb=" O SER M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 174 removed outlier: 3.668A pdb=" N PHE M 164 " --> pdb=" O ARG M 160 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL M 165 " --> pdb=" O TYR M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 192 No H-bonds generated for 'chain 'M' and resid 190 through 192' Processing helix chain 'M' and resid 194 through 212 removed outlier: 3.639A pdb=" N TYR M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG M 210 " --> pdb=" O TYR M 206 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG M 211 " --> pdb=" O GLU M 207 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 265 No H-bonds generated for 'chain 'M' and resid 263 through 265' Processing helix chain 'M' and resid 277 through 288 removed outlier: 4.081A pdb=" N MET M 283 " --> pdb=" O TYR M 280 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER M 288 " --> pdb=" O TYR M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 332 through 347 removed outlier: 3.519A pdb=" N TYR M 346 " --> pdb=" O ILE M 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 175 Processing helix chain 'G' and resid 181 through 194 Processing helix chain 'G' and resid 207 through 219 removed outlier: 3.677A pdb=" N ARG G 212 " --> pdb=" O THR G 208 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG G 213 " --> pdb=" O PHE G 209 " (cutoff:3.500A) removed outlier: 3.666A 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: 3.522A pdb=" N GLN G 265 " --> pdb=" O ASN G 261 " (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: 3.757A pdb=" N ARG G 348 " --> pdb=" O TYR G 344 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG G 349 " --> pdb=" O ALA G 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 344 through 349' Processing helix chain 'G' and resid 362 through 370 Processing helix chain 'G' and resid 375 through 394 Processing helix chain 'G' and resid 401 through 403 No H-bonds generated for 'chain 'G' and resid 401 through 403' Processing helix chain 'G' and resid 422 through 431 Processing helix chain 'G' and resid 433 through 440 Processing helix chain 'G' and resid 445 through 456 Processing helix chain 'H' and resid 170 through 175 Processing helix chain 'H' and resid 181 through 194 removed outlier: 3.744A pdb=" N ILE H 193 " --> pdb=" O LYS H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 219 removed outlier: 3.879A pdb=" N ARG H 212 " --> pdb=" O THR H 208 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG H 213 " --> pdb=" O PHE H 209 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR H 216 " --> pdb=" O ARG H 212 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU H 217 " --> pdb=" O ARG H 213 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR H 219 " --> pdb=" O ALA H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 241 No H-bonds generated for 'chain 'H' and resid 238 through 241' Processing helix chain 'H' and resid 258 through 266 Processing helix chain 'H' and resid 286 through 296 removed outlier: 6.974A pdb=" N GLU H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL H 293 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N MET H 294 " --> pdb=" O PHE H 290 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N MET H 295 " --> pdb=" O GLY H 291 " (cutoff:3.500A) removed outlier: 3.811A 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: 3.578A pdb=" N LEU H 368 " --> pdb=" O PHE H 364 " (cutoff:3.500A) Processing helix chain 'H' and resid 375 through 394 Processing helix chain 'H' and resid 401 through 403 No H-bonds generated for 'chain 'H' and resid 401 through 403' Processing helix chain 'H' and resid 408 through 411 No H-bonds generated for 'chain 'H' and resid 408 through 411' Processing helix chain 'H' and resid 422 through 431 Processing helix chain 'H' and resid 433 through 441 Processing helix chain 'H' and resid 445 through 456 Processing helix chain 'I' and resid 170 through 174 Processing helix chain 'I' and resid 181 through 194 Processing helix chain 'I' and resid 207 through 219 removed outlier: 3.875A pdb=" N ARG I 212 " --> pdb=" O THR I 208 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG I 213 " --> pdb=" O PHE I 209 " (cutoff:3.500A) removed outlier: 3.594A 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 removed outlier: 3.557A pdb=" N GLU I 268 " --> pdb=" O GLN I 264 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 296 removed outlier: 6.476A pdb=" N GLU I 292 " --> pdb=" O LYS I 288 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET I 294 " --> pdb=" O PHE I 290 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N MET I 295 " --> pdb=" O GLY I 291 " (cutoff:3.500A) removed outlier: 3.596A 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: 3.928A pdb=" N ARG I 349 " --> pdb=" O ALA I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 371 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: 3.551A 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: 6.606A pdb=" N GLU J 292 " --> pdb=" O LYS J 288 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL J 293 " --> pdb=" O VAL J 289 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N MET J 294 " --> pdb=" O PHE J 290 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N MET J 295 " --> pdb=" O GLY J 291 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU J 296 " --> pdb=" O GLU J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 304 through 306 No H-bonds generated for 'chain 'J' and resid 304 through 306' Processing helix chain 'J' and resid 346 through 349 No H-bonds generated for 'chain 'J' and resid 346 through 349' Processing helix chain 'J' and resid 362 through 371 Processing helix chain 'J' and resid 375 through 394 removed outlier: 3.569A pdb=" N GLN J 383 " --> pdb=" O GLU J 379 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU J 388 " --> pdb=" O LYS J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 408 through 411 No H-bonds generated for 'chain 'J' and resid 408 through 411' Processing helix chain 'J' and resid 422 through 431 removed outlier: 3.611A pdb=" N MET J 430 " --> pdb=" O ASN J 426 " (cutoff:3.500A) Processing helix chain 'J' and resid 433 through 440 Processing helix chain 'J' and resid 445 through 456 removed outlier: 3.627A pdb=" N LEU J 456 " --> pdb=" O THR J 452 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 194 removed outlier: 3.554A pdb=" N LEU K 188 " --> pdb=" O ILE K 184 " (cutoff:3.500A) removed outlier: 3.814A 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 268 removed outlier: 3.611A pdb=" N GLU K 268 " --> pdb=" O GLN K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 283 No H-bonds generated for 'chain 'K' and resid 281 through 283' Processing helix chain 'K' and resid 286 through 294 removed outlier: 6.868A pdb=" N GLU K 292 " --> pdb=" O LYS K 288 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL K 293 " --> pdb=" O VAL K 289 " (cutoff:3.500A) removed outlier: 4.829A 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: 3.538A pdb=" N ARG K 348 " --> pdb=" O TYR K 344 " (cutoff:3.500A) removed outlier: 3.754A 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 Processing helix chain 'L' and resid 181 through 194 removed outlier: 3.595A pdb=" N LEU L 188 " --> pdb=" O ILE L 184 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE L 193 " --> pdb=" O LYS L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 207 through 219 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 269 removed outlier: 3.517A pdb=" N GLU L 268 " --> pdb=" O GLN L 264 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN L 269 " --> pdb=" O GLN L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 295 removed outlier: 7.046A pdb=" N GLU L 292 " --> pdb=" O LYS L 288 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL L 293 " --> pdb=" O VAL L 289 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N MET L 294 " --> pdb=" O PHE L 290 " (cutoff:3.500A) removed outlier: 5.106A 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: 4.165A pdb=" N GLU L 427 " --> pdb=" O GLN L 423 " (cutoff:3.500A) removed outlier: 3.864A 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: 3.600A pdb=" N TRP L 451 " --> pdb=" O LYS L 447 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS L 454 " --> pdb=" O LYS L 450 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU L 455 " --> pdb=" O TRP L 451 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU L 456 " --> pdb=" O THR L 452 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 19 removed outlier: 3.649A pdb=" N TYR N 12 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR N 13 " --> pdb=" O ARG N 9 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET N 14 " --> pdb=" O ASN N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 56 removed outlier: 3.808A pdb=" N LEU N 51 " --> pdb=" O ASN N 47 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG N 56 " --> pdb=" O GLN N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 83 Processing helix chain 'N' and resid 104 through 118 removed outlier: 3.695A pdb=" N ILE N 109 " --> pdb=" O ALA N 105 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS N 110 " --> pdb=" O ASN N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 135 Processing helix chain 'N' and resid 147 through 155 removed outlier: 3.572A pdb=" N LEU N 153 " --> pdb=" O HIS N 149 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN N 154 " --> pdb=" O PHE N 150 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY N 155 " --> pdb=" O SER N 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 174 removed outlier: 3.668A pdb=" N PHE N 164 " --> pdb=" O ARG N 160 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL N 165 " --> pdb=" O TYR N 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 192 No H-bonds generated for 'chain 'N' and resid 190 through 192' Processing helix chain 'N' and resid 194 through 212 removed outlier: 3.638A pdb=" N TYR N 206 " --> pdb=" O GLN N 202 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG N 210 " --> pdb=" O TYR N 206 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG N 211 " --> pdb=" O GLU N 207 " (cutoff:3.500A) Processing helix chain 'N' and resid 263 through 265 No H-bonds generated for 'chain 'N' and resid 263 through 265' Processing helix chain 'N' and resid 277 through 288 removed outlier: 4.081A pdb=" N MET N 283 " --> pdb=" O TYR N 280 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER N 288 " --> pdb=" O TYR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 332 through 347 removed outlier: 3.520A 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: 8.791A pdb=" N ILE A 197 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 328 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU A 199 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY A 330 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR A 274 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE A 329 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE A 276 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU A 331 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 6.833A 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: 6.462A pdb=" N ILE B 328 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU B 199 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY B 330 " --> pdb=" O LEU B 199 " (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: 6.538A pdb=" N ILE C 328 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU C 199 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY C 330 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLY C 201 " --> pdb=" O GLY C 330 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N MET C 332 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 243 through 247 Processing sheet with id= G, first strand: chain 'D' and resid 351 through 354 removed outlier: 3.652A pdb=" N SER D 351 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE D 328 " --> pdb=" O ILE D 197 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU D 199 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY D 330 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLY D 201 " --> pdb=" O GLY D 330 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N MET D 332 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 245 through 247 Processing sheet with id= I, first strand: chain 'E' and resid 351 through 354 removed outlier: 3.848A pdb=" N SER E 351 " --> pdb=" O ASN E 196 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N ILE E 197 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE E 328 " --> pdb=" O ILE E 197 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU E 199 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY E 330 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLY E 201 " --> pdb=" O GLY E 330 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N MET E 332 " --> pdb=" O GLY E 201 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR E 274 " --> pdb=" O TYR E 327 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE E 329 " --> pdb=" O TYR E 274 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N PHE E 276 " --> pdb=" O ILE E 329 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU E 331 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE E 278 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ASN E 333 " --> pdb=" O ILE E 278 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 243 through 247 Processing sheet with id= K, first strand: chain 'F' and resid 351 through 353 removed outlier: 6.590A pdb=" N ILE F 328 " --> pdb=" O ILE F 197 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU F 199 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 6.535A 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: 3.604A pdb=" N ASP M 61 " --> pdb=" O ASN M 100 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN M 100 " --> pdb=" O ASP M 61 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU M 67 " --> pdb=" O SER M 94 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'M' and resid 217 through 219 Processing sheet with id= O, first strand: chain 'M' and resid 255 through 258 removed outlier: 3.726A pdb=" N ILE M 302 " --> pdb=" O ASP M 257 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASP M 320 " --> pdb=" O GLY M 299 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N LEU M 301 " --> pdb=" O ASP M 320 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY M 322 " --> pdb=" O LEU M 301 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N TYR M 303 " --> pdb=" O GLY M 322 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS M 324 " --> pdb=" O TYR M 303 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N HIS M 305 " --> pdb=" O CYS M 324 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL M 326 " --> pdb=" O HIS M 305 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 351 through 354 removed outlier: 8.791A pdb=" N ILE G 197 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE G 328 " --> pdb=" O ILE G 197 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU G 199 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLY G 330 " --> pdb=" O LEU G 199 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR G 274 " --> pdb=" O TYR G 327 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE G 329 " --> pdb=" O TYR G 274 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE G 276 " --> pdb=" O ILE G 329 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU G 331 " --> pdb=" O PHE G 276 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE G 278 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 243 through 247 Processing sheet with id= R, first strand: chain 'H' and resid 351 through 354 removed outlier: 6.462A pdb=" N ILE H 328 " --> pdb=" O ILE H 197 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU H 199 " --> pdb=" O ILE H 328 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY H 330 " --> pdb=" O LEU H 199 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 243 through 247 Processing sheet with id= T, first strand: chain 'I' and resid 351 through 354 removed outlier: 6.538A pdb=" N ILE I 328 " --> pdb=" O ILE I 197 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU I 199 " --> pdb=" O ILE I 328 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY I 330 " --> pdb=" O LEU I 199 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N GLY I 201 " --> pdb=" O GLY I 330 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N MET I 332 " --> pdb=" O GLY I 201 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 243 through 247 Processing sheet with id= V, first strand: chain 'J' and resid 351 through 354 removed outlier: 3.653A pdb=" N SER J 351 " --> pdb=" O ASN J 196 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE J 328 " --> pdb=" O ILE J 197 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU J 199 " --> pdb=" O ILE J 328 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY J 330 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLY J 201 " --> pdb=" O GLY J 330 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N MET J 332 " --> pdb=" O GLY J 201 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 245 through 247 Processing sheet with id= X, first strand: chain 'K' and resid 351 through 354 removed outlier: 3.848A pdb=" N SER K 351 " --> pdb=" O ASN K 196 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N ILE K 197 " --> pdb=" O VAL K 326 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE K 328 " --> pdb=" O ILE K 197 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU K 199 " --> pdb=" O ILE K 328 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY K 330 " --> pdb=" O LEU K 199 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLY K 201 " --> pdb=" O GLY K 330 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET K 332 " --> pdb=" O GLY K 201 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR K 274 " --> pdb=" O TYR K 327 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE K 329 " --> pdb=" O TYR K 274 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N PHE K 276 " --> pdb=" O ILE K 329 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU K 331 " --> pdb=" O PHE K 276 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE K 278 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ASN K 333 " --> pdb=" O ILE K 278 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 243 through 247 Processing sheet with id= Z, first strand: chain 'L' and resid 351 through 353 removed outlier: 6.591A pdb=" N ILE L 328 " --> pdb=" O ILE L 197 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU L 199 " --> pdb=" O ILE L 328 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY L 330 " --> pdb=" O LEU L 199 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 243 through 247 Processing sheet with id= AB, first strand: chain 'N' and resid 61 through 69 removed outlier: 3.604A pdb=" N ASP N 61 " --> pdb=" O ASN N 100 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN N 100 " --> pdb=" O ASP N 61 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU N 67 " --> pdb=" O SER N 94 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'N' and resid 217 through 219 Processing sheet with id= AD, first strand: chain 'N' and resid 255 through 258 removed outlier: 3.725A pdb=" N ILE N 302 " --> pdb=" O ASP N 257 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP N 320 " --> pdb=" O GLY N 299 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N LEU N 301 " --> pdb=" O ASP N 320 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY N 322 " --> pdb=" O LEU N 301 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N TYR N 303 " --> pdb=" O GLY N 322 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N CYS N 324 " --> pdb=" O TYR N 303 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N HIS N 305 " --> pdb=" O CYS N 324 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL N 326 " --> pdb=" O HIS N 305 " (cutoff:3.500A) 1110 hydrogen bonds defined for protein. 3228 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: 23.27 Time building geometry restraints manager: 45.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 33306 1.02 - 1.22: 62 1.22 - 1.42: 14937 1.42 - 1.61: 19835 1.61 - 1.81: 252 Bond restraints: 68392 Sorted by residual: bond pdb=" N3B GNP A1001 " pdb=" PG GNP A1001 " ideal model delta sigma weight residual 1.801 1.542 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" N3B GNP G1001 " pdb=" PG GNP G1001 " ideal model delta sigma weight residual 1.801 1.542 0.259 2.00e-02 2.50e+03 1.68e+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 C1001 " pdb=" PG GNP C1001 " 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 B1001 " pdb=" PG GNP B1001 " ideal model delta sigma weight residual 1.801 1.587 0.214 2.00e-02 2.50e+03 1.14e+02 ... (remaining 68387 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.05: 763 105.05 - 112.29: 76109 112.29 - 119.53: 18068 119.53 - 126.77: 27994 126.77 - 134.01: 432 Bond angle restraints: 123366 Sorted by residual: angle pdb=" O1A GNP H1001 " pdb=" PA GNP H1001 " pdb=" O2A GNP H1001 " ideal model delta sigma weight residual 121.48 107.51 13.97 3.00e+00 1.11e-01 2.17e+01 angle pdb=" O3A GNP G1001 " pdb=" PA GNP G1001 " pdb=" O5' GNP G1001 " ideal model delta sigma weight residual 97.31 111.27 -13.96 3.00e+00 1.11e-01 2.16e+01 angle pdb=" O3A GNP A1001 " pdb=" PA GNP A1001 " pdb=" O5' GNP A1001 " ideal model delta sigma weight residual 97.31 111.27 -13.96 3.00e+00 1.11e-01 2.16e+01 angle pdb=" O1A GNP B1001 " pdb=" PA GNP B1001 " pdb=" O2A GNP B1001 " ideal model delta sigma weight residual 121.48 107.55 13.93 3.00e+00 1.11e-01 2.16e+01 angle pdb=" O1A GNP C1001 " pdb=" PA GNP C1001 " pdb=" O2A GNP C1001 " ideal model delta sigma weight residual 121.48 108.37 13.11 3.00e+00 1.11e-01 1.91e+01 ... (remaining 123361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 27091 35.96 - 71.92: 459 71.92 - 107.89: 28 107.89 - 143.85: 2 143.85 - 179.81: 10 Dihedral angle restraints: 27590 sinusoidal: 12952 harmonic: 14638 Sorted by residual: 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 0.00 179.81 -179.81 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 0.00 179.81 -179.81 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG K 404 " pdb=" NE ARG K 404 " pdb=" CZ ARG K 404 " pdb=" NH1 ARG K 404 " ideal model delta sinusoidal sigma weight residual 0.00 -179.81 179.81 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 27587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4012 0.058 - 0.116: 910 0.116 - 0.174: 70 0.174 - 0.232: 8 0.232 - 0.290: 8 Chirality restraints: 5008 Sorted by residual: 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 -2.73 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C4' GNP A1001 " pdb=" C3' GNP A1001 " pdb=" C5' GNP A1001 " pdb=" O4' GNP A1001 " both_signs ideal model delta sigma weight residual False -2.44 -2.73 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C3' GDP F1001 " pdb=" C4' GDP F1001 " pdb=" O3' GDP F1001 " pdb=" C2' GDP F1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 5005 not shown) Planarity restraints: 10012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 322 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO C 323 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 323 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 323 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 322 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO I 323 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO I 323 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 323 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 209 " -0.016 2.00e-02 2.50e+03 1.24e-02 4.58e+00 pdb=" CG PHE H 209 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE H 209 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE H 209 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE H 209 " 0.002 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 " -0.003 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 ... (remaining 10009 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 3243 2.18 - 2.79: 138009 2.79 - 3.39: 183077 3.39 - 4.00: 237622 4.00 - 4.60: 380695 Nonbonded interactions: 942646 Sorted by model distance: nonbonded pdb=" O ARG I 283 " pdb=" HH TYR N 62 " model vdw 1.580 1.850 nonbonded pdb="HH12 ARG I 246 " pdb=" O GLY N 74 " model vdw 1.594 1.850 nonbonded pdb=" H ASN A 248 " pdb=" O GLY A 251 " model vdw 1.638 1.850 nonbonded pdb=" H ASN G 248 " pdb=" O GLY G 251 " model vdw 1.638 1.850 nonbonded pdb=" O PRO A 357 " pdb=" HD1 HIS A 407 " model vdw 1.652 1.850 ... (remaining 942641 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: 0.580 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: 1.070 Extract box with map and model: 7.330 Check model and map are aligned: 0.770 Process input model: 163.050 Find NCS groups from input model: 3.490 Set up NCS constraints: 0.210 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 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 0.259 35024 Z= 0.599 Angle : 0.973 13.969 47382 Z= 0.483 Chirality : 0.048 0.290 5008 Planarity : 0.005 0.055 6102 Dihedral : 14.601 179.811 13200 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.12), residues: 4084 helix: -0.29 (0.11), residues: 1622 sheet: 0.27 (0.22), residues: 526 loop : -0.47 (0.14), residues: 1936 *********************** 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 1210 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1184 time to evaluate : 4.451 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 outliers start: 26 outliers final: 7 residues processed: 1198 average time/residue: 1.0395 time to fit residues: 1940.5476 Evaluate side-chains 662 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 655 time to evaluate : 4.318 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.7690 time to fit residues: 14.6587 ------------------------------------------------------------------------------- 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: 10.0000 chunk 309 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 208 optimal weight: 0.9990 chunk 165 optimal weight: 9.9990 chunk 319 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 238 optimal weight: 7.9990 chunk 370 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS B 453 ASN E 299 HIS F 299 HIS ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 ASN M 284 ASN ** G 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 453 ASN ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 299 HIS L 383 GLN L 426 ASN N 10 ASN N 284 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 35024 Z= 0.233 Angle : 0.591 5.936 47382 Z= 0.309 Chirality : 0.039 0.160 5008 Planarity : 0.004 0.050 6102 Dihedral : 9.767 180.000 4630 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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: 0.75 (0.12), residues: 1700 sheet: 0.13 (0.22), residues: 558 loop : -0.34 (0.14), residues: 1826 *********************** 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 841 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 840 time to evaluate : 4.268 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 outliers start: 1 outliers final: 1 residues processed: 841 average time/residue: 0.9998 time to fit residues: 1325.7710 Evaluate side-chains 582 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 581 time to evaluate : 4.470 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6870 time to fit residues: 6.9701 ------------------------------------------------------------------------------- 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: 0.9980 chunk 308 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 371 optimal weight: 20.0000 chunk 400 optimal weight: 4.9990 chunk 330 optimal weight: 5.9990 chunk 368 optimal weight: 20.0000 chunk 126 optimal weight: 0.8980 chunk 297 optimal weight: 4.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 448 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 GLN ** E 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 ASN M 119 HIS G 448 GLN ** G 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 363 GLN N 119 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.124 35024 Z= 0.276 Angle : 0.579 7.125 47382 Z= 0.302 Chirality : 0.039 0.153 5008 Planarity : 0.004 0.064 6102 Dihedral : 9.558 179.114 4630 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.13), residues: 4084 helix: 0.74 (0.12), residues: 1728 sheet: 0.23 (0.21), residues: 590 loop : -0.26 (0.14), residues: 1766 *********************** 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 724 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 720 time to evaluate : 4.384 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 outliers start: 4 outliers final: 0 residues processed: 724 average time/residue: 0.9547 time to fit residues: 1103.1409 Evaluate side-chains 504 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 4.314 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3761 ------------------------------------------------------------------------------- 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: 8.9990 chunk 279 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 249 optimal weight: 6.9990 chunk 372 optimal weight: 8.9990 chunk 394 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 353 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 312 HIS ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 35024 Z= 0.300 Angle : 0.587 7.807 47382 Z= 0.305 Chirality : 0.039 0.170 5008 Planarity : 0.004 0.050 6102 Dihedral : 9.137 179.087 4630 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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: 0.05 (0.13), residues: 4084 helix: 0.63 (0.12), residues: 1722 sheet: 0.00 (0.21), residues: 592 loop : -0.43 (0.14), residues: 1770 *********************** 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 679 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 679 time to evaluate : 4.313 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 outliers start: 0 outliers final: 0 residues processed: 679 average time/residue: 0.8908 time to fit residues: 975.5172 Evaluate side-chains 510 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 510 time to evaluate : 4.328 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 293 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 336 optimal weight: 7.9990 chunk 272 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 353 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- 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 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 261 ASN ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 261 ASN ** G 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN ** G 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 315 ASN N 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 35024 Z= 0.280 Angle : 0.569 5.934 47382 Z= 0.296 Chirality : 0.039 0.156 5008 Planarity : 0.004 0.048 6102 Dihedral : 8.813 179.175 4630 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.13), residues: 4084 helix: 0.56 (0.12), residues: 1714 sheet: -0.24 (0.21), residues: 566 loop : -0.63 (0.14), residues: 1804 *********************** 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 671 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 667 time to evaluate : 4.357 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 outliers start: 4 outliers final: 1 residues processed: 671 average time/residue: 0.9035 time to fit residues: 982.2450 Evaluate side-chains 493 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 492 time to evaluate : 4.328 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5997 time to fit residues: 6.5240 ------------------------------------------------------------------------------- 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: 1.9990 chunk 355 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 231 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 394 optimal weight: 5.9990 chunk 327 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 ASN ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 261 ASN ** G 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN ** G 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.6318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 35024 Z= 0.247 Angle : 0.548 6.093 47382 Z= 0.283 Chirality : 0.039 0.182 5008 Planarity : 0.004 0.037 6102 Dihedral : 8.611 179.574 4630 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.13), residues: 4084 helix: 0.55 (0.12), residues: 1726 sheet: -0.28 (0.21), residues: 566 loop : -0.69 (0.14), residues: 1792 *********************** 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 669 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 665 time to evaluate : 4.869 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 outliers start: 4 outliers final: 0 residues processed: 667 average time/residue: 0.8945 time to fit residues: 964.0833 Evaluate side-chains 500 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 500 time to evaluate : 4.451 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3829 ------------------------------------------------------------------------------- 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: 1.9990 chunk 44 optimal weight: 8.9990 chunk 224 optimal weight: 5.9990 chunk 288 optimal weight: 0.1980 chunk 223 optimal weight: 0.5980 chunk 332 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 393 optimal weight: 2.9990 chunk 246 optimal weight: 10.0000 chunk 239 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 231 GLN ** G 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN ** G 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 228 ASN N 193 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.6536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 35024 Z= 0.198 Angle : 0.519 6.267 47382 Z= 0.264 Chirality : 0.039 0.171 5008 Planarity : 0.003 0.038 6102 Dihedral : 8.487 179.639 4630 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % 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: -0.05 (0.13), residues: 4084 helix: 0.67 (0.12), residues: 1730 sheet: -0.19 (0.21), residues: 566 loop : -0.58 (0.14), residues: 1788 *********************** 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 666 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 663 time to evaluate : 4.364 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 outliers start: 3 outliers final: 0 residues processed: 665 average time/residue: 0.8577 time to fit residues: 928.7895 Evaluate side-chains 490 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 490 time to evaluate : 4.326 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3510 ------------------------------------------------------------------------------- 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: 8.9990 chunk 157 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 267 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 309 optimal weight: 0.3980 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN ** G 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.6690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 35024 Z= 0.198 Angle : 0.511 6.126 47382 Z= 0.260 Chirality : 0.038 0.162 5008 Planarity : 0.003 0.036 6102 Dihedral : 8.433 179.940 4630 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % 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: 0.03 (0.13), residues: 4084 helix: 0.84 (0.12), residues: 1706 sheet: -0.28 (0.21), residues: 566 loop : -0.59 (0.14), residues: 1812 *********************** 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 642 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 640 time to evaluate : 4.357 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 outliers start: 2 outliers final: 0 residues processed: 642 average time/residue: 0.8872 time to fit residues: 933.5934 Evaluate side-chains 495 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 495 time to evaluate : 4.512 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6655 ------------------------------------------------------------------------------- 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: 1.9990 chunk 376 optimal weight: 6.9990 chunk 343 optimal weight: 6.9990 chunk 366 optimal weight: 9.9990 chunk 220 optimal weight: 0.6980 chunk 159 optimal weight: 9.9990 chunk 287 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 331 optimal weight: 3.9990 chunk 346 optimal weight: 6.9990 chunk 365 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 ASN ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN ** G 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 228 ASN ** K 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 35024 Z= 0.295 Angle : 0.576 6.341 47382 Z= 0.299 Chirality : 0.040 0.181 5008 Planarity : 0.004 0.049 6102 Dihedral : 8.594 179.637 4630 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.13), residues: 4084 helix: 0.56 (0.12), residues: 1726 sheet: -0.63 (0.21), residues: 586 loop : -0.79 (0.14), residues: 1772 *********************** 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 631 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 627 time to evaluate : 4.373 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 outliers start: 4 outliers final: 0 residues processed: 629 average time/residue: 0.8733 time to fit residues: 900.0959 Evaluate side-chains 467 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 4.414 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 9.9990 chunk 387 optimal weight: 7.9990 chunk 236 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 269 optimal weight: 9.9990 chunk 406 optimal weight: 0.3980 chunk 374 optimal weight: 5.9990 chunk 323 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 250 optimal weight: 6.9990 chunk 198 optimal weight: 6.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 ASN ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN ** G 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.7050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 35024 Z= 0.191 Angle : 0.513 6.310 47382 Z= 0.261 Chirality : 0.039 0.176 5008 Planarity : 0.003 0.040 6102 Dihedral : 8.421 179.764 4630 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.13), residues: 4084 helix: 0.78 (0.13), residues: 1718 sheet: -0.52 (0.21), residues: 582 loop : -0.62 (0.14), residues: 1784 ********************** 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 637 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 633 time to evaluate : 4.385 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 outliers start: 4 outliers final: 0 residues processed: 635 average time/residue: 0.8692 time to fit residues: 897.7737 Evaluate side-chains 498 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 498 time to evaluate : 4.314 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3179 ------------------------------------------------------------------------------- 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: 3.9990 chunk 344 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 298 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 324 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 332 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN ** G 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 196 ASN ** K 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.107290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.090355 restraints weight = 245310.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.094123 restraints weight = 105576.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.096488 restraints weight = 59813.539| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.7174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 35024 Z= 0.192 Angle : 0.511 6.299 47382 Z= 0.261 Chirality : 0.039 0.173 5008 Planarity : 0.003 0.035 6102 Dihedral : 8.367 179.572 4630 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % 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: 0.00 (0.13), residues: 4084 helix: 0.91 (0.13), residues: 1692 sheet: -0.53 (0.21), residues: 582 loop : -0.60 (0.14), residues: 1810 =============================================================================== Job complete usr+sys time: 15801.33 seconds wall clock time: 273 minutes 57.47 seconds (16437.47 seconds total)