Starting phenix.real_space_refine on Fri Feb 16 13:54:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz7_0313/02_2024/6hz7_0313_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz7_0313/02_2024/6hz7_0313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz7_0313/02_2024/6hz7_0313.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz7_0313/02_2024/6hz7_0313.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz7_0313/02_2024/6hz7_0313_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hz7_0313/02_2024/6hz7_0313_trim_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 30 5.49 5 Mg 6 5.21 5 S 156 5.16 5 C 21872 2.51 5 N 5748 2.21 5 O 6402 1.98 5 H 33368 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ARG 226": not complete - not flipped Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 387": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 314": "OE1" <-> "OE2" Residue "B ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 348": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B GLU 438": "OE1" <-> "OE2" Residue "B GLU 439": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 280": "OE1" <-> "OE2" Residue "C ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "D ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 365": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 387": "OE1" <-> "OE2" Residue "D ARG 404": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 181": "OE1" <-> "OE2" Residue "E ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 226": not complete - not flipped Residue "E 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 TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 242": "OE1" <-> "OE2" Residue "M GLU 251": "OE1" <-> "OE2" Residue "M TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 331": "OE1" <-> "OE2" Residue "M GLU 338": "OE1" <-> "OE2" Residue "G GLU 185": "OE1" <-> "OE2" Residue "G ARG 226": not complete - not flipped Residue "G GLU 280": "OE1" <-> "OE2" Residue "G GLU 292": "OE1" <-> "OE2" Residue "G ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 317": "OE1" <-> "OE2" Residue "G ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 387": "OE1" <-> "OE2" Residue "H GLU 185": "OE1" <-> "OE2" Residue "H ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 221": "OE1" <-> "OE2" Residue "H ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 239": "OE1" <-> "OE2" Residue "H GLU 271": "OE1" <-> "OE2" Residue "H GLU 280": "OE1" <-> "OE2" Residue "H ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 314": "OE1" <-> "OE2" Residue "H ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 348": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 395": "OE1" <-> "OE2" Residue "H GLU 427": "OE1" <-> "OE2" Residue "H GLU 438": "OE1" <-> "OE2" Residue "H GLU 439": "OE1" <-> "OE2" Residue "I GLU 171": "OE1" <-> "OE2" Residue "I GLU 181": "OE1" <-> "OE2" Residue "I GLU 185": "OE1" <-> "OE2" Residue "I PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 280": "OE1" <-> "OE2" Residue "I ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 292": "OE1" <-> "OE2" Residue "I ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 304": "OE1" <-> "OE2" Residue "I GLU 317": "OE1" <-> "OE2" Residue "I ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 324": "OE1" <-> "OE2" Residue "I ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 438": "OE1" <-> "OE2" Residue "I GLU 439": "OE1" <-> "OE2" Residue "J GLU 181": "OE1" <-> "OE2" Residue "J GLU 268": "OE1" <-> "OE2" Residue "J ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 304": "OE1" <-> "OE2" Residue "J TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 318": "OE1" <-> "OE2" Residue "J ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 365": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 387": "OE1" <-> "OE2" Residue "J ARG 404": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 181": "OE1" <-> "OE2" Residue "K ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 226": not complete - not flipped Residue "K 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 TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 242": "OE1" <-> "OE2" Residue "N GLU 251": "OE1" <-> "OE2" Residue "N TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 331": "OE1" <-> "OE2" Residue "N GLU 338": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 67582 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4720 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "B" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4719 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "C" Number of atoms: 4717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4717 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "D" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4633 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "E" Number of atoms: 4637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4637 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain: "F" Number of atoms: 4644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4644 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain: "M" Number of atoms: 5538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5538 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 323} Chain breaks: 2 Chain: "G" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4720 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "H" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4719 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "I" Number of atoms: 4717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4717 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "J" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4633 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "K" Number of atoms: 4637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4637 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain: "L" Number of atoms: 4644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4644 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain: "N" Number of atoms: 5538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5538 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 323} Chain breaks: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.67, per 1000 atoms: 0.32 Number of scatterers: 67582 At special positions: 0 Unit cell: (185.85, 136.5, 123.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 156 16.00 P 30 15.00 Mg 6 11.99 O 6402 8.00 N 5748 7.00 C 21872 6.00 H 33368 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 41.92 Conformation dependent library (CDL) restraints added in 6.1 seconds 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 198 helices and 30 sheets defined 44.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.51 Creating SS restraints... Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 207 through 219 removed outlier: 3.643A pdb=" N ARG A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 258 through 268 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 286 through 289 No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 291 through 297 removed outlier: 3.845A pdb=" N MET A 297 " --> pdb=" O MET A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 337 through 340 Processing helix chain 'A' and resid 344 through 349 removed outlier: 3.712A pdb=" N ARG A 348 " --> pdb=" O TYR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 375 through 394 Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 408 through 411 No H-bonds generated for 'chain 'A' and resid 408 through 411' Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 445 through 456 removed outlier: 3.521A pdb=" N LYS A 454 " --> pdb=" O LYS A 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.653A pdb=" N ILE B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 219 removed outlier: 3.897A pdb=" N ARG B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 No H-bonds generated for 'chain 'B' and resid 238 through 241' Processing helix chain 'B' and resid 258 through 268 removed outlier: 3.607A pdb=" N GLN B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 removed outlier: 6.690A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N MET B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N MET B 295 " --> pdb=" O GLY B 291 " (cutoff:3.500A) removed outlier: 4.060A 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: 3.640A pdb=" N PHE B 367 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 3.587A 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: 4.047A pdb=" N ARG C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 216 " --> pdb=" O ARG C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 241 No H-bonds generated for 'chain 'C' and resid 238 through 241' Processing helix chain 'C' and resid 258 through 268 Processing helix chain 'C' and resid 286 through 296 removed outlier: 6.588A pdb=" N GLU C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N MET C 294 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET C 295 " --> pdb=" O GLY C 291 " (cutoff:3.500A) removed outlier: 3.680A 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: 3.630A pdb=" N ARG C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 370 Processing helix chain 'C' and resid 375 through 394 Processing helix chain 'C' and resid 401 through 403 No H-bonds generated for 'chain 'C' and resid 401 through 403' Processing helix chain 'C' and resid 408 through 411 No H-bonds generated for 'chain 'C' and resid 408 through 411' Processing helix chain 'C' and resid 422 through 431 Processing helix chain 'C' and resid 433 through 440 Processing helix chain 'C' and resid 445 through 456 removed outlier: 3.595A pdb=" N LEU C 456 " --> pdb=" O THR C 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.544A 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: 6.395A pdb=" N GLU D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N MET D 295 " --> pdb=" O GLY D 291 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 344 through 349 Processing helix chain 'D' and resid 362 through 371 Processing helix chain 'D' and resid 375 through 392 Processing helix chain 'D' and resid 422 through 431 removed outlier: 3.505A pdb=" N ILE D 428 " --> pdb=" O TRP D 424 " (cutoff:3.500A) removed outlier: 3.569A 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: 3.666A pdb=" N LEU D 456 " --> pdb=" O THR D 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.697A pdb=" N LEU E 188 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 3.991A 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: 3.551A 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: 7.068A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL E 293 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 5.002A 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: 3.505A pdb=" N ARG E 348 " --> pdb=" O TYR E 344 " (cutoff:3.500A) removed outlier: 3.802A 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: 3.590A pdb=" N LEU F 188 " --> pdb=" O ILE F 184 " (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: 3.670A pdb=" N GLU F 268 " --> pdb=" O GLN F 264 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN F 269 " --> pdb=" O GLN F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 295 removed outlier: 6.922A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL F 293 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N MET F 294 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 5.219A 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: 4.299A pdb=" N GLU F 427 " --> pdb=" O GLN F 423 " (cutoff:3.500A) removed outlier: 3.965A 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: 3.551A pdb=" N LYS F 450 " --> pdb=" O TYR F 446 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP F 451 " --> pdb=" O LYS F 447 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS F 454 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU F 455 " --> pdb=" O TRP F 451 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU F 456 " --> pdb=" O THR F 452 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 19 removed outlier: 3.861A pdb=" N TYR M 12 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR M 13 " --> pdb=" O ARG M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 56 removed outlier: 3.811A pdb=" N LEU M 51 " --> pdb=" O ASN M 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG M 56 " --> pdb=" O GLN M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 84 Processing helix chain 'M' and resid 104 through 118 Processing helix chain 'M' and resid 124 through 136 removed outlier: 3.562A pdb=" N SER M 132 " --> pdb=" O ASP M 128 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU M 133 " --> pdb=" O GLU M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 155 removed outlier: 3.558A pdb=" N LEU M 153 " --> pdb=" O HIS M 149 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLY M 155 " --> pdb=" O SER M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 174 removed outlier: 3.862A pdb=" N PHE M 164 " --> pdb=" O ARG M 160 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL M 165 " --> pdb=" O TYR M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 212 removed outlier: 3.813A pdb=" N ARG M 210 " --> pdb=" O TYR M 206 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG M 211 " --> pdb=" O GLU M 207 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 288 removed outlier: 4.103A pdb=" N MET M 283 " --> pdb=" O TYR M 280 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER M 288 " --> pdb=" O TYR M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 332 through 347 removed outlier: 3.615A pdb=" N TYR M 346 " --> pdb=" O ILE M 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 174 Processing helix chain 'G' and resid 181 through 194 Processing helix chain 'G' and resid 207 through 219 removed outlier: 3.643A pdb=" N ARG G 212 " --> pdb=" O THR G 208 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG G 213 " --> pdb=" O PHE G 209 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR G 216 " --> pdb=" O ARG G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 241 No H-bonds generated for 'chain 'G' and resid 238 through 241' Processing helix chain 'G' and resid 258 through 268 Processing helix chain 'G' and resid 281 through 283 No H-bonds generated for 'chain 'G' and resid 281 through 283' Processing helix chain 'G' and resid 286 through 289 No H-bonds generated for 'chain 'G' and resid 286 through 289' Processing helix chain 'G' and resid 291 through 297 removed outlier: 3.847A pdb=" N MET G 297 " --> pdb=" O MET G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 306 No H-bonds generated for 'chain 'G' and resid 304 through 306' Processing helix chain 'G' and resid 337 through 340 Processing helix chain 'G' and resid 344 through 349 removed outlier: 3.711A pdb=" N ARG G 348 " --> pdb=" O TYR G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 371 Processing helix chain 'G' and resid 375 through 394 Processing helix chain 'G' and resid 401 through 403 No H-bonds generated for 'chain 'G' and resid 401 through 403' Processing helix chain 'G' and resid 408 through 411 No H-bonds generated for 'chain 'G' and resid 408 through 411' Processing helix chain 'G' and resid 422 through 431 Processing helix chain 'G' and resid 433 through 440 Processing helix chain 'G' and resid 445 through 456 removed outlier: 3.522A pdb=" N LYS G 454 " --> pdb=" O LYS G 450 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 175 Processing helix chain 'H' and resid 181 through 194 removed outlier: 3.653A pdb=" N ILE H 193 " --> pdb=" O LYS H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 219 removed outlier: 3.897A pdb=" N ARG H 212 " --> pdb=" O THR H 208 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG H 213 " --> pdb=" O PHE H 209 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR H 216 " --> pdb=" O ARG H 212 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU H 217 " --> pdb=" O ARG H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 241 No H-bonds generated for 'chain 'H' and resid 238 through 241' Processing helix chain 'H' and resid 258 through 268 removed outlier: 3.607A pdb=" N GLN H 265 " --> pdb=" O ASN H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 296 removed outlier: 6.690A pdb=" N GLU H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL H 293 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N MET H 294 " --> pdb=" O PHE H 290 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N MET H 295 " --> pdb=" O GLY H 291 " (cutoff:3.500A) removed outlier: 4.060A 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: 3.640A pdb=" N PHE H 367 " --> pdb=" O GLN H 363 " (cutoff:3.500A) removed outlier: 3.588A 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: 4.047A pdb=" N ARG I 212 " --> pdb=" O THR I 208 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG I 213 " --> pdb=" O PHE I 209 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR I 216 " --> pdb=" O ARG I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 241 No H-bonds generated for 'chain 'I' and resid 238 through 241' Processing helix chain 'I' and resid 258 through 268 Processing helix chain 'I' and resid 286 through 296 removed outlier: 6.587A pdb=" N GLU I 292 " --> pdb=" O LYS I 288 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N MET I 294 " --> pdb=" O PHE I 290 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET I 295 " --> pdb=" O GLY I 291 " (cutoff:3.500A) removed outlier: 3.681A 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: 3.629A pdb=" N ARG I 349 " --> pdb=" O ALA I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 370 Processing helix chain 'I' and resid 375 through 394 Processing helix chain 'I' and resid 401 through 403 No H-bonds generated for 'chain 'I' and resid 401 through 403' Processing helix chain 'I' and resid 408 through 411 No H-bonds generated for 'chain 'I' and resid 408 through 411' Processing helix chain 'I' and resid 422 through 431 Processing helix chain 'I' and resid 433 through 440 Processing helix chain 'I' and resid 445 through 456 removed outlier: 3.595A pdb=" N LEU I 456 " --> pdb=" O THR I 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 194 removed outlier: 3.545A 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: 6.395A pdb=" N GLU J 292 " --> pdb=" O LYS J 288 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL J 293 " --> pdb=" O VAL J 289 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N MET J 294 " --> pdb=" O PHE J 290 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N MET J 295 " --> pdb=" O GLY J 291 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU J 296 " --> pdb=" O GLU J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 304 through 306 No H-bonds generated for 'chain 'J' and resid 304 through 306' Processing helix chain 'J' and resid 344 through 349 Processing helix chain 'J' and resid 362 through 371 Processing helix chain 'J' and resid 375 through 392 Processing helix chain 'J' and resid 422 through 431 removed outlier: 3.506A pdb=" N ILE J 428 " --> pdb=" O TRP J 424 " (cutoff:3.500A) removed outlier: 3.568A 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: 3.665A pdb=" N LEU J 456 " --> pdb=" O THR J 452 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 194 removed outlier: 3.697A pdb=" N LEU K 188 " --> pdb=" O ILE K 184 " (cutoff:3.500A) removed outlier: 3.991A 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: 3.551A 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: 7.068A pdb=" N GLU K 292 " --> pdb=" O LYS K 288 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL K 293 " --> pdb=" O VAL K 289 " (cutoff:3.500A) removed outlier: 5.001A 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: 3.505A pdb=" N ARG K 348 " --> pdb=" O TYR K 344 " (cutoff:3.500A) removed outlier: 3.802A 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: 3.590A pdb=" N LEU L 188 " --> pdb=" O ILE L 184 " (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: 3.669A pdb=" N GLU L 268 " --> pdb=" O GLN L 264 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN L 269 " --> pdb=" O GLN L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 295 removed outlier: 6.922A pdb=" N GLU L 292 " --> pdb=" O LYS L 288 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL L 293 " --> pdb=" O VAL L 289 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N MET L 294 " --> pdb=" O PHE L 290 " (cutoff:3.500A) removed outlier: 5.220A 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: 4.299A pdb=" N GLU L 427 " --> pdb=" O GLN L 423 " (cutoff:3.500A) removed outlier: 3.966A 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: 3.551A pdb=" N LYS L 450 " --> pdb=" O TYR L 446 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP L 451 " --> pdb=" O LYS L 447 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS L 454 " --> pdb=" O LYS L 450 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU L 455 " --> pdb=" O TRP L 451 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU L 456 " --> pdb=" O THR L 452 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 19 removed outlier: 3.860A pdb=" N TYR N 12 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR N 13 " --> pdb=" O ARG N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 56 removed outlier: 3.811A pdb=" N LEU N 51 " --> pdb=" O ASN N 47 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG N 56 " --> pdb=" O GLN N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 84 Processing helix chain 'N' and resid 104 through 118 Processing helix chain 'N' and resid 124 through 136 removed outlier: 3.562A pdb=" N SER N 132 " --> pdb=" O ASP N 128 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU N 133 " --> pdb=" O GLU N 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 155 removed outlier: 3.559A pdb=" N LEU N 153 " --> pdb=" O HIS N 149 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLY N 155 " --> pdb=" O SER N 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 174 removed outlier: 3.862A pdb=" N PHE N 164 " --> pdb=" O ARG N 160 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL N 165 " --> pdb=" O TYR N 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 212 removed outlier: 3.814A pdb=" N ARG N 210 " --> pdb=" O TYR N 206 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG N 211 " --> pdb=" O GLU N 207 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 288 removed outlier: 4.103A pdb=" N MET N 283 " --> pdb=" O TYR N 280 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER N 288 " --> pdb=" O TYR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 332 through 347 removed outlier: 3.615A 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: 8.677A pdb=" N ILE A 197 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE A 328 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU A 199 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY A 330 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR A 274 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE A 329 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHE A 276 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU A 331 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE A 278 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 243 through 247 Processing sheet with id= C, first strand: chain 'B' and resid 351 through 354 removed outlier: 8.922A pdb=" N ILE B 197 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE B 328 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N LEU B 199 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY B 330 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR B 274 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE B 329 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE B 276 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N LEU B 331 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE B 278 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 243 through 247 Processing sheet with id= E, first strand: chain 'C' and resid 351 through 354 removed outlier: 6.609A pdb=" N ILE C 328 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LEU C 199 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY C 330 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY C 201 " --> pdb=" O GLY C 330 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N MET C 332 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 243 through 247 Processing sheet with id= G, first strand: chain 'D' and resid 351 through 354 removed outlier: 6.673A pdb=" N ILE D 328 " --> pdb=" O ILE D 197 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU D 199 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY D 330 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLY D 201 " --> pdb=" O GLY D 330 " (cutoff:3.500A) removed outlier: 5.841A 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: 3.820A pdb=" N SER E 351 " --> pdb=" O ASN E 196 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE E 328 " --> pdb=" O ILE E 197 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LEU E 199 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY E 330 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLY E 201 " --> pdb=" O GLY E 330 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N MET E 332 " --> pdb=" O GLY E 201 " (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: 9.209A pdb=" N ILE F 197 " --> pdb=" O VAL F 326 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE F 328 " --> pdb=" O ILE F 197 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU F 199 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY F 330 " --> pdb=" O LEU F 199 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR F 274 " --> pdb=" O TYR F 327 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE F 329 " --> pdb=" O TYR F 274 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE F 276 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU F 331 " --> pdb=" O PHE F 276 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE F 278 " --> pdb=" O LEU F 331 " (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: 3.986A pdb=" N ASN M 100 " --> pdb=" O ASP M 61 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'M' and resid 217 through 219 Processing sheet with id= O, first strand: chain 'M' and resid 253 through 259 removed outlier: 3.580A pdb=" N ILE M 302 " --> pdb=" O ASP M 257 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS M 259 " --> pdb=" O ILE M 302 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP M 320 " --> pdb=" O GLY M 299 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LEU M 301 " --> pdb=" O ASP M 320 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY M 322 " --> pdb=" O LEU M 301 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N TYR M 303 " --> pdb=" O GLY M 322 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N CYS M 324 " --> pdb=" O TYR M 303 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N HIS M 305 " --> pdb=" O CYS M 324 " (cutoff:3.500A) removed outlier: 5.212A 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: 8.676A pdb=" N ILE G 197 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE G 328 " --> pdb=" O ILE G 197 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU G 199 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY G 330 " --> pdb=" O LEU G 199 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR G 274 " --> pdb=" O TYR G 327 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE G 329 " --> pdb=" O TYR G 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE G 276 " --> pdb=" O ILE G 329 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU G 331 " --> pdb=" O PHE G 276 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE G 278 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 243 through 247 Processing sheet with id= R, first strand: chain 'H' and resid 351 through 354 removed outlier: 8.921A pdb=" N ILE H 197 " --> pdb=" O VAL H 326 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE H 328 " --> pdb=" O ILE H 197 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU H 199 " --> pdb=" O ILE H 328 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY H 330 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR H 274 " --> pdb=" O TYR H 327 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE H 329 " --> pdb=" O TYR H 274 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE H 276 " --> pdb=" O ILE H 329 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N LEU H 331 " --> pdb=" O PHE H 276 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE H 278 " --> pdb=" O LEU H 331 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 243 through 247 Processing sheet with id= T, first strand: chain 'I' and resid 351 through 354 removed outlier: 6.609A pdb=" N ILE I 328 " --> pdb=" O ILE I 197 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LEU I 199 " --> pdb=" O ILE I 328 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY I 330 " --> pdb=" O LEU I 199 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY I 201 " --> pdb=" O GLY I 330 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N MET I 332 " --> pdb=" O GLY I 201 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 243 through 247 Processing sheet with id= V, first strand: chain 'J' and resid 351 through 354 removed outlier: 6.672A pdb=" N ILE J 328 " --> pdb=" O ILE J 197 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU J 199 " --> pdb=" O ILE J 328 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY J 330 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLY J 201 " --> pdb=" O GLY J 330 " (cutoff:3.500A) removed outlier: 5.841A 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: 3.820A pdb=" N SER K 351 " --> pdb=" O ASN K 196 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE K 328 " --> pdb=" O ILE K 197 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LEU K 199 " --> pdb=" O ILE K 328 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY K 330 " --> pdb=" O LEU K 199 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLY K 201 " --> pdb=" O GLY K 330 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N MET K 332 " --> pdb=" O GLY K 201 " (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: 9.210A pdb=" N ILE L 197 " --> pdb=" O VAL L 326 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE L 328 " --> pdb=" O ILE L 197 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU L 199 " --> pdb=" O ILE L 328 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY L 330 " --> pdb=" O LEU L 199 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR L 274 " --> pdb=" O TYR L 327 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE L 329 " --> pdb=" O TYR L 274 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE L 276 " --> pdb=" O ILE L 329 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU L 331 " --> pdb=" O PHE L 276 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE L 278 " --> pdb=" O LEU L 331 " (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: 3.986A pdb=" N ASN N 100 " --> pdb=" O ASP N 61 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'N' and resid 217 through 219 Processing sheet with id= AD, first strand: chain 'N' and resid 253 through 259 removed outlier: 3.579A pdb=" N ILE N 302 " --> pdb=" O ASP N 257 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS N 259 " --> pdb=" O ILE N 302 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP N 320 " --> pdb=" O GLY N 299 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LEU N 301 " --> pdb=" O ASP N 320 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY N 322 " --> pdb=" O LEU N 301 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N TYR N 303 " --> pdb=" O GLY N 322 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N CYS N 324 " --> pdb=" O TYR N 303 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N HIS N 305 " --> pdb=" O CYS N 324 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL N 326 " --> pdb=" O HIS N 305 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3264 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: 24.07 Time building geometry restraints manager: 44.27 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: 14924 1.42 - 1.61: 19848 1.61 - 1.81: 252 Bond restraints: 68392 Sorted by residual: bond pdb=" N3B GNP C1001 " pdb=" PG GNP C1001 " ideal model delta sigma weight residual 1.801 1.553 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" N3B GNP I1001 " pdb=" PG GNP I1001 " ideal model delta sigma weight residual 1.801 1.553 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" N3B GNP G1001 " pdb=" PG GNP G1001 " ideal model delta sigma weight residual 1.801 1.556 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" N3B GNP A1001 " pdb=" PG GNP A1001 " ideal model delta sigma weight residual 1.801 1.557 0.244 2.00e-02 2.50e+03 1.48e+02 bond pdb=" N3B GNP B1001 " pdb=" PG GNP B1001 " ideal model delta sigma weight residual 1.801 1.584 0.217 2.00e-02 2.50e+03 1.18e+02 ... (remaining 68387 not shown) Histogram of bond angle deviations from ideal: 58.70 - 75.27: 10 75.27 - 91.84: 16 91.84 - 108.41: 22233 108.41 - 124.98: 99483 124.98 - 141.55: 1624 Bond angle restraints: 123366 Sorted by residual: angle pdb=" C ASP K 176 " pdb=" N LEU K 177 " pdb=" H LEU K 177 " ideal model delta sigma weight residual 124.71 68.10 56.62 3.00e+00 1.11e-01 3.56e+02 angle pdb=" CA LEU K 177 " pdb=" N LEU K 177 " pdb=" H LEU K 177 " ideal model delta sigma weight residual 114.41 58.70 55.71 3.00e+00 1.11e-01 3.45e+02 angle pdb=" C LYS K 371 " pdb=" N LYS K 372 " pdb=" H LYS K 372 " ideal model delta sigma weight residual 123.95 69.32 54.63 3.00e+00 1.11e-01 3.32e+02 angle pdb=" CA LYS K 372 " pdb=" N LYS K 372 " pdb=" H LYS K 372 " ideal model delta sigma weight residual 113.65 59.03 54.62 3.00e+00 1.11e-01 3.31e+02 angle pdb=" C SER K 419 " pdb=" CA SER K 419 " pdb=" HA SER K 419 " ideal model delta sigma weight residual 109.00 69.63 39.37 3.00e+00 1.11e-01 1.72e+02 ... (remaining 123361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 31464 36.00 - 71.99: 767 71.99 - 107.99: 27 107.99 - 143.99: 2 143.99 - 179.98: 10 Dihedral angle restraints: 32270 sinusoidal: 17632 harmonic: 14638 Sorted by residual: dihedral pdb=" CD ARG E 226 " pdb=" NE ARG E 226 " pdb=" CZ ARG E 226 " pdb=" NH1 ARG E 226 " ideal model delta sinusoidal sigma weight residual 0.00 179.98 -179.98 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG K 226 " pdb=" NE ARG K 226 " pdb=" CZ ARG K 226 " pdb=" NH1 ARG K 226 " ideal model delta sinusoidal sigma weight residual 0.00 -179.96 179.96 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG G 226 " pdb=" NE ARG G 226 " pdb=" CZ ARG G 226 " pdb=" NH1 ARG G 226 " ideal model delta sinusoidal sigma weight residual 0.00 -179.93 179.93 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 32267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4155 0.061 - 0.122: 764 0.122 - 0.183: 75 0.183 - 0.244: 8 0.244 - 0.305: 6 Chirality restraints: 5008 Sorted by residual: chirality pdb=" C4' GNP A1001 " pdb=" C3' GNP A1001 " pdb=" C5' GNP A1001 " pdb=" O4' GNP A1001 " both_signs ideal model delta sigma weight residual False -2.44 -2.74 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C4' GNP G1001 " pdb=" C3' GNP G1001 " pdb=" C5' GNP G1001 " pdb=" O4' GNP G1001 " both_signs ideal model delta sigma weight residual False -2.44 -2.74 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C4' GDP F1001 " pdb=" C5' GDP F1001 " pdb=" O4' GDP F1001 " pdb=" C3' GDP F1001 " both_signs ideal model delta sigma weight residual False -2.50 -2.77 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 5005 not shown) Planarity restraints: 10012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN E 243 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C GLN E 243 " 0.042 2.00e-02 2.50e+03 pdb=" O GLN E 243 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY E 244 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN K 243 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C GLN K 243 " -0.042 2.00e-02 2.50e+03 pdb=" O GLN K 243 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY K 244 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL I 322 " 0.039 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO I 323 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO I 323 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 323 " 0.032 5.00e-02 4.00e+02 ... (remaining 10009 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 2282 2.16 - 2.77: 130403 2.77 - 3.38: 187861 3.38 - 3.99: 238313 3.99 - 4.60: 384165 Nonbonded interactions: 943024 Sorted by model distance: nonbonded pdb=" H LEU K 177 " pdb=" HA LEU K 177 " model vdw 1.544 1.816 nonbonded pdb=" H ASN A 248 " pdb=" O GLY A 251 " model vdw 1.617 1.850 nonbonded pdb=" H ASN G 248 " pdb=" O GLY G 251 " model vdw 1.617 1.850 nonbonded pdb="HH12 ARG I 246 " pdb=" O GLY N 74 " model vdw 1.624 1.850 nonbonded pdb="HE21 GLN A 231 " pdb=" O GLY B 291 " model vdw 1.627 1.850 ... (remaining 943019 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 271 or (resid 272 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ3)) or resid 273 through 383 or (resid 384 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or n \ ame NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HD2 or name HD3 or name HE2 or name HE3)) or resid 385 or (resid 386 and (na \ me N or name CA or name C or name O or name CB or name CG or name OD1 or name ND \ 2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 387 throu \ gh 403 or (resid 404 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or n \ ame HE )) or resid 405 through 406 or (resid 407 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resi \ d 408 through 453 or (resid 454 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name CE or name NZ or name H or name HA or name H \ B2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or na \ me HE3 or name HZ2)) or resid 455 through 457)) selection = (chain 'B' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 225 or (resid 226 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name N \ H2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name \ HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 227 through 271 \ or (resid 272 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3 \ )) or resid 273 through 383 or (resid 384 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD or name CE or name NZ or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3)) or resid 385 or (resid 386 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or n \ ame HB2 or name HB3 or name HD21)) or resid 387 through 403 or (resid 404 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE )) or resid 405 thro \ ugh 406 or (resid 407 and (name N or name CA or name C or name O or name CB or n \ ame CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or n \ ame HB2 or name HB3 or name HD2 or name HE1)) or resid 408 through 453 or (resid \ 454 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name CE or name NZ or name H or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ2)) or res \ id 455 through 457)) selection = (chain 'C' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 225 or (resid 226 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name N \ H2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name \ HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 227 through 271 \ or (resid 272 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3 \ )) or resid 273 through 383 or (resid 384 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD or name CE or name NZ or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3)) or resid 385 or (resid 386 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or n \ ame HB2 or name HB3 or name HD21)) or resid 387 through 403 or (resid 404 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE )) or resid 405 thro \ ugh 406 or (resid 407 and (name N or name CA or name C or name O or name CB or n \ ame CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or n \ ame HB2 or name HB3 or name HD2 or name HE1)) or resid 408 through 457)) selection = (chain 'D' and (resid 174 through 207 or (resid 208 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 209 through 225 or (resid 22 \ 6 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or \ name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 \ or name HH12)) or resid 227 through 383 or (resid 384 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name CE or name NZ or name \ H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or nam \ e HD3 or name HE2 or name HE3)) or resid 385 or (resid 386 and (name N or name C \ A or name C or name O or name CB or name CG or name OD1 or name ND2 or name H or \ name HA or name HB2 or name HB3 or name HD21)) or resid 387 through 403 or (res \ id 404 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB \ 2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE )) or r \ esid 405 through 406 or (resid 407 and (name N or name CA or name C or name O or \ name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or \ name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 408 through \ 453 or (resid 454 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ2)) or resid 455 through 457)) selection = (chain 'E' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 207 or (resid 208 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name H \ G21 or name HG22 or name HG23)) or resid 209 through 271 or (resid 272 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name CE or \ name NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) or resid 273 through \ 403 or (resid 404 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or nam \ e HE )) or resid 405 through 406 or (resid 407 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 408 through 453 or (resid 454 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name CE or name NZ or name H or name HA or name HB2 \ or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name \ HE3 or name HZ2)) or resid 455 through 457)) selection = (chain 'F' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 207 or (resid 208 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name H \ G21 or name HG22 or name HG23)) or resid 209 through 225 or (resid 226 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name NE or \ name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH \ 12)) or resid 227 through 271 or (resid 272 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name CE or name NZ or name H or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or na \ me HE2 or name HE3 or name HZ3)) or resid 273 through 383 or (resid 384 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name CE o \ r name NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 o \ r name HD2 or name HD3 or name HE2 or name HE3)) or resid 385 or (resid 386 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 387 th \ rough 403 or (resid 404 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or n \ ame HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 o \ r name HE )) or resid 405 through 406 or (resid 407 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 408 through 453 or (resid 454 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name CE or name NZ or name H or name HA or nam \ e HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or \ name HE3 or name HZ2)) or resid 455 through 457)) selection = (chain 'G' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 271 or (resid 272 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ3)) or resid 273 through 383 or (resid 384 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or n \ ame NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HD2 or name HD3 or name HE2 or name HE3)) or resid 385 or (resid 386 and (na \ me N or name CA or name C or name O or name CB or name CG or name OD1 or name ND \ 2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 387 throu \ gh 403 or (resid 404 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or n \ ame HE )) or resid 405 through 406 or (resid 407 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resi \ d 408 through 453 or (resid 454 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name CE or name NZ or name H or name HA or name H \ B2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or na \ me HE3 or name HZ2)) or resid 455 through 457)) selection = (chain 'H' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 225 or (resid 226 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name N \ H2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name \ HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 227 through 271 \ or (resid 272 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3 \ )) or resid 273 through 383 or (resid 384 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD or name CE or name NZ or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3)) or resid 385 or (resid 386 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or n \ ame HB2 or name HB3 or name HD21)) or resid 387 through 403 or (resid 404 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE )) or resid 405 thro \ ugh 406 or (resid 407 and (name N or name CA or name C or name O or name CB or n \ ame CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or n \ ame HB2 or name HB3 or name HD2 or name HE1)) or resid 408 through 453 or (resid \ 454 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name CE or name NZ or name H or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ2)) or res \ id 455 through 457)) selection = (chain 'I' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 225 or (resid 226 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name N \ H2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name \ HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 227 through 271 \ or (resid 272 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3 \ )) or resid 273 through 383 or (resid 384 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD or name CE or name NZ or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3)) or resid 385 or (resid 386 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or n \ ame HB2 or name HB3 or name HD21)) or resid 387 through 403 or (resid 404 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE )) or resid 405 thro \ ugh 406 or (resid 407 and (name N or name CA or name C or name O or name CB or n \ ame CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or n \ ame HB2 or name HB3 or name HD2 or name HE1)) or resid 408 through 457)) selection = (chain 'J' and (resid 174 through 207 or (resid 208 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 209 through 225 or (resid 22 \ 6 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or \ name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 \ or name HH12)) or resid 227 through 383 or (resid 384 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name CE or name NZ or name \ H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or nam \ e HD3 or name HE2 or name HE3)) or resid 385 or (resid 386 and (name N or name C \ A or name C or name O or name CB or name CG or name OD1 or name ND2 or name H or \ name HA or name HB2 or name HB3 or name HD21)) or resid 387 through 403 or (res \ id 404 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB \ 2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE )) or r \ esid 405 through 406 or (resid 407 and (name N or name CA or name C or name O or \ name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or \ name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 408 through \ 453 or (resid 454 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name \ HZ2)) or resid 455 through 457)) selection = (chain 'K' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 207 or (resid 208 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name H \ G21 or name HG22 or name HG23)) or resid 209 through 271 or (resid 272 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name CE or \ name NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) or resid 273 through \ 403 or (resid 404 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or nam \ e HE )) or resid 405 through 406 or (resid 407 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 408 through 453 or (resid 454 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name CE or name NZ or name H or name HA or name HB2 \ or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name \ HE3 or name HZ2)) or resid 455 through 457)) selection = (chain 'L' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 207 or (resid 208 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name H \ G21 or name HG22 or name HG23)) or resid 209 through 225 or (resid 226 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name NE or \ name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH \ 12)) or resid 227 through 271 or (resid 272 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name CE or name NZ or name H or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or na \ me HE2 or name HE3 or name HZ3)) or resid 273 through 383 or (resid 384 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name CE o \ r name NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 o \ r name HD2 or name HD3 or name HE2 or name HE3)) or resid 385 or (resid 386 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 387 th \ rough 403 or (resid 404 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or n \ ame HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 o \ r name HE )) or resid 405 through 406 or (resid 407 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 408 through 453 or (resid 454 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name CE or name NZ or name H or name HA or nam \ e HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or \ name HE3 or name HZ2)) or resid 455 through 457)) } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.740 Extract box with map and model: 5.600 Check model and map are aligned: 0.740 Set scattering table: 0.480 Process input model: 168.520 Find NCS groups from input model: 2.990 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 182.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 0.008 0.248 35024 Z= 0.545 Angle : 0.973 14.294 47382 Z= 0.481 Chirality : 0.048 0.305 5008 Planarity : 0.005 0.058 6102 Dihedral : 14.637 179.984 13368 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.59 % Allowed : 5.54 % Favored : 93.86 % 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: -0.47 (0.12), residues: 4084 helix: -0.24 (0.11), residues: 1596 sheet: 0.03 (0.21), residues: 540 loop : -0.32 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 306 HIS 0.014 0.002 HIS A 233 PHE 0.035 0.003 PHE H 209 TYR 0.029 0.003 TYR L 238 ARG 0.010 0.001 ARG N 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 1265 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1243 time to evaluate : 4.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 SER cc_start: 0.7680 (p) cc_final: 0.7386 (p) REVERT: A 312 TYR cc_start: 0.8192 (m-80) cc_final: 0.7977 (m-10) REVERT: A 387 GLU cc_start: 0.8446 (tt0) cc_final: 0.7749 (tp30) REVERT: A 438 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8024 (tp30) REVERT: B 240 ASP cc_start: 0.8550 (m-30) cc_final: 0.8076 (t0) REVERT: B 242 ILE cc_start: 0.8923 (mt) cc_final: 0.8642 (mt) REVERT: B 280 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8312 (mm-30) REVERT: B 288 LYS cc_start: 0.8659 (tttt) cc_final: 0.8426 (ttpt) REVERT: B 301 LYS cc_start: 0.9185 (mttp) cc_final: 0.8825 (mtmm) REVERT: C 186 THR cc_start: 0.8805 (m) cc_final: 0.8278 (m) REVERT: C 198 ILE cc_start: 0.9239 (mt) cc_final: 0.9031 (mt) REVERT: C 446 TYR cc_start: 0.8305 (t80) cc_final: 0.7999 (t80) REVERT: D 182 THR cc_start: 0.8936 (p) cc_final: 0.8683 (t) REVERT: D 189 LYS cc_start: 0.8872 (mttt) cc_final: 0.8221 (tptt) REVERT: D 197 ILE cc_start: 0.9350 (pt) cc_final: 0.9005 (mp) REVERT: D 299 HIS cc_start: 0.8738 (p-80) cc_final: 0.8239 (p90) REVERT: D 401 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8341 (mtmm) REVERT: D 438 GLU cc_start: 0.8653 (tt0) cc_final: 0.8402 (tm-30) REVERT: D 444 ASP cc_start: 0.6820 (t0) cc_final: 0.6175 (m-30) REVERT: E 227 VAL cc_start: 0.9379 (t) cc_final: 0.9170 (p) REVERT: E 228 ASN cc_start: 0.8597 (t0) cc_final: 0.7801 (m-40) REVERT: E 288 LYS cc_start: 0.8960 (mmtt) cc_final: 0.8690 (tptp) REVERT: E 306 TRP cc_start: 0.8466 (m100) cc_final: 0.8139 (m100) REVERT: E 320 PHE cc_start: 0.8625 (t80) cc_final: 0.7641 (t80) REVERT: E 442 PHE cc_start: 0.7873 (t80) cc_final: 0.7466 (t80) REVERT: F 252 PHE cc_start: 0.8076 (m-80) cc_final: 0.7707 (m-80) REVERT: F 360 ASP cc_start: 0.6675 (p0) cc_final: 0.5213 (t0) REVERT: F 385 MET cc_start: 0.8650 (mmm) cc_final: 0.8431 (tpp) REVERT: F 387 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7752 (tp30) REVERT: M 12 TYR cc_start: 0.8869 (t80) cc_final: 0.8296 (t80) REVERT: M 17 TYR cc_start: 0.8629 (m-80) cc_final: 0.8367 (m-10) REVERT: M 61 ASP cc_start: 0.7897 (t0) cc_final: 0.7608 (t0) REVERT: M 73 LYS cc_start: 0.9000 (ttmt) cc_final: 0.8419 (ttmm) REVERT: M 124 SER cc_start: 0.7705 (p) cc_final: 0.7112 (m) REVERT: M 129 GLU cc_start: 0.8578 (tt0) cc_final: 0.8139 (tp30) REVERT: M 140 ILE cc_start: 0.8000 (mt) cc_final: 0.7698 (mt) REVERT: M 153 LEU cc_start: 0.8548 (tp) cc_final: 0.8329 (tt) REVERT: M 170 LYS cc_start: 0.9268 (tttt) cc_final: 0.8883 (ttpt) REVERT: M 202 GLN cc_start: 0.8977 (mt0) cc_final: 0.8560 (mt0) REVERT: M 253 ILE cc_start: 0.8205 (tt) cc_final: 0.7922 (mt) REVERT: M 257 ASP cc_start: 0.7755 (m-30) cc_final: 0.7529 (m-30) REVERT: M 337 GLN cc_start: 0.8689 (tt0) cc_final: 0.8283 (tp40) REVERT: G 197 ILE cc_start: 0.8663 (tt) cc_final: 0.8403 (tp) REVERT: G 213 ARG cc_start: 0.7748 (mtt180) cc_final: 0.7522 (mmt180) REVERT: G 382 CYS cc_start: 0.7298 (m) cc_final: 0.6910 (m) REVERT: G 428 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8431 (tt) REVERT: H 236 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.8737 (m-10) REVERT: H 238 TYR cc_start: 0.8684 (t80) cc_final: 0.8405 (t80) REVERT: H 240 ASP cc_start: 0.8767 (m-30) cc_final: 0.8436 (t70) REVERT: H 280 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8244 (mm-30) REVERT: H 331 LEU cc_start: 0.9188 (mt) cc_final: 0.8841 (mp) REVERT: I 186 THR cc_start: 0.8723 (m) cc_final: 0.8451 (m) REVERT: I 200 GLN cc_start: 0.9099 (pt0) cc_final: 0.8594 (pt0) REVERT: I 231 GLN cc_start: 0.7943 (tt0) cc_final: 0.6726 (tt0) REVERT: I 277 ILE cc_start: 0.9206 (mt) cc_final: 0.8916 (mt) REVERT: J 189 LYS cc_start: 0.9075 (mttt) cc_final: 0.8575 (tptt) REVERT: J 197 ILE cc_start: 0.9160 (pt) cc_final: 0.8958 (mp) REVERT: J 274 TYR cc_start: 0.6469 (m-80) cc_final: 0.6230 (m-80) REVERT: J 440 TYR cc_start: 0.9015 (m-10) cc_final: 0.8416 (m-80) REVERT: J 444 ASP cc_start: 0.7322 (t0) cc_final: 0.7004 (m-30) REVERT: K 227 VAL cc_start: 0.9252 (t) cc_final: 0.8932 (p) REVERT: K 228 ASN cc_start: 0.8480 (t0) cc_final: 0.7931 (m-40) REVERT: K 288 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8566 (mmmt) REVERT: K 321 TYR cc_start: 0.7870 (p90) cc_final: 0.7103 (p90) REVERT: K 385 MET cc_start: 0.7568 (mmm) cc_final: 0.7345 (mmt) REVERT: K 442 PHE cc_start: 0.7843 (t80) cc_final: 0.7464 (t80) REVERT: L 333 ASN cc_start: 0.8268 (t0) cc_final: 0.7589 (t0) REVERT: L 341 VAL cc_start: 0.8685 (t) cc_final: 0.8472 (m) REVERT: L 366 ASN cc_start: 0.7401 (m-40) cc_final: 0.6932 (t0) REVERT: L 386 ASN cc_start: 0.7020 (m-40) cc_final: 0.6694 (t0) REVERT: L 446 TYR cc_start: 0.5660 (t80) cc_final: 0.5256 (t80) REVERT: N 12 TYR cc_start: 0.8878 (t80) cc_final: 0.8383 (t80) REVERT: N 17 TYR cc_start: 0.8624 (m-80) cc_final: 0.8401 (m-10) REVERT: N 61 ASP cc_start: 0.7859 (t0) cc_final: 0.7624 (t0) REVERT: N 73 LYS cc_start: 0.8957 (ttmt) cc_final: 0.8328 (ttmm) REVERT: N 116 LEU cc_start: 0.8797 (tp) cc_final: 0.8562 (tp) REVERT: N 124 SER cc_start: 0.7692 (p) cc_final: 0.7001 (m) REVERT: N 129 GLU cc_start: 0.8546 (tt0) cc_final: 0.8312 (tp30) REVERT: N 140 ILE cc_start: 0.8081 (mt) cc_final: 0.7848 (mt) REVERT: N 153 LEU cc_start: 0.8417 (tp) cc_final: 0.8183 (tt) REVERT: N 170 LYS cc_start: 0.9228 (tttt) cc_final: 0.8839 (ttmt) REVERT: N 202 GLN cc_start: 0.9026 (mt0) cc_final: 0.8618 (mt0) REVERT: N 253 ILE cc_start: 0.8405 (tt) cc_final: 0.8099 (mt) REVERT: N 257 ASP cc_start: 0.7598 (m-30) cc_final: 0.7384 (m-30) REVERT: N 337 GLN cc_start: 0.8731 (tt0) cc_final: 0.8396 (tm-30) outliers start: 22 outliers final: 7 residues processed: 1253 average time/residue: 1.0164 time to fit residues: 1984.0988 Evaluate side-chains 782 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 773 time to evaluate : 4.097 ------------------------------------------------------------------------------- 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: 3.9990 chunk 309 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 208 optimal weight: 0.6980 chunk 165 optimal weight: 7.9990 chunk 319 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 238 optimal weight: 9.9990 chunk 370 optimal weight: 0.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 ASN F 383 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 453 ASN H 228 ASN H 264 GLN J 269 GLN K 333 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35024 Z= 0.252 Angle : 0.626 12.019 47382 Z= 0.336 Chirality : 0.040 0.360 5008 Planarity : 0.005 0.104 6102 Dihedral : 10.201 179.732 4798 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.08 % Allowed : 1.97 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.12), residues: 4084 helix: 0.44 (0.12), residues: 1710 sheet: 0.18 (0.22), residues: 530 loop : -0.33 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 424 HIS 0.014 0.001 HIS H 233 PHE 0.021 0.002 PHE D 377 TYR 0.024 0.002 TYR F 344 ARG 0.011 0.001 ARG F 347 *********************** 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 904 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 901 time to evaluate : 4.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.8073 (ttp) cc_final: 0.7431 (ppp) REVERT: A 401 LYS cc_start: 0.8585 (ttmt) cc_final: 0.8350 (ttpp) REVERT: A 419 SER cc_start: 0.8434 (p) cc_final: 0.8160 (m) REVERT: A 438 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8155 (tp30) REVERT: A 439 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8491 (mt-10) REVERT: B 196 ASN cc_start: 0.8393 (m-40) cc_final: 0.7996 (m-40) REVERT: B 240 ASP cc_start: 0.8585 (m-30) cc_final: 0.8279 (t0) REVERT: B 280 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8199 (mm-30) REVERT: B 288 LYS cc_start: 0.8884 (tttt) cc_final: 0.8609 (ttpt) REVERT: B 301 LYS cc_start: 0.9161 (mttp) cc_final: 0.8920 (mtmm) REVERT: B 321 TYR cc_start: 0.8816 (p90) cc_final: 0.8400 (p90) REVERT: B 438 GLU cc_start: 0.8403 (pt0) cc_final: 0.8130 (tm-30) REVERT: C 196 ASN cc_start: 0.8285 (m-40) cc_final: 0.7688 (m-40) REVERT: D 189 LYS cc_start: 0.9012 (mttt) cc_final: 0.8494 (tptt) REVERT: D 197 ILE cc_start: 0.9308 (pt) cc_final: 0.8951 (mp) REVERT: D 390 GLN cc_start: 0.9237 (mt0) cc_final: 0.8924 (tm-30) REVERT: D 401 LYS cc_start: 0.8476 (mppt) cc_final: 0.8221 (mtmm) REVERT: D 438 GLU cc_start: 0.8834 (tt0) cc_final: 0.8284 (tm-30) REVERT: D 444 ASP cc_start: 0.6846 (t0) cc_final: 0.6084 (m-30) REVERT: E 228 ASN cc_start: 0.8612 (t0) cc_final: 0.7866 (m110) REVERT: E 263 CYS cc_start: 0.9322 (m) cc_final: 0.9056 (m) REVERT: E 267 LYS cc_start: 0.8795 (ttpt) cc_final: 0.8381 (ttmm) REVERT: E 288 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8576 (tptp) REVERT: E 306 TRP cc_start: 0.8446 (m100) cc_final: 0.8201 (m100) REVERT: E 320 PHE cc_start: 0.8580 (t80) cc_final: 0.8308 (t80) REVERT: F 288 LYS cc_start: 0.8939 (mttt) cc_final: 0.8601 (tptt) REVERT: F 387 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8058 (tp30) REVERT: M 12 TYR cc_start: 0.8965 (t80) cc_final: 0.8248 (t80) REVERT: M 40 ASP cc_start: 0.7566 (m-30) cc_final: 0.7026 (t70) REVERT: M 73 LYS cc_start: 0.9031 (ttmt) cc_final: 0.8767 (ttmm) REVERT: M 101 GLU cc_start: 0.8462 (pm20) cc_final: 0.8210 (pm20) REVERT: M 170 LYS cc_start: 0.9212 (tttt) cc_final: 0.8887 (ttpt) REVERT: M 253 ILE cc_start: 0.8392 (tt) cc_final: 0.8018 (mt) REVERT: M 337 GLN cc_start: 0.8677 (tt0) cc_final: 0.8338 (tm-30) REVERT: G 213 ARG cc_start: 0.7805 (mtt180) cc_final: 0.7561 (mmt180) REVERT: G 289 VAL cc_start: 0.8913 (t) cc_final: 0.8535 (t) REVERT: H 196 ASN cc_start: 0.8439 (m-40) cc_final: 0.8151 (m-40) REVERT: H 280 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8158 (mm-30) REVERT: H 331 LEU cc_start: 0.9216 (mt) cc_final: 0.8893 (mp) REVERT: I 200 GLN cc_start: 0.9117 (pt0) cc_final: 0.8898 (pt0) REVERT: I 277 ILE cc_start: 0.9298 (mt) cc_final: 0.9019 (mt) REVERT: I 427 GLU cc_start: 0.8196 (pp20) cc_final: 0.7991 (pp20) REVERT: J 189 LYS cc_start: 0.9260 (mttt) cc_final: 0.8668 (tptt) REVERT: J 197 ILE cc_start: 0.9209 (pt) cc_final: 0.8911 (mp) REVERT: J 405 ILE cc_start: 0.8906 (mm) cc_final: 0.8703 (mm) REVERT: J 440 TYR cc_start: 0.8991 (m-10) cc_final: 0.8445 (m-10) REVERT: K 213 ARG cc_start: 0.7923 (mmt90) cc_final: 0.7682 (ttm170) REVERT: K 228 ASN cc_start: 0.8313 (t0) cc_final: 0.7785 (m-40) REVERT: K 263 CYS cc_start: 0.9429 (m) cc_final: 0.8992 (m) REVERT: K 267 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8106 (ttmm) REVERT: K 288 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8571 (mmmt) REVERT: K 385 MET cc_start: 0.7633 (mmm) cc_final: 0.7247 (mmt) REVERT: K 442 PHE cc_start: 0.7899 (t80) cc_final: 0.7630 (t80) REVERT: L 288 LYS cc_start: 0.8945 (mttt) cc_final: 0.8404 (tptt) REVERT: L 366 ASN cc_start: 0.7648 (m-40) cc_final: 0.7257 (t0) REVERT: L 386 ASN cc_start: 0.7121 (m-40) cc_final: 0.6899 (t0) REVERT: L 439 GLU cc_start: 0.8899 (tp30) cc_final: 0.8695 (tt0) REVERT: N 12 TYR cc_start: 0.8992 (t80) cc_final: 0.8376 (t80) REVERT: N 40 ASP cc_start: 0.7630 (m-30) cc_final: 0.7098 (t70) REVERT: N 73 LYS cc_start: 0.8968 (ttmt) cc_final: 0.8718 (ttmm) REVERT: N 101 GLU cc_start: 0.8544 (pm20) cc_final: 0.8219 (pm20) REVERT: N 170 LYS cc_start: 0.9115 (tttt) cc_final: 0.8828 (ttpt) REVERT: N 253 ILE cc_start: 0.8527 (tt) cc_final: 0.8206 (mt) REVERT: N 337 GLN cc_start: 0.8672 (tt0) cc_final: 0.8314 (tm-30) REVERT: N 347 LEU cc_start: 0.7132 (tp) cc_final: 0.6873 (tt) outliers start: 3 outliers final: 1 residues processed: 903 average time/residue: 0.9665 time to fit residues: 1369.2682 Evaluate side-chains 672 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 671 time to evaluate : 4.151 ------------------------------------------------------------------------------- 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: 9.9990 chunk 114 optimal weight: 4.9990 chunk 308 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 371 optimal weight: 6.9990 chunk 400 optimal weight: 6.9990 chunk 330 optimal weight: 2.9990 chunk 368 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 297 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 GLN A 453 ASN ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 284 ASN ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 261 ASN ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN H 315 ASN ** I 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 ASN K 389 ASN L 299 HIS ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 202 GLN N 284 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 35024 Z= 0.370 Angle : 0.670 12.057 47382 Z= 0.356 Chirality : 0.041 0.366 5008 Planarity : 0.005 0.066 6102 Dihedral : 9.983 179.681 4798 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.05 % Allowed : 2.24 % Favored : 97.70 % 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: -0.47 (0.12), residues: 4084 helix: -0.04 (0.11), residues: 1766 sheet: -0.05 (0.20), residues: 612 loop : -0.52 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 424 HIS 0.007 0.002 HIS N 275 PHE 0.037 0.002 PHE D 178 TYR 0.021 0.002 TYR F 344 ARG 0.008 0.001 ARG H 253 *********************** 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 747 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 745 time to evaluate : 4.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.8133 (ttp) cc_final: 0.7278 (ppp) REVERT: A 419 SER cc_start: 0.8487 (p) cc_final: 0.8254 (m) REVERT: A 438 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8313 (tp30) REVERT: B 196 ASN cc_start: 0.8596 (m-40) cc_final: 0.8247 (m-40) REVERT: B 272 LYS cc_start: 0.7573 (mttp) cc_final: 0.7260 (mtmm) REVERT: B 301 LYS cc_start: 0.9186 (mttp) cc_final: 0.8863 (mttp) REVERT: B 321 TYR cc_start: 0.9060 (p90) cc_final: 0.8467 (p90) REVERT: B 371 LYS cc_start: 0.7764 (mttt) cc_final: 0.7538 (tptp) REVERT: B 439 GLU cc_start: 0.8236 (tp30) cc_final: 0.8031 (tp30) REVERT: C 196 ASN cc_start: 0.8548 (m-40) cc_final: 0.8105 (m-40) REVERT: D 189 LYS cc_start: 0.9102 (mttt) cc_final: 0.8600 (tptt) REVERT: D 197 ILE cc_start: 0.9444 (pt) cc_final: 0.9182 (mp) REVERT: D 390 GLN cc_start: 0.9292 (mt0) cc_final: 0.8959 (tm-30) REVERT: D 401 LYS cc_start: 0.8507 (mppt) cc_final: 0.8249 (mtmm) REVERT: D 438 GLU cc_start: 0.8949 (tt0) cc_final: 0.8379 (tm-30) REVERT: E 263 CYS cc_start: 0.9444 (m) cc_final: 0.9107 (m) REVERT: E 306 TRP cc_start: 0.8498 (m100) cc_final: 0.8245 (m100) REVERT: E 442 PHE cc_start: 0.8026 (t80) cc_final: 0.7586 (t80) REVERT: F 189 LYS cc_start: 0.8845 (mttt) cc_final: 0.8615 (mmtm) REVERT: F 288 LYS cc_start: 0.8948 (mttt) cc_final: 0.8654 (tptt) REVERT: F 347 ARG cc_start: 0.8642 (ttm110) cc_final: 0.8312 (mtp85) REVERT: M 40 ASP cc_start: 0.7684 (m-30) cc_final: 0.7313 (t70) REVERT: M 73 LYS cc_start: 0.9159 (ttmt) cc_final: 0.8457 (ttmm) REVERT: M 170 LYS cc_start: 0.9262 (tttt) cc_final: 0.8901 (ttpt) REVERT: M 253 ILE cc_start: 0.8303 (tt) cc_final: 0.7969 (mt) REVERT: M 337 GLN cc_start: 0.8781 (tt0) cc_final: 0.8442 (tm-30) REVERT: M 341 ASP cc_start: 0.8266 (t70) cc_final: 0.7919 (t70) REVERT: M 347 LEU cc_start: 0.7165 (tp) cc_final: 0.6878 (tt) REVERT: G 294 MET cc_start: 0.8682 (ptp) cc_final: 0.8423 (ptp) REVERT: G 382 CYS cc_start: 0.7192 (m) cc_final: 0.6909 (m) REVERT: H 196 ASN cc_start: 0.8602 (m-40) cc_final: 0.8254 (m-40) REVERT: H 280 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8095 (mm-30) REVERT: H 331 LEU cc_start: 0.9210 (mt) cc_final: 0.8697 (mp) REVERT: H 390 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8520 (tm-30) REVERT: I 196 ASN cc_start: 0.8516 (m-40) cc_final: 0.8307 (m-40) REVERT: I 239 GLU cc_start: 0.9335 (mp0) cc_final: 0.8956 (mp0) REVERT: I 329 ILE cc_start: 0.9361 (mt) cc_final: 0.8876 (tt) REVERT: J 189 LYS cc_start: 0.9296 (mttt) cc_final: 0.8613 (tppt) REVERT: J 274 TYR cc_start: 0.7119 (m-80) cc_final: 0.6870 (m-80) REVERT: J 440 TYR cc_start: 0.9086 (m-10) cc_final: 0.8648 (m-10) REVERT: K 213 ARG cc_start: 0.7972 (mmt90) cc_final: 0.7751 (ttm170) REVERT: K 263 CYS cc_start: 0.9439 (m) cc_final: 0.9070 (m) REVERT: K 288 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8619 (mmmt) REVERT: K 332 MET cc_start: 0.9350 (ttm) cc_final: 0.9055 (ttp) REVERT: K 385 MET cc_start: 0.7610 (mmm) cc_final: 0.7161 (mmt) REVERT: L 288 LYS cc_start: 0.8988 (mttt) cc_final: 0.8573 (tptt) REVERT: L 366 ASN cc_start: 0.7739 (m-40) cc_final: 0.7391 (t0) REVERT: L 386 ASN cc_start: 0.6893 (m-40) cc_final: 0.6562 (t0) REVERT: N 40 ASP cc_start: 0.7916 (m-30) cc_final: 0.7548 (t70) REVERT: N 73 LYS cc_start: 0.9143 (ttmt) cc_final: 0.8431 (ttmm) REVERT: N 170 LYS cc_start: 0.9237 (tttt) cc_final: 0.8902 (ttpt) REVERT: N 253 ILE cc_start: 0.8343 (tt) cc_final: 0.8005 (mt) REVERT: N 337 GLN cc_start: 0.8751 (tt0) cc_final: 0.8402 (tm-30) REVERT: N 347 LEU cc_start: 0.7128 (tp) cc_final: 0.6911 (tt) outliers start: 2 outliers final: 0 residues processed: 747 average time/residue: 0.9407 time to fit residues: 1111.8595 Evaluate side-chains 594 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 594 time to evaluate : 4.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 9.9990 chunk 279 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 249 optimal weight: 8.9990 chunk 372 optimal weight: 4.9990 chunk 394 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 353 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 GLN A 453 ASN ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 202 GLN G 200 GLN H 315 ASN K 333 ASN N 3 GLN N 148 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 35024 Z= 0.288 Angle : 0.589 12.117 47382 Z= 0.313 Chirality : 0.040 0.360 5008 Planarity : 0.005 0.074 6102 Dihedral : 9.591 179.750 4798 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.08 % Allowed : 2.11 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.13), residues: 4084 helix: 0.16 (0.12), residues: 1732 sheet: -0.12 (0.20), residues: 630 loop : -0.49 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 424 HIS 0.007 0.001 HIS L 407 PHE 0.020 0.002 PHE G 410 TYR 0.043 0.002 TYR A 236 ARG 0.016 0.001 ARG G 404 *********************** 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 739 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 736 time to evaluate : 4.172 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: A 419 SER cc_start: 0.8512 (p) cc_final: 0.8252 (m) REVERT: A 421 ASP cc_start: 0.8350 (p0) cc_final: 0.8105 (p0) REVERT: A 438 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8441 (tp30) REVERT: A 449 GLN cc_start: 0.8528 (tp40) cc_final: 0.8321 (tp40) REVERT: B 196 ASN cc_start: 0.8647 (m-40) cc_final: 0.8269 (m-40) REVERT: B 239 GLU cc_start: 0.9136 (mp0) cc_final: 0.8851 (mp0) REVERT: B 263 CYS cc_start: 0.8381 (m) cc_final: 0.8097 (m) REVERT: B 272 LYS cc_start: 0.7612 (mttp) cc_final: 0.7377 (mtmm) REVERT: B 276 PHE cc_start: 0.7894 (t80) cc_final: 0.7363 (t80) REVERT: B 321 TYR cc_start: 0.9123 (p90) cc_final: 0.8440 (p90) REVERT: B 339 LEU cc_start: 0.9182 (mt) cc_final: 0.8802 (mt) REVERT: B 439 GLU cc_start: 0.8204 (tp30) cc_final: 0.7935 (tp30) REVERT: D 189 LYS cc_start: 0.9134 (mttt) cc_final: 0.8613 (tptt) REVERT: D 197 ILE cc_start: 0.9498 (pt) cc_final: 0.9220 (mp) REVERT: D 390 GLN cc_start: 0.9281 (mt0) cc_final: 0.8921 (tm-30) REVERT: D 401 LYS cc_start: 0.8477 (mppt) cc_final: 0.8169 (mtmm) REVERT: D 438 GLU cc_start: 0.9029 (tt0) cc_final: 0.8300 (tm-30) REVERT: E 263 CYS cc_start: 0.9452 (m) cc_final: 0.8914 (t) REVERT: E 306 TRP cc_start: 0.8554 (m100) cc_final: 0.8191 (m100) REVERT: E 332 MET cc_start: 0.9245 (ttm) cc_final: 0.8990 (ttp) REVERT: F 288 LYS cc_start: 0.8923 (mttt) cc_final: 0.8626 (tptt) REVERT: F 321 TYR cc_start: 0.9053 (p90) cc_final: 0.8709 (p90) REVERT: F 347 ARG cc_start: 0.8571 (ttm110) cc_final: 0.8279 (mtp85) REVERT: M 40 ASP cc_start: 0.7708 (m-30) cc_final: 0.7360 (t70) REVERT: M 73 LYS cc_start: 0.9238 (ttmt) cc_final: 0.8330 (ttmm) REVERT: M 124 SER cc_start: 0.8352 (m) cc_final: 0.7488 (m) REVERT: M 160 ARG cc_start: 0.8464 (ttm170) cc_final: 0.8105 (tmt170) REVERT: M 170 LYS cc_start: 0.9258 (tttt) cc_final: 0.8862 (ttpt) REVERT: M 189 ASP cc_start: 0.7257 (t0) cc_final: 0.7041 (t0) REVERT: M 194 GLU cc_start: 0.8615 (pp20) cc_final: 0.8243 (pp20) REVERT: M 207 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8561 (mm-30) REVERT: M 253 ILE cc_start: 0.8221 (tt) cc_final: 0.7866 (mt) REVERT: M 337 GLN cc_start: 0.8759 (tt0) cc_final: 0.8426 (tm-30) REVERT: M 341 ASP cc_start: 0.8244 (t70) cc_final: 0.7989 (t70) REVERT: M 347 LEU cc_start: 0.7143 (tp) cc_final: 0.6824 (tt) REVERT: G 197 ILE cc_start: 0.8888 (tp) cc_final: 0.8679 (tp) REVERT: G 382 CYS cc_start: 0.7379 (m) cc_final: 0.7097 (m) REVERT: H 196 ASN cc_start: 0.8621 (m-40) cc_final: 0.8209 (m-40) REVERT: H 280 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8084 (mm-30) REVERT: H 331 LEU cc_start: 0.9215 (mt) cc_final: 0.8962 (mp) REVERT: H 390 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8507 (tm-30) REVERT: J 189 LYS cc_start: 0.9328 (mttt) cc_final: 0.8717 (tppt) REVERT: J 440 TYR cc_start: 0.9152 (m-10) cc_final: 0.8797 (m-10) REVERT: K 213 ARG cc_start: 0.7988 (mmt90) cc_final: 0.7587 (ttm170) REVERT: K 263 CYS cc_start: 0.9497 (m) cc_final: 0.9035 (m) REVERT: K 267 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8207 (tppp) REVERT: K 288 LYS cc_start: 0.8880 (mmtt) cc_final: 0.8615 (mmmt) REVERT: K 317 GLU cc_start: 0.7749 (tp30) cc_final: 0.7548 (tp30) REVERT: K 327 TYR cc_start: 0.8890 (m-80) cc_final: 0.8513 (m-80) REVERT: K 332 MET cc_start: 0.9433 (ttm) cc_final: 0.8977 (ttp) REVERT: K 385 MET cc_start: 0.7442 (mmm) cc_final: 0.7057 (mmt) REVERT: L 288 LYS cc_start: 0.8949 (mttt) cc_final: 0.8610 (tptt) REVERT: L 366 ASN cc_start: 0.7874 (m-40) cc_final: 0.7644 (t0) REVERT: L 386 ASN cc_start: 0.6720 (m-40) cc_final: 0.6443 (t0) REVERT: N 40 ASP cc_start: 0.7749 (m-30) cc_final: 0.7372 (t70) REVERT: N 73 LYS cc_start: 0.9172 (ttmt) cc_final: 0.8510 (ttmm) REVERT: N 170 LYS cc_start: 0.9213 (tttt) cc_final: 0.8878 (ttpt) REVERT: N 253 ILE cc_start: 0.8255 (tt) cc_final: 0.7925 (mt) REVERT: N 302 ILE cc_start: 0.9300 (tt) cc_final: 0.8970 (tp) REVERT: N 337 GLN cc_start: 0.8775 (tt0) cc_final: 0.8411 (tm-30) REVERT: N 347 LEU cc_start: 0.7121 (tp) cc_final: 0.6890 (tt) outliers start: 3 outliers final: 0 residues processed: 739 average time/residue: 0.9338 time to fit residues: 1087.4440 Evaluate side-chains 577 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 577 time to evaluate : 4.112 ------------------------------------------------------------------------------- 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: 4.9990 chunk 5 optimal weight: 0.0870 chunk 293 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 336 optimal weight: 5.9990 chunk 272 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 chunk 353 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 261 ASN ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN H 231 GLN H 315 ASN K 333 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 35024 Z= 0.325 Angle : 0.610 12.170 47382 Z= 0.322 Chirality : 0.040 0.359 5008 Planarity : 0.005 0.072 6102 Dihedral : 9.500 179.442 4798 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.05 % Allowed : 1.57 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.13), residues: 4084 helix: 0.02 (0.12), residues: 1750 sheet: -0.30 (0.19), residues: 672 loop : -0.56 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 332 HIS 0.011 0.002 HIS F 407 PHE 0.019 0.002 PHE G 410 TYR 0.029 0.002 TYR H 440 ARG 0.006 0.001 ARG C 337 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8168 Ramachandran restraints generated. 4084 Oldfield, 0 Emsley, 4084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue LYS 384 is missing expected H atoms. Skipping. Evaluate side-chains 682 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 680 time to evaluate : 4.161 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: A 419 SER cc_start: 0.8478 (p) cc_final: 0.8224 (m) REVERT: A 421 ASP cc_start: 0.8289 (p0) cc_final: 0.8072 (p0) REVERT: A 438 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8422 (tp30) REVERT: B 196 ASN cc_start: 0.8655 (m-40) cc_final: 0.8310 (m-40) REVERT: B 239 GLU cc_start: 0.9127 (mp0) cc_final: 0.8834 (mp0) REVERT: B 272 LYS cc_start: 0.7690 (mttp) cc_final: 0.7466 (mtmm) REVERT: B 394 LYS cc_start: 0.8773 (ptmt) cc_final: 0.8569 (ptmm) REVERT: C 196 ASN cc_start: 0.8572 (m-40) cc_final: 0.7701 (m-40) REVERT: D 189 LYS cc_start: 0.9147 (mttt) cc_final: 0.8561 (tptt) REVERT: D 197 ILE cc_start: 0.9525 (pt) cc_final: 0.9280 (mp) REVERT: D 390 GLN cc_start: 0.9250 (mt0) cc_final: 0.8902 (tm-30) REVERT: D 401 LYS cc_start: 0.8526 (mppt) cc_final: 0.8201 (mtmm) REVERT: D 438 GLU cc_start: 0.9054 (tt0) cc_final: 0.8286 (tm-30) REVERT: E 263 CYS cc_start: 0.9475 (m) cc_final: 0.8984 (t) REVERT: E 306 TRP cc_start: 0.8678 (m100) cc_final: 0.8288 (m100) REVERT: E 332 MET cc_start: 0.9318 (ttm) cc_final: 0.9036 (ttp) REVERT: F 288 LYS cc_start: 0.8854 (mttt) cc_final: 0.8614 (tptt) REVERT: F 321 TYR cc_start: 0.9104 (p90) cc_final: 0.8780 (p90) REVERT: M 73 LYS cc_start: 0.8843 (ttmt) cc_final: 0.8431 (ttmm) REVERT: M 124 SER cc_start: 0.8274 (m) cc_final: 0.7361 (m) REVERT: M 128 ASP cc_start: 0.8255 (m-30) cc_final: 0.8054 (m-30) REVERT: M 160 ARG cc_start: 0.8588 (ttm170) cc_final: 0.8145 (tmt170) REVERT: M 170 LYS cc_start: 0.9310 (tttt) cc_final: 0.8912 (ttpt) REVERT: M 189 ASP cc_start: 0.7349 (t0) cc_final: 0.7119 (t0) REVERT: M 194 GLU cc_start: 0.8686 (pp20) cc_final: 0.8464 (pp20) REVERT: M 253 ILE cc_start: 0.8206 (tt) cc_final: 0.7886 (mt) REVERT: M 337 GLN cc_start: 0.8810 (tt0) cc_final: 0.8442 (tm-30) REVERT: M 341 ASP cc_start: 0.8197 (t70) cc_final: 0.7950 (t70) REVERT: G 294 MET cc_start: 0.8587 (ptp) cc_final: 0.8326 (ptp) REVERT: G 382 CYS cc_start: 0.7710 (m) cc_final: 0.7416 (m) REVERT: G 432 ASP cc_start: 0.7436 (m-30) cc_final: 0.7187 (m-30) REVERT: H 196 ASN cc_start: 0.8673 (m-40) cc_final: 0.8247 (m-40) REVERT: H 280 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8033 (mm-30) REVERT: H 294 MET cc_start: 0.8130 (ttm) cc_final: 0.7785 (ttm) REVERT: H 331 LEU cc_start: 0.9218 (mt) cc_final: 0.8959 (mp) REVERT: H 339 LEU cc_start: 0.9349 (mt) cc_final: 0.9006 (mt) REVERT: H 440 TYR cc_start: 0.8487 (m-80) cc_final: 0.7816 (m-80) REVERT: I 196 ASN cc_start: 0.8682 (m-40) cc_final: 0.8480 (m-40) REVERT: I 239 GLU cc_start: 0.9380 (mp0) cc_final: 0.8998 (mp0) REVERT: J 189 LYS cc_start: 0.9333 (mttt) cc_final: 0.8918 (tptt) REVERT: J 440 TYR cc_start: 0.9152 (m-10) cc_final: 0.8798 (m-10) REVERT: K 263 CYS cc_start: 0.9523 (m) cc_final: 0.9107 (m) REVERT: K 267 LYS cc_start: 0.8901 (ttpt) cc_final: 0.8314 (tppp) REVERT: K 288 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8669 (mmmt) REVERT: K 327 TYR cc_start: 0.8877 (m-80) cc_final: 0.8391 (m-80) REVERT: K 332 MET cc_start: 0.9356 (ttm) cc_final: 0.8877 (ttp) REVERT: K 385 MET cc_start: 0.7452 (mmm) cc_final: 0.7001 (mmt) REVERT: L 229 MET cc_start: 0.7597 (tmm) cc_final: 0.7157 (tmm) REVERT: L 288 LYS cc_start: 0.8992 (mttt) cc_final: 0.8650 (tptt) REVERT: L 366 ASN cc_start: 0.7962 (m-40) cc_final: 0.7748 (t0) REVERT: L 386 ASN cc_start: 0.6834 (m-40) cc_final: 0.6593 (t0) REVERT: N 40 ASP cc_start: 0.7851 (m-30) cc_final: 0.7481 (t70) REVERT: N 73 LYS cc_start: 0.9205 (ttmt) cc_final: 0.8272 (ttmm) REVERT: N 160 ARG cc_start: 0.8544 (ttm170) cc_final: 0.8061 (tmt170) REVERT: N 170 LYS cc_start: 0.9249 (tttt) cc_final: 0.8895 (ttpt) REVERT: N 194 GLU cc_start: 0.8657 (pp20) cc_final: 0.8436 (pp20) REVERT: N 253 ILE cc_start: 0.8185 (tt) cc_final: 0.7881 (mt) REVERT: N 337 GLN cc_start: 0.8776 (tt0) cc_final: 0.8440 (tm-30) outliers start: 2 outliers final: 1 residues processed: 682 average time/residue: 0.9118 time to fit residues: 987.1427 Evaluate side-chains 545 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 544 time to evaluate : 4.093 ------------------------------------------------------------------------------- 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: 8.9990 chunk 355 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 394 optimal weight: 4.9990 chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN H 315 ASN K 333 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 35024 Z= 0.202 Angle : 0.536 12.204 47382 Z= 0.279 Chirality : 0.039 0.355 5008 Planarity : 0.004 0.050 6102 Dihedral : 9.044 179.972 4798 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.05 % Allowed : 0.84 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.13), residues: 4084 helix: 0.36 (0.12), residues: 1728 sheet: -0.03 (0.20), residues: 626 loop : -0.50 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 451 HIS 0.008 0.001 HIS F 407 PHE 0.020 0.001 PHE C 178 TYR 0.032 0.001 TYR G 236 ARG 0.004 0.000 ARG G 348 *********************** 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 703 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 701 time to evaluate : 4.189 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: A 419 SER cc_start: 0.8441 (p) cc_final: 0.8201 (m) REVERT: A 421 ASP cc_start: 0.8283 (p0) cc_final: 0.7917 (p0) REVERT: A 438 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8417 (tp30) REVERT: A 449 GLN cc_start: 0.8480 (tp40) cc_final: 0.8244 (tp40) REVERT: B 196 ASN cc_start: 0.8595 (m-40) cc_final: 0.7906 (m-40) REVERT: B 239 GLU cc_start: 0.9078 (mp0) cc_final: 0.8613 (mp0) REVERT: B 321 TYR cc_start: 0.9185 (p90) cc_final: 0.8723 (p90) REVERT: B 394 LYS cc_start: 0.8790 (ptmt) cc_final: 0.8576 (ptmm) REVERT: C 178 PHE cc_start: 0.7709 (m-80) cc_final: 0.7492 (m-10) REVERT: C 196 ASN cc_start: 0.8518 (m-40) cc_final: 0.8199 (m-40) REVERT: C 395 GLU cc_start: 0.8424 (pt0) cc_final: 0.7960 (pm20) REVERT: D 189 LYS cc_start: 0.9134 (mttt) cc_final: 0.8614 (tptt) REVERT: D 197 ILE cc_start: 0.9511 (pt) cc_final: 0.9268 (mp) REVERT: D 390 GLN cc_start: 0.9260 (mt0) cc_final: 0.8906 (tm-30) REVERT: D 401 LYS cc_start: 0.8586 (mppt) cc_final: 0.8307 (mtmm) REVERT: D 438 GLU cc_start: 0.9068 (tt0) cc_final: 0.8320 (tm-30) REVERT: E 263 CYS cc_start: 0.9470 (m) cc_final: 0.9109 (m) REVERT: E 306 TRP cc_start: 0.8566 (m100) cc_final: 0.8170 (m100) REVERT: E 332 MET cc_start: 0.9313 (ttm) cc_final: 0.9042 (ttp) REVERT: F 288 LYS cc_start: 0.8862 (mttt) cc_final: 0.8608 (tptt) REVERT: F 321 TYR cc_start: 0.9089 (p90) cc_final: 0.8770 (p90) REVERT: M 73 LYS cc_start: 0.8822 (ttmt) cc_final: 0.8405 (ttmm) REVERT: M 124 SER cc_start: 0.8336 (m) cc_final: 0.7347 (m) REVERT: M 160 ARG cc_start: 0.8535 (ttm170) cc_final: 0.8190 (tmt170) REVERT: M 170 LYS cc_start: 0.9254 (tttt) cc_final: 0.8878 (ttpt) REVERT: M 189 ASP cc_start: 0.7319 (t0) cc_final: 0.7074 (t0) REVERT: M 194 GLU cc_start: 0.8716 (pp20) cc_final: 0.8365 (pp20) REVERT: M 213 LEU cc_start: 0.9094 (mt) cc_final: 0.8842 (mp) REVERT: M 253 ILE cc_start: 0.8150 (tt) cc_final: 0.7841 (mt) REVERT: M 337 GLN cc_start: 0.8791 (tt0) cc_final: 0.8385 (tm-30) REVERT: M 341 ASP cc_start: 0.8198 (t70) cc_final: 0.7942 (t70) REVERT: G 432 ASP cc_start: 0.7457 (m-30) cc_final: 0.7181 (m-30) REVERT: H 196 ASN cc_start: 0.8629 (m-40) cc_final: 0.8211 (m-40) REVERT: H 280 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8084 (mm-30) REVERT: H 294 MET cc_start: 0.8107 (ttm) cc_final: 0.7769 (ttm) REVERT: I 196 ASN cc_start: 0.8663 (m-40) cc_final: 0.8462 (m-40) REVERT: I 239 GLU cc_start: 0.9347 (mp0) cc_final: 0.8960 (mp0) REVERT: J 189 LYS cc_start: 0.9334 (mttt) cc_final: 0.8906 (tptt) REVERT: J 440 TYR cc_start: 0.9146 (m-10) cc_final: 0.8834 (m-10) REVERT: K 200 GLN cc_start: 0.9109 (pt0) cc_final: 0.8800 (pm20) REVERT: K 263 CYS cc_start: 0.9530 (m) cc_final: 0.9001 (m) REVERT: K 267 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8323 (tppp) REVERT: K 288 LYS cc_start: 0.8909 (mmtt) cc_final: 0.8658 (mmmt) REVERT: K 327 TYR cc_start: 0.8857 (m-80) cc_final: 0.8434 (m-80) REVERT: K 332 MET cc_start: 0.9355 (ttm) cc_final: 0.8947 (ttp) REVERT: K 385 MET cc_start: 0.7435 (mmm) cc_final: 0.7016 (mmt) REVERT: L 198 ILE cc_start: 0.8686 (mt) cc_final: 0.8301 (tp) REVERT: L 229 MET cc_start: 0.7556 (tmm) cc_final: 0.7145 (tmm) REVERT: L 288 LYS cc_start: 0.8974 (mttt) cc_final: 0.8672 (tptt) REVERT: N 40 ASP cc_start: 0.7725 (m-30) cc_final: 0.7339 (t70) REVERT: N 73 LYS cc_start: 0.8763 (ttmt) cc_final: 0.8296 (ttmm) REVERT: N 160 ARG cc_start: 0.8521 (ttm170) cc_final: 0.8071 (tmt170) REVERT: N 170 LYS cc_start: 0.9212 (tttt) cc_final: 0.8848 (ttpt) REVERT: N 189 ASP cc_start: 0.7351 (t0) cc_final: 0.7119 (t0) REVERT: N 194 GLU cc_start: 0.8694 (pp20) cc_final: 0.8400 (pp20) REVERT: N 253 ILE cc_start: 0.8154 (tt) cc_final: 0.7891 (mt) REVERT: N 337 GLN cc_start: 0.8742 (tt0) cc_final: 0.8406 (tm-30) REVERT: N 347 LEU cc_start: 0.6991 (tp) cc_final: 0.6527 (tt) outliers start: 2 outliers final: 0 residues processed: 703 average time/residue: 0.8917 time to fit residues: 999.5034 Evaluate side-chains 563 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 563 time to evaluate : 4.099 ------------------------------------------------------------------------------- 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: 5.9990 chunk 44 optimal weight: 4.9990 chunk 224 optimal weight: 0.9990 chunk 288 optimal weight: 5.9990 chunk 223 optimal weight: 0.9990 chunk 332 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 393 optimal weight: 6.9990 chunk 246 optimal weight: 10.0000 chunk 239 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN H 315 ASN K 333 ASN N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.6203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35024 Z= 0.208 Angle : 0.535 12.211 47382 Z= 0.277 Chirality : 0.039 0.355 5008 Planarity : 0.004 0.054 6102 Dihedral : 8.775 179.841 4798 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.08 % Allowed : 0.95 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.13), residues: 4084 helix: 0.47 (0.12), residues: 1744 sheet: 0.04 (0.20), residues: 626 loop : -0.43 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 451 HIS 0.011 0.001 HIS E 407 PHE 0.021 0.001 PHE J 352 TYR 0.031 0.001 TYR G 236 ARG 0.006 0.000 ARG F 404 *********************** 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 690 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 687 time to evaluate : 4.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 SER cc_start: 0.8407 (p) cc_final: 0.8181 (m) REVERT: A 421 ASP cc_start: 0.8336 (p0) cc_final: 0.7922 (p0) REVERT: A 438 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8464 (tp30) REVERT: A 449 GLN cc_start: 0.8458 (tp40) cc_final: 0.8180 (tp40) REVERT: B 196 ASN cc_start: 0.8636 (m-40) cc_final: 0.8304 (m-40) REVERT: B 321 TYR cc_start: 0.9223 (p90) cc_final: 0.8822 (p90) REVERT: B 394 LYS cc_start: 0.8865 (ptmt) cc_final: 0.8619 (ptmm) REVERT: D 189 LYS cc_start: 0.9141 (mttt) cc_final: 0.8549 (tptt) REVERT: D 390 GLN cc_start: 0.9281 (mt0) cc_final: 0.8782 (tm-30) REVERT: D 401 LYS cc_start: 0.8618 (mppt) cc_final: 0.8347 (mtmm) REVERT: D 438 GLU cc_start: 0.9070 (tt0) cc_final: 0.8356 (tm-30) REVERT: E 263 CYS cc_start: 0.9470 (m) cc_final: 0.9050 (m) REVERT: E 306 TRP cc_start: 0.8563 (m100) cc_final: 0.8182 (m100) REVERT: E 332 MET cc_start: 0.9277 (ttm) cc_final: 0.9030 (ttp) REVERT: E 442 PHE cc_start: 0.8057 (t80) cc_final: 0.7700 (t80) REVERT: F 288 LYS cc_start: 0.8940 (mttt) cc_final: 0.8585 (tptt) REVERT: F 321 TYR cc_start: 0.9083 (p90) cc_final: 0.8773 (p90) REVERT: M 73 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8425 (ttmm) REVERT: M 124 SER cc_start: 0.8401 (m) cc_final: 0.7483 (m) REVERT: M 160 ARG cc_start: 0.8596 (ttm170) cc_final: 0.8242 (tmt170) REVERT: M 170 LYS cc_start: 0.9259 (tttt) cc_final: 0.8910 (ttpt) REVERT: M 189 ASP cc_start: 0.7329 (t0) cc_final: 0.7067 (t0) REVERT: M 194 GLU cc_start: 0.8707 (pp20) cc_final: 0.8362 (pp20) REVERT: M 213 LEU cc_start: 0.9095 (mt) cc_final: 0.8840 (mp) REVERT: M 253 ILE cc_start: 0.8151 (tt) cc_final: 0.7851 (mt) REVERT: M 337 GLN cc_start: 0.8778 (tt0) cc_final: 0.8394 (tm-30) REVERT: M 341 ASP cc_start: 0.8193 (t70) cc_final: 0.7941 (t70) REVERT: G 197 ILE cc_start: 0.8720 (tp) cc_final: 0.8497 (tp) REVERT: G 432 ASP cc_start: 0.7531 (m-30) cc_final: 0.7284 (m-30) REVERT: H 196 ASN cc_start: 0.8618 (m-40) cc_final: 0.8214 (m-40) REVERT: H 239 GLU cc_start: 0.8793 (mp0) cc_final: 0.8552 (mp0) REVERT: H 280 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8118 (mm-30) REVERT: H 294 MET cc_start: 0.8113 (ttm) cc_final: 0.7667 (ttm) REVERT: H 339 LEU cc_start: 0.9397 (mt) cc_final: 0.9080 (mt) REVERT: H 448 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7677 (tm-30) REVERT: I 239 GLU cc_start: 0.9344 (mp0) cc_final: 0.8951 (mp0) REVERT: I 281 ILE cc_start: 0.9460 (tt) cc_final: 0.9154 (tp) REVERT: I 320 PHE cc_start: 0.8561 (t80) cc_final: 0.8356 (t80) REVERT: J 189 LYS cc_start: 0.9326 (mttt) cc_final: 0.8926 (tptt) REVERT: J 440 TYR cc_start: 0.9149 (m-10) cc_final: 0.8830 (m-10) REVERT: K 263 CYS cc_start: 0.9508 (m) cc_final: 0.8992 (t) REVERT: K 267 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8387 (tppp) REVERT: K 288 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8653 (mmmt) REVERT: K 317 GLU cc_start: 0.8369 (tp30) cc_final: 0.8047 (tp30) REVERT: K 332 MET cc_start: 0.9313 (ttm) cc_final: 0.8962 (ttp) REVERT: K 352 PHE cc_start: 0.7769 (m-80) cc_final: 0.7454 (m-80) REVERT: K 379 GLU cc_start: 0.8056 (tp30) cc_final: 0.7836 (mm-30) REVERT: K 385 MET cc_start: 0.7400 (mmm) cc_final: 0.6951 (mmt) REVERT: K 427 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7998 (tm-30) REVERT: L 198 ILE cc_start: 0.8711 (mt) cc_final: 0.8279 (tp) REVERT: L 229 MET cc_start: 0.7503 (tmm) cc_final: 0.7112 (tmm) REVERT: L 288 LYS cc_start: 0.8988 (mttt) cc_final: 0.8727 (tptt) REVERT: N 40 ASP cc_start: 0.7783 (m-30) cc_final: 0.7368 (t70) REVERT: N 73 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8346 (ttmm) REVERT: N 160 ARG cc_start: 0.8558 (ttm170) cc_final: 0.7861 (tmm160) REVERT: N 170 LYS cc_start: 0.9224 (tttt) cc_final: 0.8890 (ttpt) REVERT: N 194 GLU cc_start: 0.8687 (pp20) cc_final: 0.8311 (pp20) REVERT: N 201 TYR cc_start: 0.9061 (t80) cc_final: 0.8840 (t80) REVERT: N 211 ARG cc_start: 0.7427 (mmm160) cc_final: 0.6676 (mmm-85) REVERT: N 253 ILE cc_start: 0.8212 (tt) cc_final: 0.7927 (mt) REVERT: N 337 GLN cc_start: 0.8760 (tt0) cc_final: 0.8414 (tm-30) outliers start: 3 outliers final: 1 residues processed: 690 average time/residue: 0.8973 time to fit residues: 989.1911 Evaluate side-chains 555 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 554 time to evaluate : 4.117 ------------------------------------------------------------------------------- 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: 0.7980 chunk 157 optimal weight: 9.9990 chunk 234 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 250 optimal weight: 9.9990 chunk 267 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 309 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 315 ASN K 333 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.6369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35024 Z= 0.180 Angle : 0.517 12.214 47382 Z= 0.266 Chirality : 0.039 0.355 5008 Planarity : 0.004 0.049 6102 Dihedral : 8.596 179.855 4798 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.05 % Allowed : 0.41 % Favored : 99.54 % 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: 0.23 (0.13), residues: 4084 helix: 0.72 (0.12), residues: 1740 sheet: 0.10 (0.21), residues: 626 loop : -0.28 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 424 HIS 0.011 0.001 HIS E 407 PHE 0.020 0.001 PHE G 178 TYR 0.028 0.001 TYR G 236 ARG 0.006 0.000 ARG F 404 *********************** 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 694 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 692 time to evaluate : 4.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 SER cc_start: 0.8369 (p) cc_final: 0.8146 (m) REVERT: A 421 ASP cc_start: 0.8350 (p0) cc_final: 0.7940 (p0) REVERT: A 438 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8453 (tp30) REVERT: A 449 GLN cc_start: 0.8440 (tp40) cc_final: 0.8125 (tp40) REVERT: B 196 ASN cc_start: 0.8604 (m-40) cc_final: 0.8267 (m-40) REVERT: B 321 TYR cc_start: 0.9176 (p90) cc_final: 0.8887 (p90) REVERT: B 394 LYS cc_start: 0.8875 (ptmt) cc_final: 0.8607 (ptmm) REVERT: C 178 PHE cc_start: 0.7701 (m-80) cc_final: 0.7330 (m-10) REVERT: D 189 LYS cc_start: 0.9133 (mttt) cc_final: 0.8550 (tptt) REVERT: D 390 GLN cc_start: 0.9272 (mt0) cc_final: 0.8780 (tm-30) REVERT: D 401 LYS cc_start: 0.8601 (mppt) cc_final: 0.8344 (mtmm) REVERT: D 438 GLU cc_start: 0.9029 (tt0) cc_final: 0.8341 (tm-30) REVERT: E 263 CYS cc_start: 0.9341 (m) cc_final: 0.8954 (m) REVERT: E 306 TRP cc_start: 0.8578 (m100) cc_final: 0.8216 (m100) REVERT: E 332 MET cc_start: 0.9260 (ttm) cc_final: 0.9010 (ttp) REVERT: E 442 PHE cc_start: 0.8018 (t80) cc_final: 0.7693 (t80) REVERT: F 288 LYS cc_start: 0.8881 (mttt) cc_final: 0.8555 (tptt) REVERT: F 321 TYR cc_start: 0.9086 (p90) cc_final: 0.8785 (p90) REVERT: M 40 ASP cc_start: 0.7487 (m-30) cc_final: 0.7077 (t70) REVERT: M 73 LYS cc_start: 0.8810 (ttmt) cc_final: 0.8407 (ttmm) REVERT: M 124 SER cc_start: 0.8423 (m) cc_final: 0.7478 (m) REVERT: M 170 LYS cc_start: 0.9240 (tttt) cc_final: 0.8881 (ttpt) REVERT: M 189 ASP cc_start: 0.7329 (t0) cc_final: 0.7068 (t0) REVERT: M 194 GLU cc_start: 0.8734 (pp20) cc_final: 0.8364 (pp20) REVERT: M 213 LEU cc_start: 0.9060 (mt) cc_final: 0.8798 (mp) REVERT: M 253 ILE cc_start: 0.8138 (tt) cc_final: 0.7825 (mt) REVERT: M 337 GLN cc_start: 0.8805 (tt0) cc_final: 0.8424 (tm-30) REVERT: M 341 ASP cc_start: 0.8157 (t70) cc_final: 0.7919 (t70) REVERT: G 432 ASP cc_start: 0.7537 (m-30) cc_final: 0.7285 (m-30) REVERT: H 196 ASN cc_start: 0.8606 (m-40) cc_final: 0.8200 (m-40) REVERT: H 280 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8041 (mm-30) REVERT: H 294 MET cc_start: 0.8118 (ttm) cc_final: 0.7797 (ttm) REVERT: H 339 LEU cc_start: 0.9417 (mt) cc_final: 0.9111 (mt) REVERT: H 448 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7599 (tm-30) REVERT: I 196 ASN cc_start: 0.8695 (m-40) cc_final: 0.8464 (m-40) REVERT: I 239 GLU cc_start: 0.9348 (mp0) cc_final: 0.8932 (mp0) REVERT: I 320 PHE cc_start: 0.8545 (t80) cc_final: 0.8316 (t80) REVERT: J 189 LYS cc_start: 0.9318 (mttt) cc_final: 0.8909 (tptt) REVERT: J 299 HIS cc_start: 0.8793 (p90) cc_final: 0.8562 (p90) REVERT: J 440 TYR cc_start: 0.9162 (m-10) cc_final: 0.8869 (m-10) REVERT: K 263 CYS cc_start: 0.9466 (m) cc_final: 0.8937 (t) REVERT: K 288 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8669 (mmmt) REVERT: K 317 GLU cc_start: 0.8282 (tp30) cc_final: 0.7956 (tp30) REVERT: K 327 TYR cc_start: 0.8798 (m-80) cc_final: 0.8306 (m-80) REVERT: K 332 MET cc_start: 0.9314 (ttm) cc_final: 0.8956 (ttp) REVERT: K 379 GLU cc_start: 0.8069 (tp30) cc_final: 0.7833 (mm-30) REVERT: K 385 MET cc_start: 0.7425 (mmm) cc_final: 0.6969 (mmt) REVERT: K 427 GLU cc_start: 0.8243 (tm-30) cc_final: 0.8007 (tm-30) REVERT: L 198 ILE cc_start: 0.8739 (mt) cc_final: 0.8317 (tp) REVERT: L 229 MET cc_start: 0.7494 (tmm) cc_final: 0.7129 (tmm) REVERT: L 288 LYS cc_start: 0.9003 (mttt) cc_final: 0.8744 (tptt) REVERT: N 40 ASP cc_start: 0.7760 (m-30) cc_final: 0.7341 (t70) REVERT: N 73 LYS cc_start: 0.8799 (ttmt) cc_final: 0.8339 (ttmm) REVERT: N 160 ARG cc_start: 0.8545 (ttm170) cc_final: 0.7837 (tmm160) REVERT: N 170 LYS cc_start: 0.9195 (tttt) cc_final: 0.8853 (ttpt) REVERT: N 194 GLU cc_start: 0.8711 (pp20) cc_final: 0.8322 (pp20) REVERT: N 211 ARG cc_start: 0.7463 (mmm160) cc_final: 0.6772 (mmm-85) REVERT: N 253 ILE cc_start: 0.8182 (tt) cc_final: 0.7907 (mt) REVERT: N 337 GLN cc_start: 0.8763 (tt0) cc_final: 0.8439 (tm-30) outliers start: 2 outliers final: 0 residues processed: 694 average time/residue: 0.9070 time to fit residues: 1010.0342 Evaluate side-chains 550 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 550 time to evaluate : 4.100 ------------------------------------------------------------------------------- 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: 7.9990 chunk 376 optimal weight: 5.9990 chunk 343 optimal weight: 0.6980 chunk 366 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 287 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 331 optimal weight: 0.5980 chunk 346 optimal weight: 6.9990 chunk 365 optimal weight: 5.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 261 ASN J 299 HIS K 333 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 10 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35024 Z= 0.209 Angle : 0.529 12.210 47382 Z= 0.272 Chirality : 0.039 0.357 5008 Planarity : 0.004 0.073 6102 Dihedral : 8.554 179.804 4798 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.13), residues: 4084 helix: 0.77 (0.12), residues: 1740 sheet: 0.10 (0.21), residues: 626 loop : -0.30 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 332 HIS 0.011 0.001 HIS E 407 PHE 0.019 0.001 PHE J 352 TYR 0.026 0.001 TYR G 236 ARG 0.014 0.000 ARG M 211 *********************** 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 683 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 682 time to evaluate : 4.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 SER cc_start: 0.8332 (p) cc_final: 0.8118 (m) REVERT: A 421 ASP cc_start: 0.8375 (p0) cc_final: 0.7944 (p0) REVERT: A 430 MET cc_start: 0.8811 (mmp) cc_final: 0.8455 (mmm) REVERT: A 438 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8493 (tp30) REVERT: A 449 GLN cc_start: 0.8425 (tp40) cc_final: 0.8152 (tp40) REVERT: B 196 ASN cc_start: 0.8589 (m-40) cc_final: 0.8181 (m-40) REVERT: B 263 CYS cc_start: 0.8545 (m) cc_final: 0.8305 (m) REVERT: B 294 MET cc_start: 0.8242 (ttm) cc_final: 0.7945 (ttm) REVERT: B 394 LYS cc_start: 0.8884 (ptmt) cc_final: 0.8633 (ptmm) REVERT: C 178 PHE cc_start: 0.7802 (m-80) cc_final: 0.7389 (m-10) REVERT: C 320 PHE cc_start: 0.8489 (t80) cc_final: 0.8273 (t80) REVERT: D 189 LYS cc_start: 0.9152 (mttt) cc_final: 0.8562 (tptt) REVERT: D 390 GLN cc_start: 0.9273 (mt0) cc_final: 0.8775 (tm-30) REVERT: D 401 LYS cc_start: 0.8609 (mppt) cc_final: 0.8334 (mtmm) REVERT: D 438 GLU cc_start: 0.9018 (tt0) cc_final: 0.8328 (tm-30) REVERT: E 263 CYS cc_start: 0.9339 (m) cc_final: 0.8961 (m) REVERT: E 306 TRP cc_start: 0.8619 (m100) cc_final: 0.8244 (m100) REVERT: E 332 MET cc_start: 0.9239 (ttm) cc_final: 0.8987 (ttp) REVERT: E 442 PHE cc_start: 0.8009 (t80) cc_final: 0.7658 (t80) REVERT: F 288 LYS cc_start: 0.8866 (mttt) cc_final: 0.8511 (tptt) REVERT: F 321 TYR cc_start: 0.9084 (p90) cc_final: 0.8776 (p90) REVERT: M 40 ASP cc_start: 0.7571 (m-30) cc_final: 0.7083 (t70) REVERT: M 73 LYS cc_start: 0.8839 (ttmt) cc_final: 0.8396 (ttmm) REVERT: M 124 SER cc_start: 0.8388 (m) cc_final: 0.7438 (m) REVERT: M 170 LYS cc_start: 0.9245 (tttt) cc_final: 0.8900 (ttpt) REVERT: M 189 ASP cc_start: 0.7344 (t0) cc_final: 0.7094 (t0) REVERT: M 194 GLU cc_start: 0.8746 (pp20) cc_final: 0.8372 (pp20) REVERT: M 213 LEU cc_start: 0.9059 (mt) cc_final: 0.8773 (mp) REVERT: M 253 ILE cc_start: 0.8135 (tt) cc_final: 0.7824 (mt) REVERT: M 337 GLN cc_start: 0.8798 (tt0) cc_final: 0.8407 (tm-30) REVERT: M 341 ASP cc_start: 0.8171 (t70) cc_final: 0.7931 (t70) REVERT: G 231 GLN cc_start: 0.7388 (tt0) cc_final: 0.6856 (tt0) REVERT: G 280 GLU cc_start: 0.8203 (mt-10) cc_final: 0.6597 (mt-10) REVERT: G 379 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8363 (mt-10) REVERT: G 432 ASP cc_start: 0.7615 (m-30) cc_final: 0.7358 (m-30) REVERT: H 196 ASN cc_start: 0.8601 (m-40) cc_final: 0.8181 (m-40) REVERT: H 262 PHE cc_start: 0.8726 (t80) cc_final: 0.8514 (t80) REVERT: H 280 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8067 (mm-30) REVERT: H 294 MET cc_start: 0.8061 (ttm) cc_final: 0.7634 (ttm) REVERT: H 339 LEU cc_start: 0.9423 (mt) cc_final: 0.9119 (mt) REVERT: H 448 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7664 (tm-30) REVERT: I 239 GLU cc_start: 0.9354 (mp0) cc_final: 0.9110 (mp0) REVERT: I 281 ILE cc_start: 0.9482 (tt) cc_final: 0.9150 (tp) REVERT: I 320 PHE cc_start: 0.8569 (t80) cc_final: 0.8303 (t80) REVERT: J 189 LYS cc_start: 0.9315 (mttt) cc_final: 0.8914 (tptt) REVERT: J 196 ASN cc_start: 0.8368 (m-40) cc_final: 0.8156 (m-40) REVERT: J 440 TYR cc_start: 0.9146 (m-10) cc_final: 0.8848 (m-10) REVERT: K 263 CYS cc_start: 0.9469 (m) cc_final: 0.8955 (t) REVERT: K 288 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8670 (mmmt) REVERT: K 327 TYR cc_start: 0.8786 (m-80) cc_final: 0.8146 (m-80) REVERT: K 332 MET cc_start: 0.9300 (ttm) cc_final: 0.8949 (ttp) REVERT: K 379 GLU cc_start: 0.8131 (tp30) cc_final: 0.7890 (mm-30) REVERT: K 385 MET cc_start: 0.7452 (mmm) cc_final: 0.6993 (mmt) REVERT: K 427 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7886 (tm-30) REVERT: L 198 ILE cc_start: 0.8743 (mt) cc_final: 0.8311 (tp) REVERT: L 229 MET cc_start: 0.7535 (tmm) cc_final: 0.7164 (tmm) REVERT: L 288 LYS cc_start: 0.8995 (mttt) cc_final: 0.8717 (tptt) REVERT: N 40 ASP cc_start: 0.7607 (m-30) cc_final: 0.7197 (t70) REVERT: N 73 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8346 (ttmm) REVERT: N 170 LYS cc_start: 0.9223 (tttt) cc_final: 0.8886 (ttpt) REVERT: N 194 GLU cc_start: 0.8725 (pp20) cc_final: 0.8328 (pp20) REVERT: N 253 ILE cc_start: 0.8141 (tt) cc_final: 0.7869 (mt) REVERT: N 337 GLN cc_start: 0.8851 (tt0) cc_final: 0.8502 (tm-30) outliers start: 1 outliers final: 0 residues processed: 683 average time/residue: 0.8627 time to fit residues: 946.6182 Evaluate side-chains 551 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 551 time to evaluate : 4.113 ------------------------------------------------------------------------------- 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: 4.9990 chunk 236 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 406 optimal weight: 3.9990 chunk 374 optimal weight: 10.0000 chunk 323 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 ASN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.6730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35024 Z= 0.273 Angle : 0.567 12.172 47382 Z= 0.296 Chirality : 0.039 0.359 5008 Planarity : 0.004 0.055 6102 Dihedral : 8.618 179.698 4798 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.03 % Allowed : 0.16 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.13), residues: 4084 helix: 0.63 (0.12), residues: 1730 sheet: -0.10 (0.20), residues: 630 loop : -0.45 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 424 HIS 0.012 0.002 HIS K 407 PHE 0.033 0.002 PHE D 352 TYR 0.027 0.002 TYR G 236 ARG 0.011 0.001 ARG M 211 ********************** 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 648 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 647 time to evaluate : 4.230 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: A 430 MET cc_start: 0.8828 (mmp) cc_final: 0.8513 (mmm) REVERT: A 438 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8558 (tp30) REVERT: A 449 GLN cc_start: 0.8458 (tp40) cc_final: 0.8162 (tp40) REVERT: B 263 CYS cc_start: 0.8566 (m) cc_final: 0.8352 (m) REVERT: B 281 ILE cc_start: 0.9419 (pt) cc_final: 0.9123 (mt) REVERT: B 294 MET cc_start: 0.8147 (ttm) cc_final: 0.7666 (ttm) REVERT: B 321 TYR cc_start: 0.9197 (p90) cc_final: 0.8981 (p90) REVERT: B 394 LYS cc_start: 0.8901 (ptmt) cc_final: 0.8641 (ptmm) REVERT: C 178 PHE cc_start: 0.7977 (m-80) cc_final: 0.7523 (m-10) REVERT: D 189 LYS cc_start: 0.9173 (mttt) cc_final: 0.8579 (tptt) REVERT: D 390 GLN cc_start: 0.9286 (mt0) cc_final: 0.8794 (tm-30) REVERT: D 401 LYS cc_start: 0.8629 (mppt) cc_final: 0.8370 (mtmm) REVERT: D 438 GLU cc_start: 0.9020 (tt0) cc_final: 0.8247 (tm-30) REVERT: E 263 CYS cc_start: 0.9339 (m) cc_final: 0.8898 (t) REVERT: E 306 TRP cc_start: 0.8712 (m100) cc_final: 0.8390 (m100) REVERT: E 332 MET cc_start: 0.9280 (ttm) cc_final: 0.9036 (ttp) REVERT: E 442 PHE cc_start: 0.8035 (t80) cc_final: 0.7674 (t80) REVERT: F 288 LYS cc_start: 0.8894 (mttt) cc_final: 0.8537 (tptt) REVERT: F 321 TYR cc_start: 0.9065 (p90) cc_final: 0.8737 (p90) REVERT: M 40 ASP cc_start: 0.7518 (m-30) cc_final: 0.6989 (t70) REVERT: M 73 LYS cc_start: 0.8890 (ttmt) cc_final: 0.8413 (ttmm) REVERT: M 124 SER cc_start: 0.8468 (m) cc_final: 0.7513 (m) REVERT: M 170 LYS cc_start: 0.9265 (tttt) cc_final: 0.8920 (ttpt) REVERT: M 194 GLU cc_start: 0.8785 (pp20) cc_final: 0.8460 (pp20) REVERT: M 253 ILE cc_start: 0.8070 (tt) cc_final: 0.7750 (mt) REVERT: M 337 GLN cc_start: 0.8828 (tt0) cc_final: 0.8467 (tm-30) REVERT: M 341 ASP cc_start: 0.8189 (t70) cc_final: 0.7950 (t70) REVERT: G 432 ASP cc_start: 0.7703 (m-30) cc_final: 0.7392 (m-30) REVERT: H 196 ASN cc_start: 0.8622 (m-40) cc_final: 0.8212 (m-40) REVERT: H 280 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8149 (mm-30) REVERT: H 294 MET cc_start: 0.8037 (ttm) cc_final: 0.7575 (ttm) REVERT: H 339 LEU cc_start: 0.9398 (mt) cc_final: 0.9114 (mt) REVERT: H 448 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7734 (tm-30) REVERT: I 281 ILE cc_start: 0.9507 (tt) cc_final: 0.9201 (tp) REVERT: I 320 PHE cc_start: 0.8648 (t80) cc_final: 0.8313 (t80) REVERT: J 189 LYS cc_start: 0.9321 (mttt) cc_final: 0.8910 (tptt) REVERT: J 262 PHE cc_start: 0.8919 (t80) cc_final: 0.8705 (t80) REVERT: J 440 TYR cc_start: 0.9169 (m-10) cc_final: 0.8860 (m-10) REVERT: K 263 CYS cc_start: 0.9489 (m) cc_final: 0.9023 (t) REVERT: K 288 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8665 (mmmt) REVERT: K 332 MET cc_start: 0.9292 (ttm) cc_final: 0.8949 (ttp) REVERT: K 379 GLU cc_start: 0.8020 (tp30) cc_final: 0.7738 (mm-30) REVERT: K 385 MET cc_start: 0.7422 (mmm) cc_final: 0.6947 (mmt) REVERT: K 427 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7708 (tm-30) REVERT: L 198 ILE cc_start: 0.8691 (mt) cc_final: 0.8261 (tp) REVERT: L 288 LYS cc_start: 0.8965 (mttt) cc_final: 0.8717 (tptt) REVERT: N 40 ASP cc_start: 0.7821 (m-30) cc_final: 0.7238 (t70) REVERT: N 52 GLN cc_start: 0.8656 (mt0) cc_final: 0.7969 (tm-30) REVERT: N 73 LYS cc_start: 0.8882 (ttmt) cc_final: 0.8426 (ttmm) REVERT: N 122 LEU cc_start: 0.7207 (tp) cc_final: 0.6706 (tp) REVERT: N 170 LYS cc_start: 0.9261 (tttt) cc_final: 0.8914 (ttpt) REVERT: N 194 GLU cc_start: 0.8757 (pp20) cc_final: 0.8419 (pp20) REVERT: N 253 ILE cc_start: 0.8176 (tt) cc_final: 0.7890 (mt) REVERT: N 337 GLN cc_start: 0.8856 (tt0) cc_final: 0.8498 (tm-30) outliers start: 1 outliers final: 0 residues processed: 648 average time/residue: 0.8690 time to fit residues: 911.1744 Evaluate side-chains 526 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 526 time to evaluate : 4.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 10.0000 chunk 344 optimal weight: 10.0000 chunk 99 optimal weight: 0.0370 chunk 298 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 324 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 332 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 GLN A 453 ASN ** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 ASN N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.097608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.080653 restraints weight = 292164.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.084379 restraints weight = 127815.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.086770 restraints weight = 72800.626| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.6839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35024 Z= 0.211 Angle : 0.532 12.183 47382 Z= 0.275 Chirality : 0.039 0.356 5008 Planarity : 0.004 0.062 6102 Dihedral : 8.433 179.765 4798 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.05 % Allowed : 0.08 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.13), residues: 4084 helix: 0.72 (0.12), residues: 1730 sheet: -0.04 (0.21), residues: 626 loop : -0.37 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 451 HIS 0.011 0.001 HIS K 407 PHE 0.022 0.001 PHE D 178 TYR 0.029 0.001 TYR H 236 ARG 0.012 0.000 ARG M 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16381.03 seconds wall clock time: 284 minutes 1.34 seconds (17041.34 seconds total)