Starting phenix.real_space_refine on Mon Mar 11 21:05:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3q_18133/03_2024/8q3q_18133_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3q_18133/03_2024/8q3q_18133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3q_18133/03_2024/8q3q_18133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3q_18133/03_2024/8q3q_18133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3q_18133/03_2024/8q3q_18133_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3q_18133/03_2024/8q3q_18133_updated.pdb" } resolution = 3.3 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= 0.014 sd= 0.065 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 18 5.21 5 S 306 5.16 5 C 37548 2.51 5 N 10638 2.21 5 O 11376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 211": "OE1" <-> "OE2" Residue "a GLU 215": "OE1" <-> "OE2" Residue "a GLU 226": "OE1" <-> "OE2" Residue "a GLU 248": "OE1" <-> "OE2" Residue "a ASP 265": "OD1" <-> "OD2" Residue "a TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 328": "OD1" <-> "OD2" Residue "a GLU 329": "OE1" <-> "OE2" Residue "a GLU 334": "OE1" <-> "OE2" Residue "a GLU 342": "OE1" <-> "OE2" Residue "a TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 368": "OE1" <-> "OE2" Residue "a GLU 375": "OE1" <-> "OE2" Residue "a ASP 410": "OD1" <-> "OD2" Residue "r TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 211": "OE1" <-> "OE2" Residue "r GLU 215": "OE1" <-> "OE2" Residue "r GLU 226": "OE1" <-> "OE2" Residue "r GLU 248": "OE1" <-> "OE2" Residue "r ASP 265": "OD1" <-> "OD2" Residue "r TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 328": "OD1" <-> "OD2" Residue "r GLU 329": "OE1" <-> "OE2" Residue "r GLU 334": "OE1" <-> "OE2" Residue "r GLU 342": "OE1" <-> "OE2" Residue "r TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 368": "OE1" <-> "OE2" Residue "r GLU 375": "OE1" <-> "OE2" Residue "r ASP 410": "OD1" <-> "OD2" Residue "q TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 211": "OE1" <-> "OE2" Residue "q GLU 215": "OE1" <-> "OE2" Residue "q GLU 226": "OE1" <-> "OE2" Residue "q GLU 248": "OE1" <-> "OE2" Residue "q ASP 265": "OD1" <-> "OD2" Residue "q TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 328": "OD1" <-> "OD2" Residue "q GLU 329": "OE1" <-> "OE2" Residue "q GLU 334": "OE1" <-> "OE2" Residue "q GLU 342": "OE1" <-> "OE2" Residue "q TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 368": "OE1" <-> "OE2" Residue "q GLU 375": "OE1" <-> "OE2" Residue "q ASP 410": "OD1" <-> "OD2" Residue "p TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 211": "OE1" <-> "OE2" Residue "p GLU 215": "OE1" <-> "OE2" Residue "p GLU 226": "OE1" <-> "OE2" Residue "p GLU 248": "OE1" <-> "OE2" Residue "p ASP 265": "OD1" <-> "OD2" Residue "p TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 328": "OD1" <-> "OD2" Residue "p GLU 329": "OE1" <-> "OE2" Residue "p GLU 334": "OE1" <-> "OE2" Residue "p GLU 342": "OE1" <-> "OE2" Residue "p TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 368": "OE1" <-> "OE2" Residue "p GLU 375": "OE1" <-> "OE2" Residue "p ASP 410": "OD1" <-> "OD2" Residue "o TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 211": "OE1" <-> "OE2" Residue "o GLU 215": "OE1" <-> "OE2" Residue "o GLU 226": "OE1" <-> "OE2" Residue "o GLU 248": "OE1" <-> "OE2" Residue "o ASP 265": "OD1" <-> "OD2" Residue "o TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 328": "OD1" <-> "OD2" Residue "o GLU 329": "OE1" <-> "OE2" Residue "o GLU 334": "OE1" <-> "OE2" Residue "o GLU 342": "OE1" <-> "OE2" Residue "o TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 368": "OE1" <-> "OE2" Residue "o GLU 375": "OE1" <-> "OE2" Residue "o ASP 410": "OD1" <-> "OD2" Residue "n TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 211": "OE1" <-> "OE2" Residue "n GLU 215": "OE1" <-> "OE2" Residue "n GLU 226": "OE1" <-> "OE2" Residue "n GLU 248": "OE1" <-> "OE2" Residue "n ASP 265": "OD1" <-> "OD2" Residue "n TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 328": "OD1" <-> "OD2" Residue "n GLU 329": "OE1" <-> "OE2" Residue "n GLU 334": "OE1" <-> "OE2" Residue "n GLU 342": "OE1" <-> "OE2" Residue "n TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 368": "OE1" <-> "OE2" Residue "n GLU 375": "OE1" <-> "OE2" Residue "n ASP 410": "OD1" <-> "OD2" Residue "m TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 211": "OE1" <-> "OE2" Residue "m GLU 215": "OE1" <-> "OE2" Residue "m GLU 226": "OE1" <-> "OE2" Residue "m GLU 248": "OE1" <-> "OE2" Residue "m ASP 265": "OD1" <-> "OD2" Residue "m TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 328": "OD1" <-> "OD2" Residue "m GLU 329": "OE1" <-> "OE2" Residue "m GLU 334": "OE1" <-> "OE2" Residue "m GLU 342": "OE1" <-> "OE2" Residue "m TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 368": "OE1" <-> "OE2" Residue "m GLU 375": "OE1" <-> "OE2" Residue "m ASP 410": "OD1" <-> "OD2" Residue "l TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 211": "OE1" <-> "OE2" Residue "l GLU 215": "OE1" <-> "OE2" Residue "l GLU 226": "OE1" <-> "OE2" Residue "l GLU 248": "OE1" <-> "OE2" Residue "l ASP 265": "OD1" <-> "OD2" Residue "l TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 328": "OD1" <-> "OD2" Residue "l GLU 329": "OE1" <-> "OE2" Residue "l GLU 334": "OE1" <-> "OE2" Residue "l GLU 342": "OE1" <-> "OE2" Residue "l TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 368": "OE1" <-> "OE2" Residue "l GLU 375": "OE1" <-> "OE2" Residue "l ASP 410": "OD1" <-> "OD2" Residue "k TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 211": "OE1" <-> "OE2" Residue "k GLU 215": "OE1" <-> "OE2" Residue "k GLU 226": "OE1" <-> "OE2" Residue "k GLU 248": "OE1" <-> "OE2" Residue "k ASP 265": "OD1" <-> "OD2" Residue "k TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 328": "OD1" <-> "OD2" Residue "k GLU 329": "OE1" <-> "OE2" Residue "k GLU 334": "OE1" <-> "OE2" Residue "k GLU 342": "OE1" <-> "OE2" Residue "k TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 368": "OE1" <-> "OE2" Residue "k GLU 375": "OE1" <-> "OE2" Residue "k ASP 410": "OD1" <-> "OD2" Residue "j TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 211": "OE1" <-> "OE2" Residue "j GLU 215": "OE1" <-> "OE2" Residue "j GLU 226": "OE1" <-> "OE2" Residue "j GLU 248": "OE1" <-> "OE2" Residue "j ASP 265": "OD1" <-> "OD2" Residue "j TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 328": "OD1" <-> "OD2" Residue "j GLU 329": "OE1" <-> "OE2" Residue "j GLU 334": "OE1" <-> "OE2" Residue "j GLU 342": "OE1" <-> "OE2" Residue "j TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 368": "OE1" <-> "OE2" Residue "j GLU 375": "OE1" <-> "OE2" Residue "j ASP 410": "OD1" <-> "OD2" Residue "i TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 211": "OE1" <-> "OE2" Residue "i GLU 215": "OE1" <-> "OE2" Residue "i GLU 226": "OE1" <-> "OE2" Residue "i GLU 248": "OE1" <-> "OE2" Residue "i ASP 265": "OD1" <-> "OD2" Residue "i TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 328": "OD1" <-> "OD2" Residue "i GLU 329": "OE1" <-> "OE2" Residue "i GLU 334": "OE1" <-> "OE2" Residue "i GLU 342": "OE1" <-> "OE2" Residue "i TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 368": "OE1" <-> "OE2" Residue "i GLU 375": "OE1" <-> "OE2" Residue "i ASP 410": "OD1" <-> "OD2" Residue "h TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 211": "OE1" <-> "OE2" Residue "h GLU 215": "OE1" <-> "OE2" Residue "h GLU 226": "OE1" <-> "OE2" Residue "h GLU 248": "OE1" <-> "OE2" Residue "h ASP 265": "OD1" <-> "OD2" Residue "h TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 328": "OD1" <-> "OD2" Residue "h GLU 329": "OE1" <-> "OE2" Residue "h GLU 334": "OE1" <-> "OE2" Residue "h GLU 342": "OE1" <-> "OE2" Residue "h TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 368": "OE1" <-> "OE2" Residue "h GLU 375": "OE1" <-> "OE2" Residue "h ASP 410": "OD1" <-> "OD2" Residue "g TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 211": "OE1" <-> "OE2" Residue "g GLU 215": "OE1" <-> "OE2" Residue "g GLU 226": "OE1" <-> "OE2" Residue "g GLU 248": "OE1" <-> "OE2" Residue "g ASP 265": "OD1" <-> "OD2" Residue "g TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 328": "OD1" <-> "OD2" Residue "g GLU 329": "OE1" <-> "OE2" Residue "g GLU 334": "OE1" <-> "OE2" Residue "g GLU 342": "OE1" <-> "OE2" Residue "g TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 368": "OE1" <-> "OE2" Residue "g GLU 375": "OE1" <-> "OE2" Residue "g ASP 410": "OD1" <-> "OD2" Residue "f TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 211": "OE1" <-> "OE2" Residue "f GLU 215": "OE1" <-> "OE2" Residue "f GLU 226": "OE1" <-> "OE2" Residue "f GLU 248": "OE1" <-> "OE2" Residue "f ASP 265": "OD1" <-> "OD2" Residue "f TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 328": "OD1" <-> "OD2" Residue "f GLU 329": "OE1" <-> "OE2" Residue "f GLU 334": "OE1" <-> "OE2" Residue "f GLU 342": "OE1" <-> "OE2" Residue "f TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 368": "OE1" <-> "OE2" Residue "f GLU 375": "OE1" <-> "OE2" Residue "f ASP 410": "OD1" <-> "OD2" Residue "e TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 211": "OE1" <-> "OE2" Residue "e GLU 215": "OE1" <-> "OE2" Residue "e GLU 226": "OE1" <-> "OE2" Residue "e GLU 248": "OE1" <-> "OE2" Residue "e ASP 265": "OD1" <-> "OD2" Residue "e TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 328": "OD1" <-> "OD2" Residue "e GLU 329": "OE1" <-> "OE2" Residue "e GLU 334": "OE1" <-> "OE2" Residue "e GLU 342": "OE1" <-> "OE2" Residue "e TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 368": "OE1" <-> "OE2" Residue "e GLU 375": "OE1" <-> "OE2" Residue "e ASP 410": "OD1" <-> "OD2" Residue "d TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 211": "OE1" <-> "OE2" Residue "d GLU 215": "OE1" <-> "OE2" Residue "d GLU 226": "OE1" <-> "OE2" Residue "d GLU 248": "OE1" <-> "OE2" Residue "d ASP 265": "OD1" <-> "OD2" Residue "d TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 328": "OD1" <-> "OD2" Residue "d GLU 329": "OE1" <-> "OE2" Residue "d GLU 334": "OE1" <-> "OE2" Residue "d GLU 342": "OE1" <-> "OE2" Residue "d TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 368": "OE1" <-> "OE2" Residue "d GLU 375": "OE1" <-> "OE2" Residue "d ASP 410": "OD1" <-> "OD2" Residue "c TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 211": "OE1" <-> "OE2" Residue "c GLU 215": "OE1" <-> "OE2" Residue "c GLU 226": "OE1" <-> "OE2" Residue "c GLU 248": "OE1" <-> "OE2" Residue "c ASP 265": "OD1" <-> "OD2" Residue "c TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 328": "OD1" <-> "OD2" Residue "c GLU 329": "OE1" <-> "OE2" Residue "c GLU 334": "OE1" <-> "OE2" Residue "c GLU 342": "OE1" <-> "OE2" Residue "c TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 368": "OE1" <-> "OE2" Residue "c GLU 375": "OE1" <-> "OE2" Residue "c ASP 410": "OD1" <-> "OD2" Residue "b TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 211": "OE1" <-> "OE2" Residue "b GLU 215": "OE1" <-> "OE2" Residue "b GLU 226": "OE1" <-> "OE2" Residue "b GLU 248": "OE1" <-> "OE2" Residue "b ASP 265": "OD1" <-> "OD2" Residue "b TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 328": "OD1" <-> "OD2" Residue "b GLU 329": "OE1" <-> "OE2" Residue "b GLU 334": "OE1" <-> "OE2" Residue "b GLU 342": "OE1" <-> "OE2" Residue "b TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 368": "OE1" <-> "OE2" Residue "b GLU 375": "OE1" <-> "OE2" Residue "b ASP 410": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 59922 Number of models: 1 Model: "" Number of chains: 36 Chain: "a" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "r" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "q" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "p" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "o" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "n" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "m" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "l" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "k" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "j" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "i" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "h" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "g" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "f" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "e" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "d" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "c" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "b" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 23.41, per 1000 atoms: 0.39 Number of scatterers: 59922 At special positions: 0 Unit cell: (138.112, 138.112, 279.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 306 16.00 P 36 15.00 Mg 18 11.99 O 11376 8.00 N 10638 7.00 C 37548 6.00 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: 18.99 Conformation dependent library (CDL) restraints added in 8.0 seconds 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14076 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 324 helices and 36 sheets defined 43.2% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.78 Creating SS restraints... Processing helix chain 'a' and resid 3 through 8 Processing helix chain 'a' and resid 11 through 21 removed outlier: 4.304A pdb=" N THR a 16 " --> pdb=" O SER a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 31 through 45 Processing helix chain 'a' and resid 83 through 88 Processing helix chain 'a' and resid 124 through 129 removed outlier: 3.534A pdb=" N ARG a 128 " --> pdb=" O PRO a 124 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN a 129 " --> pdb=" O GLU a 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 124 through 129' Processing helix chain 'a' and resid 133 through 135 No H-bonds generated for 'chain 'a' and resid 133 through 135' Processing helix chain 'a' and resid 158 through 165 Processing helix chain 'a' and resid 184 through 198 Processing helix chain 'a' and resid 213 through 222 Processing helix chain 'a' and resid 236 through 256 removed outlier: 3.633A pdb=" N HIS a 256 " --> pdb=" O ARG a 252 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 277 Processing helix chain 'a' and resid 291 through 303 removed outlier: 3.964A pdb=" N ARG a 296 " --> pdb=" O ASN a 292 " (cutoff:3.500A) Proline residue: a 297 - end of helix Processing helix chain 'a' and resid 326 through 334 Processing helix chain 'a' and resid 347 through 352 Processing helix chain 'a' and resid 368 through 371 No H-bonds generated for 'chain 'a' and resid 368 through 371' Processing helix chain 'a' and resid 374 through 388 Processing helix chain 'a' and resid 392 through 403 Processing helix chain 'a' and resid 409 through 418 Processing helix chain 'r' and resid 3 through 8 Processing helix chain 'r' and resid 11 through 21 removed outlier: 4.304A pdb=" N THR r 16 " --> pdb=" O SER r 12 " (cutoff:3.500A) Processing helix chain 'r' and resid 31 through 45 Processing helix chain 'r' and resid 83 through 88 Processing helix chain 'r' and resid 124 through 129 removed outlier: 3.534A pdb=" N ARG r 128 " --> pdb=" O PRO r 124 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN r 129 " --> pdb=" O GLU r 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 124 through 129' Processing helix chain 'r' and resid 133 through 135 No H-bonds generated for 'chain 'r' and resid 133 through 135' Processing helix chain 'r' and resid 158 through 165 Processing helix chain 'r' and resid 184 through 198 Processing helix chain 'r' and resid 213 through 222 Processing helix chain 'r' and resid 236 through 256 removed outlier: 3.632A pdb=" N HIS r 256 " --> pdb=" O ARG r 252 " (cutoff:3.500A) Processing helix chain 'r' and resid 267 through 277 Processing helix chain 'r' and resid 291 through 303 removed outlier: 3.964A pdb=" N ARG r 296 " --> pdb=" O ASN r 292 " (cutoff:3.500A) Proline residue: r 297 - end of helix Processing helix chain 'r' and resid 326 through 334 Processing helix chain 'r' and resid 347 through 352 Processing helix chain 'r' and resid 368 through 371 No H-bonds generated for 'chain 'r' and resid 368 through 371' Processing helix chain 'r' and resid 374 through 388 Processing helix chain 'r' and resid 392 through 403 Processing helix chain 'r' and resid 409 through 418 Processing helix chain 'q' and resid 3 through 8 Processing helix chain 'q' and resid 11 through 21 removed outlier: 4.303A pdb=" N THR q 16 " --> pdb=" O SER q 12 " (cutoff:3.500A) Processing helix chain 'q' and resid 31 through 45 Processing helix chain 'q' and resid 83 through 88 Processing helix chain 'q' and resid 124 through 129 removed outlier: 3.535A pdb=" N ARG q 128 " --> pdb=" O PRO q 124 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN q 129 " --> pdb=" O GLU q 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 124 through 129' Processing helix chain 'q' and resid 133 through 135 No H-bonds generated for 'chain 'q' and resid 133 through 135' Processing helix chain 'q' and resid 158 through 165 Processing helix chain 'q' and resid 184 through 198 Processing helix chain 'q' and resid 213 through 222 Processing helix chain 'q' and resid 236 through 256 removed outlier: 3.633A pdb=" N HIS q 256 " --> pdb=" O ARG q 252 " (cutoff:3.500A) Processing helix chain 'q' and resid 267 through 277 Processing helix chain 'q' and resid 291 through 303 removed outlier: 3.964A pdb=" N ARG q 296 " --> pdb=" O ASN q 292 " (cutoff:3.500A) Proline residue: q 297 - end of helix Processing helix chain 'q' and resid 326 through 334 Processing helix chain 'q' and resid 347 through 352 Processing helix chain 'q' and resid 368 through 371 No H-bonds generated for 'chain 'q' and resid 368 through 371' Processing helix chain 'q' and resid 374 through 388 Processing helix chain 'q' and resid 392 through 403 Processing helix chain 'q' and resid 409 through 418 Processing helix chain 'p' and resid 3 through 8 Processing helix chain 'p' and resid 11 through 21 removed outlier: 4.304A pdb=" N THR p 16 " --> pdb=" O SER p 12 " (cutoff:3.500A) Processing helix chain 'p' and resid 31 through 45 Processing helix chain 'p' and resid 83 through 88 Processing helix chain 'p' and resid 124 through 129 removed outlier: 3.534A pdb=" N ARG p 128 " --> pdb=" O PRO p 124 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN p 129 " --> pdb=" O GLU p 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 124 through 129' Processing helix chain 'p' and resid 133 through 135 No H-bonds generated for 'chain 'p' and resid 133 through 135' Processing helix chain 'p' and resid 158 through 165 Processing helix chain 'p' and resid 184 through 198 Processing helix chain 'p' and resid 213 through 222 Processing helix chain 'p' and resid 236 through 256 removed outlier: 3.633A pdb=" N HIS p 256 " --> pdb=" O ARG p 252 " (cutoff:3.500A) Processing helix chain 'p' and resid 267 through 277 Processing helix chain 'p' and resid 291 through 303 removed outlier: 3.964A pdb=" N ARG p 296 " --> pdb=" O ASN p 292 " (cutoff:3.500A) Proline residue: p 297 - end of helix Processing helix chain 'p' and resid 326 through 334 Processing helix chain 'p' and resid 347 through 352 Processing helix chain 'p' and resid 368 through 371 No H-bonds generated for 'chain 'p' and resid 368 through 371' Processing helix chain 'p' and resid 374 through 388 Processing helix chain 'p' and resid 392 through 403 Processing helix chain 'p' and resid 409 through 418 Processing helix chain 'o' and resid 3 through 8 Processing helix chain 'o' and resid 11 through 21 removed outlier: 4.304A pdb=" N THR o 16 " --> pdb=" O SER o 12 " (cutoff:3.500A) Processing helix chain 'o' and resid 31 through 45 Processing helix chain 'o' and resid 83 through 88 Processing helix chain 'o' and resid 124 through 129 removed outlier: 3.535A pdb=" N ARG o 128 " --> pdb=" O PRO o 124 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN o 129 " --> pdb=" O GLU o 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 124 through 129' Processing helix chain 'o' and resid 133 through 135 No H-bonds generated for 'chain 'o' and resid 133 through 135' Processing helix chain 'o' and resid 158 through 165 Processing helix chain 'o' and resid 184 through 198 Processing helix chain 'o' and resid 213 through 222 Processing helix chain 'o' and resid 236 through 256 removed outlier: 3.632A pdb=" N HIS o 256 " --> pdb=" O ARG o 252 " (cutoff:3.500A) Processing helix chain 'o' and resid 267 through 277 Processing helix chain 'o' and resid 291 through 303 removed outlier: 3.964A pdb=" N ARG o 296 " --> pdb=" O ASN o 292 " (cutoff:3.500A) Proline residue: o 297 - end of helix Processing helix chain 'o' and resid 326 through 334 Processing helix chain 'o' and resid 347 through 352 Processing helix chain 'o' and resid 368 through 371 No H-bonds generated for 'chain 'o' and resid 368 through 371' Processing helix chain 'o' and resid 374 through 388 Processing helix chain 'o' and resid 392 through 403 Processing helix chain 'o' and resid 409 through 418 Processing helix chain 'n' and resid 3 through 8 Processing helix chain 'n' and resid 11 through 21 removed outlier: 4.304A pdb=" N THR n 16 " --> pdb=" O SER n 12 " (cutoff:3.500A) Processing helix chain 'n' and resid 31 through 45 Processing helix chain 'n' and resid 83 through 88 Processing helix chain 'n' and resid 124 through 129 removed outlier: 3.535A pdb=" N ARG n 128 " --> pdb=" O PRO n 124 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN n 129 " --> pdb=" O GLU n 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 124 through 129' Processing helix chain 'n' and resid 133 through 135 No H-bonds generated for 'chain 'n' and resid 133 through 135' Processing helix chain 'n' and resid 158 through 165 Processing helix chain 'n' and resid 184 through 198 Processing helix chain 'n' and resid 213 through 222 Processing helix chain 'n' and resid 236 through 256 removed outlier: 3.633A pdb=" N HIS n 256 " --> pdb=" O ARG n 252 " (cutoff:3.500A) Processing helix chain 'n' and resid 267 through 277 Processing helix chain 'n' and resid 291 through 303 removed outlier: 3.964A pdb=" N ARG n 296 " --> pdb=" O ASN n 292 " (cutoff:3.500A) Proline residue: n 297 - end of helix Processing helix chain 'n' and resid 326 through 334 Processing helix chain 'n' and resid 347 through 352 Processing helix chain 'n' and resid 368 through 371 No H-bonds generated for 'chain 'n' and resid 368 through 371' Processing helix chain 'n' and resid 374 through 388 Processing helix chain 'n' and resid 392 through 403 Processing helix chain 'n' and resid 409 through 418 Processing helix chain 'm' and resid 3 through 8 Processing helix chain 'm' and resid 11 through 21 removed outlier: 4.304A pdb=" N THR m 16 " --> pdb=" O SER m 12 " (cutoff:3.500A) Processing helix chain 'm' and resid 31 through 45 Processing helix chain 'm' and resid 83 through 88 Processing helix chain 'm' and resid 124 through 129 removed outlier: 3.534A pdb=" N ARG m 128 " --> pdb=" O PRO m 124 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN m 129 " --> pdb=" O GLU m 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 124 through 129' Processing helix chain 'm' and resid 133 through 135 No H-bonds generated for 'chain 'm' and resid 133 through 135' Processing helix chain 'm' and resid 158 through 165 Processing helix chain 'm' and resid 184 through 198 Processing helix chain 'm' and resid 213 through 222 Processing helix chain 'm' and resid 236 through 256 removed outlier: 3.632A pdb=" N HIS m 256 " --> pdb=" O ARG m 252 " (cutoff:3.500A) Processing helix chain 'm' and resid 267 through 277 Processing helix chain 'm' and resid 291 through 303 removed outlier: 3.964A pdb=" N ARG m 296 " --> pdb=" O ASN m 292 " (cutoff:3.500A) Proline residue: m 297 - end of helix Processing helix chain 'm' and resid 326 through 334 Processing helix chain 'm' and resid 347 through 352 Processing helix chain 'm' and resid 368 through 371 No H-bonds generated for 'chain 'm' and resid 368 through 371' Processing helix chain 'm' and resid 374 through 388 Processing helix chain 'm' and resid 392 through 403 Processing helix chain 'm' and resid 409 through 418 Processing helix chain 'l' and resid 3 through 8 Processing helix chain 'l' and resid 11 through 21 removed outlier: 4.304A pdb=" N THR l 16 " --> pdb=" O SER l 12 " (cutoff:3.500A) Processing helix chain 'l' and resid 31 through 45 Processing helix chain 'l' and resid 83 through 88 Processing helix chain 'l' and resid 124 through 129 removed outlier: 3.535A pdb=" N ARG l 128 " --> pdb=" O PRO l 124 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN l 129 " --> pdb=" O GLU l 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 124 through 129' Processing helix chain 'l' and resid 133 through 135 No H-bonds generated for 'chain 'l' and resid 133 through 135' Processing helix chain 'l' and resid 158 through 165 Processing helix chain 'l' and resid 184 through 198 Processing helix chain 'l' and resid 213 through 222 Processing helix chain 'l' and resid 236 through 256 removed outlier: 3.633A pdb=" N HIS l 256 " --> pdb=" O ARG l 252 " (cutoff:3.500A) Processing helix chain 'l' and resid 267 through 277 Processing helix chain 'l' and resid 291 through 303 removed outlier: 3.964A pdb=" N ARG l 296 " --> pdb=" O ASN l 292 " (cutoff:3.500A) Proline residue: l 297 - end of helix Processing helix chain 'l' and resid 326 through 334 Processing helix chain 'l' and resid 347 through 352 Processing helix chain 'l' and resid 368 through 371 No H-bonds generated for 'chain 'l' and resid 368 through 371' Processing helix chain 'l' and resid 374 through 388 Processing helix chain 'l' and resid 392 through 403 Processing helix chain 'l' and resid 409 through 418 Processing helix chain 'k' and resid 3 through 8 Processing helix chain 'k' and resid 11 through 21 removed outlier: 4.304A pdb=" N THR k 16 " --> pdb=" O SER k 12 " (cutoff:3.500A) Processing helix chain 'k' and resid 31 through 45 Processing helix chain 'k' and resid 83 through 88 Processing helix chain 'k' and resid 124 through 129 removed outlier: 3.535A pdb=" N ARG k 128 " --> pdb=" O PRO k 124 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN k 129 " --> pdb=" O GLU k 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 124 through 129' Processing helix chain 'k' and resid 133 through 135 No H-bonds generated for 'chain 'k' and resid 133 through 135' Processing helix chain 'k' and resid 158 through 165 Processing helix chain 'k' and resid 184 through 198 Processing helix chain 'k' and resid 213 through 222 Processing helix chain 'k' and resid 236 through 256 removed outlier: 3.632A pdb=" N HIS k 256 " --> pdb=" O ARG k 252 " (cutoff:3.500A) Processing helix chain 'k' and resid 267 through 277 Processing helix chain 'k' and resid 291 through 303 removed outlier: 3.964A pdb=" N ARG k 296 " --> pdb=" O ASN k 292 " (cutoff:3.500A) Proline residue: k 297 - end of helix Processing helix chain 'k' and resid 326 through 334 Processing helix chain 'k' and resid 347 through 352 Processing helix chain 'k' and resid 368 through 371 No H-bonds generated for 'chain 'k' and resid 368 through 371' Processing helix chain 'k' and resid 374 through 388 Processing helix chain 'k' and resid 392 through 403 Processing helix chain 'k' and resid 409 through 418 Processing helix chain 'j' and resid 3 through 8 Processing helix chain 'j' and resid 11 through 21 removed outlier: 4.305A pdb=" N THR j 16 " --> pdb=" O SER j 12 " (cutoff:3.500A) Processing helix chain 'j' and resid 31 through 45 Processing helix chain 'j' and resid 83 through 88 Processing helix chain 'j' and resid 124 through 129 removed outlier: 3.535A pdb=" N ARG j 128 " --> pdb=" O PRO j 124 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN j 129 " --> pdb=" O GLU j 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 124 through 129' Processing helix chain 'j' and resid 133 through 135 No H-bonds generated for 'chain 'j' and resid 133 through 135' Processing helix chain 'j' and resid 158 through 165 Processing helix chain 'j' and resid 184 through 198 Processing helix chain 'j' and resid 213 through 222 Processing helix chain 'j' and resid 236 through 256 removed outlier: 3.633A pdb=" N HIS j 256 " --> pdb=" O ARG j 252 " (cutoff:3.500A) Processing helix chain 'j' and resid 267 through 277 Processing helix chain 'j' and resid 291 through 303 removed outlier: 3.965A pdb=" N ARG j 296 " --> pdb=" O ASN j 292 " (cutoff:3.500A) Proline residue: j 297 - end of helix Processing helix chain 'j' and resid 326 through 334 Processing helix chain 'j' and resid 347 through 352 Processing helix chain 'j' and resid 368 through 371 No H-bonds generated for 'chain 'j' and resid 368 through 371' Processing helix chain 'j' and resid 374 through 388 Processing helix chain 'j' and resid 392 through 403 Processing helix chain 'j' and resid 409 through 418 Processing helix chain 'i' and resid 3 through 8 Processing helix chain 'i' and resid 11 through 21 removed outlier: 4.304A pdb=" N THR i 16 " --> pdb=" O SER i 12 " (cutoff:3.500A) Processing helix chain 'i' and resid 31 through 45 Processing helix chain 'i' and resid 83 through 88 Processing helix chain 'i' and resid 124 through 129 removed outlier: 3.535A pdb=" N ARG i 128 " --> pdb=" O PRO i 124 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN i 129 " --> pdb=" O GLU i 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 124 through 129' Processing helix chain 'i' and resid 133 through 135 No H-bonds generated for 'chain 'i' and resid 133 through 135' Processing helix chain 'i' and resid 158 through 165 Processing helix chain 'i' and resid 184 through 198 Processing helix chain 'i' and resid 213 through 222 Processing helix chain 'i' and resid 236 through 256 removed outlier: 3.633A pdb=" N HIS i 256 " --> pdb=" O ARG i 252 " (cutoff:3.500A) Processing helix chain 'i' and resid 267 through 277 Processing helix chain 'i' and resid 291 through 303 removed outlier: 3.964A pdb=" N ARG i 296 " --> pdb=" O ASN i 292 " (cutoff:3.500A) Proline residue: i 297 - end of helix Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 347 through 352 Processing helix chain 'i' and resid 368 through 371 No H-bonds generated for 'chain 'i' and resid 368 through 371' Processing helix chain 'i' and resid 374 through 388 Processing helix chain 'i' and resid 392 through 403 Processing helix chain 'i' and resid 409 through 418 Processing helix chain 'h' and resid 3 through 8 Processing helix chain 'h' and resid 11 through 21 removed outlier: 4.304A pdb=" N THR h 16 " --> pdb=" O SER h 12 " (cutoff:3.500A) Processing helix chain 'h' and resid 31 through 45 Processing helix chain 'h' and resid 83 through 88 Processing helix chain 'h' and resid 124 through 129 removed outlier: 3.535A pdb=" N ARG h 128 " --> pdb=" O PRO h 124 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN h 129 " --> pdb=" O GLU h 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 124 through 129' Processing helix chain 'h' and resid 133 through 135 No H-bonds generated for 'chain 'h' and resid 133 through 135' Processing helix chain 'h' and resid 158 through 165 Processing helix chain 'h' and resid 184 through 198 Processing helix chain 'h' and resid 213 through 222 Processing helix chain 'h' and resid 236 through 256 removed outlier: 3.634A pdb=" N HIS h 256 " --> pdb=" O ARG h 252 " (cutoff:3.500A) Processing helix chain 'h' and resid 267 through 277 Processing helix chain 'h' and resid 291 through 303 removed outlier: 3.964A pdb=" N ARG h 296 " --> pdb=" O ASN h 292 " (cutoff:3.500A) Proline residue: h 297 - end of helix Processing helix chain 'h' and resid 326 through 334 Processing helix chain 'h' and resid 347 through 352 Processing helix chain 'h' and resid 368 through 371 No H-bonds generated for 'chain 'h' and resid 368 through 371' Processing helix chain 'h' and resid 374 through 388 Processing helix chain 'h' and resid 392 through 403 Processing helix chain 'h' and resid 409 through 418 Processing helix chain 'g' and resid 3 through 8 Processing helix chain 'g' and resid 11 through 21 removed outlier: 4.304A pdb=" N THR g 16 " --> pdb=" O SER g 12 " (cutoff:3.500A) Processing helix chain 'g' and resid 31 through 45 Processing helix chain 'g' and resid 83 through 88 Processing helix chain 'g' and resid 124 through 129 removed outlier: 3.535A pdb=" N ARG g 128 " --> pdb=" O PRO g 124 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN g 129 " --> pdb=" O GLU g 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 124 through 129' Processing helix chain 'g' and resid 133 through 135 No H-bonds generated for 'chain 'g' and resid 133 through 135' Processing helix chain 'g' and resid 158 through 165 Processing helix chain 'g' and resid 184 through 198 Processing helix chain 'g' and resid 213 through 222 Processing helix chain 'g' and resid 236 through 256 removed outlier: 3.632A pdb=" N HIS g 256 " --> pdb=" O ARG g 252 " (cutoff:3.500A) Processing helix chain 'g' and resid 267 through 277 Processing helix chain 'g' and resid 291 through 303 removed outlier: 3.964A pdb=" N ARG g 296 " --> pdb=" O ASN g 292 " (cutoff:3.500A) Proline residue: g 297 - end of helix Processing helix chain 'g' and resid 326 through 334 Processing helix chain 'g' and resid 347 through 352 Processing helix chain 'g' and resid 368 through 371 No H-bonds generated for 'chain 'g' and resid 368 through 371' Processing helix chain 'g' and resid 374 through 388 Processing helix chain 'g' and resid 392 through 403 Processing helix chain 'g' and resid 409 through 418 Processing helix chain 'f' and resid 3 through 8 Processing helix chain 'f' and resid 11 through 21 removed outlier: 4.305A pdb=" N THR f 16 " --> pdb=" O SER f 12 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 45 Processing helix chain 'f' and resid 83 through 88 Processing helix chain 'f' and resid 124 through 129 removed outlier: 3.535A pdb=" N ARG f 128 " --> pdb=" O PRO f 124 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN f 129 " --> pdb=" O GLU f 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 124 through 129' Processing helix chain 'f' and resid 133 through 135 No H-bonds generated for 'chain 'f' and resid 133 through 135' Processing helix chain 'f' and resid 158 through 165 Processing helix chain 'f' and resid 184 through 198 Processing helix chain 'f' and resid 213 through 222 Processing helix chain 'f' and resid 236 through 256 removed outlier: 3.632A pdb=" N HIS f 256 " --> pdb=" O ARG f 252 " (cutoff:3.500A) Processing helix chain 'f' and resid 267 through 277 Processing helix chain 'f' and resid 291 through 303 removed outlier: 3.964A pdb=" N ARG f 296 " --> pdb=" O ASN f 292 " (cutoff:3.500A) Proline residue: f 297 - end of helix Processing helix chain 'f' and resid 326 through 334 Processing helix chain 'f' and resid 347 through 352 Processing helix chain 'f' and resid 368 through 371 No H-bonds generated for 'chain 'f' and resid 368 through 371' Processing helix chain 'f' and resid 374 through 388 Processing helix chain 'f' and resid 392 through 403 Processing helix chain 'f' and resid 409 through 418 Processing helix chain 'e' and resid 3 through 8 Processing helix chain 'e' and resid 11 through 21 removed outlier: 4.304A pdb=" N THR e 16 " --> pdb=" O SER e 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 31 through 45 Processing helix chain 'e' and resid 83 through 88 Processing helix chain 'e' and resid 124 through 129 removed outlier: 3.535A pdb=" N ARG e 128 " --> pdb=" O PRO e 124 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN e 129 " --> pdb=" O GLU e 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 124 through 129' Processing helix chain 'e' and resid 133 through 135 No H-bonds generated for 'chain 'e' and resid 133 through 135' Processing helix chain 'e' and resid 158 through 165 Processing helix chain 'e' and resid 184 through 198 Processing helix chain 'e' and resid 213 through 222 Processing helix chain 'e' and resid 236 through 256 removed outlier: 3.632A pdb=" N HIS e 256 " --> pdb=" O ARG e 252 " (cutoff:3.500A) Processing helix chain 'e' and resid 267 through 277 Processing helix chain 'e' and resid 291 through 303 removed outlier: 3.963A pdb=" N ARG e 296 " --> pdb=" O ASN e 292 " (cutoff:3.500A) Proline residue: e 297 - end of helix Processing helix chain 'e' and resid 326 through 334 Processing helix chain 'e' and resid 347 through 352 Processing helix chain 'e' and resid 368 through 371 No H-bonds generated for 'chain 'e' and resid 368 through 371' Processing helix chain 'e' and resid 374 through 388 Processing helix chain 'e' and resid 392 through 403 Processing helix chain 'e' and resid 409 through 418 Processing helix chain 'd' and resid 3 through 8 Processing helix chain 'd' and resid 11 through 21 removed outlier: 4.304A pdb=" N THR d 16 " --> pdb=" O SER d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 31 through 45 Processing helix chain 'd' and resid 83 through 88 Processing helix chain 'd' and resid 124 through 129 removed outlier: 3.535A pdb=" N ARG d 128 " --> pdb=" O PRO d 124 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN d 129 " --> pdb=" O GLU d 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 124 through 129' Processing helix chain 'd' and resid 133 through 135 No H-bonds generated for 'chain 'd' and resid 133 through 135' Processing helix chain 'd' and resid 158 through 165 Processing helix chain 'd' and resid 184 through 198 Processing helix chain 'd' and resid 213 through 222 Processing helix chain 'd' and resid 236 through 256 removed outlier: 3.633A pdb=" N HIS d 256 " --> pdb=" O ARG d 252 " (cutoff:3.500A) Processing helix chain 'd' and resid 267 through 277 Processing helix chain 'd' and resid 291 through 303 removed outlier: 3.963A pdb=" N ARG d 296 " --> pdb=" O ASN d 292 " (cutoff:3.500A) Proline residue: d 297 - end of helix Processing helix chain 'd' and resid 326 through 334 Processing helix chain 'd' and resid 347 through 352 Processing helix chain 'd' and resid 368 through 371 No H-bonds generated for 'chain 'd' and resid 368 through 371' Processing helix chain 'd' and resid 374 through 388 Processing helix chain 'd' and resid 392 through 403 Processing helix chain 'd' and resid 409 through 418 Processing helix chain 'c' and resid 3 through 8 Processing helix chain 'c' and resid 11 through 21 removed outlier: 4.305A pdb=" N THR c 16 " --> pdb=" O SER c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 31 through 45 Processing helix chain 'c' and resid 83 through 88 Processing helix chain 'c' and resid 124 through 129 removed outlier: 3.535A pdb=" N ARG c 128 " --> pdb=" O PRO c 124 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN c 129 " --> pdb=" O GLU c 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 124 through 129' Processing helix chain 'c' and resid 133 through 135 No H-bonds generated for 'chain 'c' and resid 133 through 135' Processing helix chain 'c' and resid 158 through 165 Processing helix chain 'c' and resid 184 through 198 Processing helix chain 'c' and resid 213 through 222 Processing helix chain 'c' and resid 236 through 256 removed outlier: 3.632A pdb=" N HIS c 256 " --> pdb=" O ARG c 252 " (cutoff:3.500A) Processing helix chain 'c' and resid 267 through 277 Processing helix chain 'c' and resid 291 through 303 removed outlier: 3.963A pdb=" N ARG c 296 " --> pdb=" O ASN c 292 " (cutoff:3.500A) Proline residue: c 297 - end of helix Processing helix chain 'c' and resid 326 through 334 Processing helix chain 'c' and resid 347 through 352 Processing helix chain 'c' and resid 368 through 371 No H-bonds generated for 'chain 'c' and resid 368 through 371' Processing helix chain 'c' and resid 374 through 388 Processing helix chain 'c' and resid 392 through 403 Processing helix chain 'c' and resid 409 through 418 Processing helix chain 'b' and resid 3 through 8 Processing helix chain 'b' and resid 11 through 21 removed outlier: 4.305A pdb=" N THR b 16 " --> pdb=" O SER b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 45 Processing helix chain 'b' and resid 83 through 88 Processing helix chain 'b' and resid 124 through 129 removed outlier: 3.535A pdb=" N ARG b 128 " --> pdb=" O PRO b 124 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN b 129 " --> pdb=" O GLU b 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 124 through 129' Processing helix chain 'b' and resid 133 through 135 No H-bonds generated for 'chain 'b' and resid 133 through 135' Processing helix chain 'b' and resid 158 through 165 Processing helix chain 'b' and resid 184 through 198 Processing helix chain 'b' and resid 213 through 222 Processing helix chain 'b' and resid 236 through 256 removed outlier: 3.632A pdb=" N HIS b 256 " --> pdb=" O ARG b 252 " (cutoff:3.500A) Processing helix chain 'b' and resid 267 through 277 Processing helix chain 'b' and resid 291 through 303 removed outlier: 3.964A pdb=" N ARG b 296 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Proline residue: b 297 - end of helix Processing helix chain 'b' and resid 326 through 334 Processing helix chain 'b' and resid 347 through 352 Processing helix chain 'b' and resid 368 through 371 No H-bonds generated for 'chain 'b' and resid 368 through 371' Processing helix chain 'b' and resid 374 through 388 Processing helix chain 'b' and resid 392 through 403 Processing helix chain 'b' and resid 409 through 418 Processing sheet with id= A, first strand: chain 'a' and resid 79 through 81 removed outlier: 3.834A pdb=" N ILE a 79 " --> pdb=" O LEU a 65 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE a 49 " --> pdb=" O ILE a 101 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS a 100 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL a 116 " --> pdb=" O LYS a 100 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'a' and resid 342 through 344 removed outlier: 6.589A pdb=" N LEU a 175 " --> pdb=" O LEU a 343 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE a 176 " --> pdb=" O ILE a 315 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA a 317 " --> pdb=" O ILE a 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA a 178 " --> pdb=" O ALA a 317 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA a 319 " --> pdb=" O ALA a 178 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR a 318 " --> pdb=" O LEU a 264 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL a 203 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU a 263 " --> pdb=" O VAL a 203 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N MET a 205 " --> pdb=" O LEU a 263 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU a 226 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LEU a 208 " --> pdb=" O GLU a 226 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL a 228 " --> pdb=" O LEU a 208 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ASP a 210 " --> pdb=" O VAL a 228 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N SER a 230 " --> pdb=" O ASP a 210 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'r' and resid 79 through 81 removed outlier: 3.833A pdb=" N ILE r 79 " --> pdb=" O LEU r 65 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE r 49 " --> pdb=" O ILE r 101 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS r 100 " --> pdb=" O VAL r 116 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL r 116 " --> pdb=" O LYS r 100 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'r' and resid 342 through 344 removed outlier: 6.589A pdb=" N LEU r 175 " --> pdb=" O LEU r 343 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE r 176 " --> pdb=" O ILE r 315 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA r 317 " --> pdb=" O ILE r 176 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA r 178 " --> pdb=" O ALA r 317 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA r 319 " --> pdb=" O ALA r 178 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR r 318 " --> pdb=" O LEU r 264 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL r 203 " --> pdb=" O ILE r 261 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU r 263 " --> pdb=" O VAL r 203 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N MET r 205 " --> pdb=" O LEU r 263 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU r 226 " --> pdb=" O VAL r 206 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU r 208 " --> pdb=" O GLU r 226 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL r 228 " --> pdb=" O LEU r 208 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASP r 210 " --> pdb=" O VAL r 228 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER r 230 " --> pdb=" O ASP r 210 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'q' and resid 79 through 81 removed outlier: 3.833A pdb=" N ILE q 79 " --> pdb=" O LEU q 65 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE q 49 " --> pdb=" O ILE q 101 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS q 100 " --> pdb=" O VAL q 116 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL q 116 " --> pdb=" O LYS q 100 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'q' and resid 342 through 344 removed outlier: 6.588A pdb=" N LEU q 175 " --> pdb=" O LEU q 343 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE q 176 " --> pdb=" O ILE q 315 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA q 317 " --> pdb=" O ILE q 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA q 178 " --> pdb=" O ALA q 317 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA q 319 " --> pdb=" O ALA q 178 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR q 318 " --> pdb=" O LEU q 264 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL q 203 " --> pdb=" O ILE q 261 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU q 263 " --> pdb=" O VAL q 203 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N MET q 205 " --> pdb=" O LEU q 263 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU q 226 " --> pdb=" O VAL q 206 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LEU q 208 " --> pdb=" O GLU q 226 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL q 228 " --> pdb=" O LEU q 208 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASP q 210 " --> pdb=" O VAL q 228 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N SER q 230 " --> pdb=" O ASP q 210 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'p' and resid 79 through 81 removed outlier: 3.833A pdb=" N ILE p 79 " --> pdb=" O LEU p 65 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE p 49 " --> pdb=" O ILE p 101 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS p 100 " --> pdb=" O VAL p 116 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL p 116 " --> pdb=" O LYS p 100 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'p' and resid 342 through 344 removed outlier: 6.588A pdb=" N LEU p 175 " --> pdb=" O LEU p 343 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE p 176 " --> pdb=" O ILE p 315 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA p 317 " --> pdb=" O ILE p 176 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA p 178 " --> pdb=" O ALA p 317 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA p 319 " --> pdb=" O ALA p 178 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR p 318 " --> pdb=" O LEU p 264 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL p 203 " --> pdb=" O ILE p 261 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU p 263 " --> pdb=" O VAL p 203 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N MET p 205 " --> pdb=" O LEU p 263 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU p 226 " --> pdb=" O VAL p 206 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LEU p 208 " --> pdb=" O GLU p 226 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL p 228 " --> pdb=" O LEU p 208 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASP p 210 " --> pdb=" O VAL p 228 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N SER p 230 " --> pdb=" O ASP p 210 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'o' and resid 79 through 81 removed outlier: 3.833A pdb=" N ILE o 79 " --> pdb=" O LEU o 65 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE o 49 " --> pdb=" O ILE o 101 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS o 100 " --> pdb=" O VAL o 116 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL o 116 " --> pdb=" O LYS o 100 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'o' and resid 342 through 344 removed outlier: 6.589A pdb=" N LEU o 175 " --> pdb=" O LEU o 343 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE o 176 " --> pdb=" O ILE o 315 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA o 317 " --> pdb=" O ILE o 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA o 178 " --> pdb=" O ALA o 317 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA o 319 " --> pdb=" O ALA o 178 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR o 318 " --> pdb=" O LEU o 264 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL o 203 " --> pdb=" O ILE o 261 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU o 263 " --> pdb=" O VAL o 203 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N MET o 205 " --> pdb=" O LEU o 263 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU o 226 " --> pdb=" O VAL o 206 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU o 208 " --> pdb=" O GLU o 226 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL o 228 " --> pdb=" O LEU o 208 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASP o 210 " --> pdb=" O VAL o 228 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER o 230 " --> pdb=" O ASP o 210 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'n' and resid 79 through 81 removed outlier: 3.833A pdb=" N ILE n 79 " --> pdb=" O LEU n 65 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE n 49 " --> pdb=" O ILE n 101 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS n 100 " --> pdb=" O VAL n 116 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL n 116 " --> pdb=" O LYS n 100 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'n' and resid 342 through 344 removed outlier: 6.588A pdb=" N LEU n 175 " --> pdb=" O LEU n 343 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE n 176 " --> pdb=" O ILE n 315 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA n 317 " --> pdb=" O ILE n 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA n 178 " --> pdb=" O ALA n 317 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA n 319 " --> pdb=" O ALA n 178 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR n 318 " --> pdb=" O LEU n 264 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL n 203 " --> pdb=" O ILE n 261 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU n 263 " --> pdb=" O VAL n 203 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N MET n 205 " --> pdb=" O LEU n 263 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU n 226 " --> pdb=" O VAL n 206 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU n 208 " --> pdb=" O GLU n 226 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL n 228 " --> pdb=" O LEU n 208 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASP n 210 " --> pdb=" O VAL n 228 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER n 230 " --> pdb=" O ASP n 210 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'm' and resid 79 through 81 removed outlier: 3.833A pdb=" N ILE m 79 " --> pdb=" O LEU m 65 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE m 49 " --> pdb=" O ILE m 101 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS m 100 " --> pdb=" O VAL m 116 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL m 116 " --> pdb=" O LYS m 100 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'm' and resid 342 through 344 removed outlier: 6.588A pdb=" N LEU m 175 " --> pdb=" O LEU m 343 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE m 176 " --> pdb=" O ILE m 315 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA m 317 " --> pdb=" O ILE m 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA m 178 " --> pdb=" O ALA m 317 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA m 319 " --> pdb=" O ALA m 178 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR m 318 " --> pdb=" O LEU m 264 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL m 203 " --> pdb=" O ILE m 261 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU m 263 " --> pdb=" O VAL m 203 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N MET m 205 " --> pdb=" O LEU m 263 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU m 226 " --> pdb=" O VAL m 206 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU m 208 " --> pdb=" O GLU m 226 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL m 228 " --> pdb=" O LEU m 208 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ASP m 210 " --> pdb=" O VAL m 228 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER m 230 " --> pdb=" O ASP m 210 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'l' and resid 79 through 81 removed outlier: 3.833A pdb=" N ILE l 79 " --> pdb=" O LEU l 65 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE l 49 " --> pdb=" O ILE l 101 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS l 100 " --> pdb=" O VAL l 116 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL l 116 " --> pdb=" O LYS l 100 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'l' and resid 342 through 344 removed outlier: 6.589A pdb=" N LEU l 175 " --> pdb=" O LEU l 343 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE l 176 " --> pdb=" O ILE l 315 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA l 317 " --> pdb=" O ILE l 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA l 178 " --> pdb=" O ALA l 317 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA l 319 " --> pdb=" O ALA l 178 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR l 318 " --> pdb=" O LEU l 264 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL l 203 " --> pdb=" O ILE l 261 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU l 263 " --> pdb=" O VAL l 203 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N MET l 205 " --> pdb=" O LEU l 263 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU l 226 " --> pdb=" O VAL l 206 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU l 208 " --> pdb=" O GLU l 226 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL l 228 " --> pdb=" O LEU l 208 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASP l 210 " --> pdb=" O VAL l 228 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER l 230 " --> pdb=" O ASP l 210 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'k' and resid 79 through 81 removed outlier: 3.833A pdb=" N ILE k 79 " --> pdb=" O LEU k 65 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE k 49 " --> pdb=" O ILE k 101 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS k 100 " --> pdb=" O VAL k 116 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL k 116 " --> pdb=" O LYS k 100 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'k' and resid 342 through 344 removed outlier: 6.588A pdb=" N LEU k 175 " --> pdb=" O LEU k 343 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE k 176 " --> pdb=" O ILE k 315 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA k 317 " --> pdb=" O ILE k 176 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA k 178 " --> pdb=" O ALA k 317 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA k 319 " --> pdb=" O ALA k 178 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR k 318 " --> pdb=" O LEU k 264 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL k 203 " --> pdb=" O ILE k 261 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU k 263 " --> pdb=" O VAL k 203 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N MET k 205 " --> pdb=" O LEU k 263 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU k 226 " --> pdb=" O VAL k 206 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU k 208 " --> pdb=" O GLU k 226 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL k 228 " --> pdb=" O LEU k 208 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ASP k 210 " --> pdb=" O VAL k 228 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER k 230 " --> pdb=" O ASP k 210 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'j' and resid 79 through 81 removed outlier: 3.834A pdb=" N ILE j 79 " --> pdb=" O LEU j 65 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE j 49 " --> pdb=" O ILE j 101 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS j 100 " --> pdb=" O VAL j 116 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL j 116 " --> pdb=" O LYS j 100 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'j' and resid 342 through 344 removed outlier: 6.588A pdb=" N LEU j 175 " --> pdb=" O LEU j 343 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE j 176 " --> pdb=" O ILE j 315 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA j 317 " --> pdb=" O ILE j 176 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA j 178 " --> pdb=" O ALA j 317 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA j 319 " --> pdb=" O ALA j 178 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR j 318 " --> pdb=" O LEU j 264 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL j 203 " --> pdb=" O ILE j 261 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU j 263 " --> pdb=" O VAL j 203 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N MET j 205 " --> pdb=" O LEU j 263 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU j 226 " --> pdb=" O VAL j 206 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LEU j 208 " --> pdb=" O GLU j 226 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL j 228 " --> pdb=" O LEU j 208 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASP j 210 " --> pdb=" O VAL j 228 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N SER j 230 " --> pdb=" O ASP j 210 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'i' and resid 79 through 81 removed outlier: 3.833A pdb=" N ILE i 79 " --> pdb=" O LEU i 65 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE i 49 " --> pdb=" O ILE i 101 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS i 100 " --> pdb=" O VAL i 116 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL i 116 " --> pdb=" O LYS i 100 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'i' and resid 342 through 344 removed outlier: 6.589A pdb=" N LEU i 175 " --> pdb=" O LEU i 343 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE i 176 " --> pdb=" O ILE i 315 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA i 317 " --> pdb=" O ILE i 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA i 178 " --> pdb=" O ALA i 317 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA i 319 " --> pdb=" O ALA i 178 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR i 318 " --> pdb=" O LEU i 264 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL i 203 " --> pdb=" O ILE i 261 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU i 263 " --> pdb=" O VAL i 203 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N MET i 205 " --> pdb=" O LEU i 263 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU i 226 " --> pdb=" O VAL i 206 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU i 208 " --> pdb=" O GLU i 226 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL i 228 " --> pdb=" O LEU i 208 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASP i 210 " --> pdb=" O VAL i 228 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER i 230 " --> pdb=" O ASP i 210 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'h' and resid 79 through 81 removed outlier: 3.833A pdb=" N ILE h 79 " --> pdb=" O LEU h 65 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE h 49 " --> pdb=" O ILE h 101 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS h 100 " --> pdb=" O VAL h 116 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL h 116 " --> pdb=" O LYS h 100 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'h' and resid 342 through 344 removed outlier: 6.589A pdb=" N LEU h 175 " --> pdb=" O LEU h 343 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE h 176 " --> pdb=" O ILE h 315 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA h 317 " --> pdb=" O ILE h 176 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA h 178 " --> pdb=" O ALA h 317 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA h 319 " --> pdb=" O ALA h 178 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR h 318 " --> pdb=" O LEU h 264 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL h 203 " --> pdb=" O ILE h 261 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU h 263 " --> pdb=" O VAL h 203 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N MET h 205 " --> pdb=" O LEU h 263 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU h 226 " --> pdb=" O VAL h 206 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU h 208 " --> pdb=" O GLU h 226 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL h 228 " --> pdb=" O LEU h 208 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASP h 210 " --> pdb=" O VAL h 228 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER h 230 " --> pdb=" O ASP h 210 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'g' and resid 79 through 81 removed outlier: 3.834A pdb=" N ILE g 79 " --> pdb=" O LEU g 65 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE g 49 " --> pdb=" O ILE g 101 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS g 100 " --> pdb=" O VAL g 116 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL g 116 " --> pdb=" O LYS g 100 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'g' and resid 342 through 344 removed outlier: 6.588A pdb=" N LEU g 175 " --> pdb=" O LEU g 343 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE g 176 " --> pdb=" O ILE g 315 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA g 317 " --> pdb=" O ILE g 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA g 178 " --> pdb=" O ALA g 317 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA g 319 " --> pdb=" O ALA g 178 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR g 318 " --> pdb=" O LEU g 264 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL g 203 " --> pdb=" O ILE g 261 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU g 263 " --> pdb=" O VAL g 203 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N MET g 205 " --> pdb=" O LEU g 263 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU g 226 " --> pdb=" O VAL g 206 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU g 208 " --> pdb=" O GLU g 226 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL g 228 " --> pdb=" O LEU g 208 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASP g 210 " --> pdb=" O VAL g 228 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER g 230 " --> pdb=" O ASP g 210 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'f' and resid 79 through 81 removed outlier: 3.833A pdb=" N ILE f 79 " --> pdb=" O LEU f 65 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE f 49 " --> pdb=" O ILE f 101 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS f 100 " --> pdb=" O VAL f 116 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL f 116 " --> pdb=" O LYS f 100 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'f' and resid 342 through 344 removed outlier: 6.588A pdb=" N LEU f 175 " --> pdb=" O LEU f 343 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE f 176 " --> pdb=" O ILE f 315 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA f 317 " --> pdb=" O ILE f 176 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA f 178 " --> pdb=" O ALA f 317 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA f 319 " --> pdb=" O ALA f 178 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR f 318 " --> pdb=" O LEU f 264 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL f 203 " --> pdb=" O ILE f 261 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU f 263 " --> pdb=" O VAL f 203 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N MET f 205 " --> pdb=" O LEU f 263 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU f 226 " --> pdb=" O VAL f 206 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LEU f 208 " --> pdb=" O GLU f 226 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL f 228 " --> pdb=" O LEU f 208 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASP f 210 " --> pdb=" O VAL f 228 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER f 230 " --> pdb=" O ASP f 210 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'e' and resid 79 through 81 removed outlier: 3.833A pdb=" N ILE e 79 " --> pdb=" O LEU e 65 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE e 49 " --> pdb=" O ILE e 101 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS e 100 " --> pdb=" O VAL e 116 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL e 116 " --> pdb=" O LYS e 100 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'e' and resid 342 through 344 removed outlier: 6.588A pdb=" N LEU e 175 " --> pdb=" O LEU e 343 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE e 176 " --> pdb=" O ILE e 315 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA e 317 " --> pdb=" O ILE e 176 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA e 178 " --> pdb=" O ALA e 317 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA e 319 " --> pdb=" O ALA e 178 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR e 318 " --> pdb=" O LEU e 264 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL e 203 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU e 263 " --> pdb=" O VAL e 203 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N MET e 205 " --> pdb=" O LEU e 263 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU e 226 " --> pdb=" O VAL e 206 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU e 208 " --> pdb=" O GLU e 226 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL e 228 " --> pdb=" O LEU e 208 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N ASP e 210 " --> pdb=" O VAL e 228 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N SER e 230 " --> pdb=" O ASP e 210 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'd' and resid 79 through 81 removed outlier: 3.833A pdb=" N ILE d 79 " --> pdb=" O LEU d 65 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE d 49 " --> pdb=" O ILE d 101 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS d 100 " --> pdb=" O VAL d 116 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL d 116 " --> pdb=" O LYS d 100 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'd' and resid 342 through 344 removed outlier: 6.588A pdb=" N LEU d 175 " --> pdb=" O LEU d 343 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE d 176 " --> pdb=" O ILE d 315 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA d 317 " --> pdb=" O ILE d 176 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA d 178 " --> pdb=" O ALA d 317 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA d 319 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR d 318 " --> pdb=" O LEU d 264 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL d 203 " --> pdb=" O ILE d 261 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU d 263 " --> pdb=" O VAL d 203 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N MET d 205 " --> pdb=" O LEU d 263 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU d 226 " --> pdb=" O VAL d 206 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU d 208 " --> pdb=" O GLU d 226 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL d 228 " --> pdb=" O LEU d 208 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASP d 210 " --> pdb=" O VAL d 228 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER d 230 " --> pdb=" O ASP d 210 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'c' and resid 79 through 81 removed outlier: 3.833A pdb=" N ILE c 79 " --> pdb=" O LEU c 65 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE c 49 " --> pdb=" O ILE c 101 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS c 100 " --> pdb=" O VAL c 116 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL c 116 " --> pdb=" O LYS c 100 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'c' and resid 342 through 344 removed outlier: 6.588A pdb=" N LEU c 175 " --> pdb=" O LEU c 343 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE c 176 " --> pdb=" O ILE c 315 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA c 317 " --> pdb=" O ILE c 176 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA c 178 " --> pdb=" O ALA c 317 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA c 319 " --> pdb=" O ALA c 178 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR c 318 " --> pdb=" O LEU c 264 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL c 203 " --> pdb=" O ILE c 261 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU c 263 " --> pdb=" O VAL c 203 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N MET c 205 " --> pdb=" O LEU c 263 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU c 226 " --> pdb=" O VAL c 206 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU c 208 " --> pdb=" O GLU c 226 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL c 228 " --> pdb=" O LEU c 208 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASP c 210 " --> pdb=" O VAL c 228 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER c 230 " --> pdb=" O ASP c 210 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'b' and resid 79 through 81 removed outlier: 3.833A pdb=" N ILE b 79 " --> pdb=" O LEU b 65 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE b 49 " --> pdb=" O ILE b 101 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS b 100 " --> pdb=" O VAL b 116 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL b 116 " --> pdb=" O LYS b 100 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'b' and resid 342 through 344 removed outlier: 6.588A pdb=" N LEU b 175 " --> pdb=" O LEU b 343 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE b 176 " --> pdb=" O ILE b 315 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA b 317 " --> pdb=" O ILE b 176 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA b 178 " --> pdb=" O ALA b 317 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA b 319 " --> pdb=" O ALA b 178 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR b 318 " --> pdb=" O LEU b 264 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL b 203 " --> pdb=" O ILE b 261 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU b 263 " --> pdb=" O VAL b 203 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N MET b 205 " --> pdb=" O LEU b 263 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU b 226 " --> pdb=" O VAL b 206 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LEU b 208 " --> pdb=" O GLU b 226 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL b 228 " --> pdb=" O LEU b 208 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N ASP b 210 " --> pdb=" O VAL b 228 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER b 230 " --> pdb=" O ASP b 210 " (cutoff:3.500A) 2178 hydrogen bonds defined for protein. 6480 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: 21.15 Time building geometry restraints manager: 20.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 20376 1.35 - 1.47: 12029 1.47 - 1.59: 27769 1.59 - 1.71: 54 1.71 - 1.82: 594 Bond restraints: 60822 Sorted by residual: bond pdb=" CB ARG r 353 " pdb=" CG ARG r 353 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.87e+00 bond pdb=" CB ARG b 353 " pdb=" CG ARG b 353 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.87e+00 bond pdb=" CB ARG o 353 " pdb=" CG ARG o 353 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.85e+00 bond pdb=" CB ARG j 353 " pdb=" CG ARG j 353 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.85e+00 bond pdb=" CB ARG h 353 " pdb=" CG ARG h 353 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.84e+00 ... (remaining 60817 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.60: 2149 107.60 - 114.70: 35845 114.70 - 121.80: 31215 121.80 - 128.90: 12547 128.90 - 136.00: 252 Bond angle restraints: 82008 Sorted by residual: angle pdb=" CA GLU c 397 " pdb=" CB GLU c 397 " pdb=" CG GLU c 397 " ideal model delta sigma weight residual 114.10 122.24 -8.14 2.00e+00 2.50e-01 1.66e+01 angle pdb=" CA GLU h 397 " pdb=" CB GLU h 397 " pdb=" CG GLU h 397 " ideal model delta sigma weight residual 114.10 122.24 -8.14 2.00e+00 2.50e-01 1.65e+01 angle pdb=" CA GLU r 397 " pdb=" CB GLU r 397 " pdb=" CG GLU r 397 " ideal model delta sigma weight residual 114.10 122.22 -8.12 2.00e+00 2.50e-01 1.65e+01 angle pdb=" CA GLU p 397 " pdb=" CB GLU p 397 " pdb=" CG GLU p 397 " ideal model delta sigma weight residual 114.10 122.22 -8.12 2.00e+00 2.50e-01 1.65e+01 angle pdb=" CA GLU b 397 " pdb=" CB GLU b 397 " pdb=" CG GLU b 397 " ideal model delta sigma weight residual 114.10 122.22 -8.12 2.00e+00 2.50e-01 1.65e+01 ... (remaining 82003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.02: 35977 33.02 - 66.03: 1589 66.03 - 99.05: 119 99.05 - 132.07: 0 132.07 - 165.08: 7 Dihedral angle restraints: 37692 sinusoidal: 15966 harmonic: 21726 Sorted by residual: dihedral pdb=" O1B ADP h1000 " pdb=" O3A ADP h1000 " pdb=" PB ADP h1000 " pdb=" PA ADP h1000 " ideal model delta sinusoidal sigma weight residual -60.00 105.08 -165.08 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" O1B ADP p1000 " pdb=" O3A ADP p1000 " pdb=" PB ADP p1000 " pdb=" PA ADP p1000 " ideal model delta sinusoidal sigma weight residual -60.00 105.08 -165.08 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" O1B ADP o1000 " pdb=" O3A ADP o1000 " pdb=" PB ADP o1000 " pdb=" PA ADP o1000 " ideal model delta sinusoidal sigma weight residual -60.00 105.07 -165.08 1 2.00e+01 2.50e-03 4.72e+01 ... (remaining 37689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 5664 0.029 - 0.058: 2249 0.058 - 0.087: 690 0.087 - 0.116: 678 0.116 - 0.145: 43 Chirality restraints: 9324 Sorted by residual: chirality pdb=" CA ASP i 322 " pdb=" N ASP i 322 " pdb=" C ASP i 322 " pdb=" CB ASP i 322 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA ASP g 322 " pdb=" N ASP g 322 " pdb=" C ASP g 322 " pdb=" CB ASP g 322 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ASP l 322 " pdb=" N ASP l 322 " pdb=" C ASP l 322 " pdb=" CB ASP l 322 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 9321 not shown) Planarity restraints: 10620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP k 381 " 0.020 2.00e-02 2.50e+03 1.64e-02 6.71e+00 pdb=" CG TRP k 381 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP k 381 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP k 381 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP k 381 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP k 381 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP k 381 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP k 381 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP k 381 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP k 381 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP f 381 " 0.020 2.00e-02 2.50e+03 1.63e-02 6.67e+00 pdb=" CG TRP f 381 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP f 381 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP f 381 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP f 381 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP f 381 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP f 381 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP f 381 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP f 381 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP f 381 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP q 381 " 0.020 2.00e-02 2.50e+03 1.63e-02 6.66e+00 pdb=" CG TRP q 381 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP q 381 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP q 381 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP q 381 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP q 381 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP q 381 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP q 381 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP q 381 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP q 381 " -0.002 2.00e-02 2.50e+03 ... (remaining 10617 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 1369 2.65 - 3.21: 58337 3.21 - 3.78: 98122 3.78 - 4.34: 129058 4.34 - 4.90: 207656 Nonbonded interactions: 494542 Sorted by model distance: nonbonded pdb=" O3B ADP o1000 " pdb="MG MG o1001 " model vdw 2.089 2.170 nonbonded pdb=" O2B ADP f1000 " pdb="MG MG f1001 " model vdw 2.089 2.170 nonbonded pdb=" O2B ADP m1000 " pdb="MG MG m1001 " model vdw 2.089 2.170 nonbonded pdb=" O3B ADP n1000 " pdb="MG MG n1001 " model vdw 2.089 2.170 nonbonded pdb=" O3B ADP h1000 " pdb="MG MG h1001 " model vdw 2.089 2.170 ... (remaining 494537 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' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } 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 individual isotropic 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: 2.640 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: 0.050 Extract box with map and model: 13.310 Check model and map are aligned: 0.680 Set scattering table: 0.420 Process input model: 123.880 Find NCS groups from input model: 3.280 Set up NCS constraints: 0.550 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 : 0.004 0.059 60822 Z= 0.242 Angle : 0.806 11.742 82008 Z= 0.386 Chirality : 0.042 0.145 9324 Planarity : 0.004 0.028 10620 Dihedral : 17.249 165.082 23616 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.07 % Allowed : 39.48 % Favored : 57.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.28 (0.10), residues: 7506 helix: 1.41 (0.09), residues: 3456 sheet: 1.26 (0.15), residues: 1188 loop : 0.10 (0.11), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.010 TRP k 381 HIS 0.003 0.001 HIS h 239 PHE 0.005 0.001 PHE p 355 TYR 0.022 0.003 TYR r 332 ARG 0.008 0.001 ARG f 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1611 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1412 time to evaluate : 5.559 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: a 21 MET cc_start: 0.8593 (ttm) cc_final: 0.8373 (ttt) REVERT: a 189 GLN cc_start: 0.8974 (mt0) cc_final: 0.8681 (mt0) REVERT: a 197 TYR cc_start: 0.8892 (t80) cc_final: 0.8467 (t80) REVERT: a 218 GLU cc_start: 0.9304 (tp30) cc_final: 0.8944 (tp30) REVERT: a 222 LEU cc_start: 0.9458 (mp) cc_final: 0.9243 (mm) REVERT: a 265 ASP cc_start: 0.8284 (t0) cc_final: 0.8021 (p0) REVERT: a 341 MET cc_start: 0.9405 (tmt) cc_final: 0.9148 (tmm) REVERT: a 405 MET cc_start: 0.8859 (ttp) cc_final: 0.8639 (ttm) REVERT: r 85 GLN cc_start: 0.8580 (mp10) cc_final: 0.8167 (mp10) REVERT: r 189 GLN cc_start: 0.9134 (mt0) cc_final: 0.8699 (mt0) REVERT: r 233 ASP cc_start: 0.8385 (p0) cc_final: 0.8184 (p0) REVERT: r 248 GLU cc_start: 0.9258 (tp30) cc_final: 0.8843 (mm-30) REVERT: r 328 ASP cc_start: 0.9364 (m-30) cc_final: 0.9123 (m-30) REVERT: r 390 MET cc_start: 0.8863 (pmm) cc_final: 0.8619 (pmm) REVERT: q 29 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8505 (ptm) REVERT: q 33 ASP cc_start: 0.8998 (m-30) cc_final: 0.8695 (m-30) REVERT: q 186 MET cc_start: 0.8987 (ptm) cc_final: 0.8681 (ppp) REVERT: q 201 ASP cc_start: 0.8928 (p0) cc_final: 0.8625 (p0) REVERT: q 241 GLN cc_start: 0.8832 (pp30) cc_final: 0.8437 (pp30) REVERT: q 248 GLU cc_start: 0.9271 (tp30) cc_final: 0.9045 (mm-30) REVERT: q 264 LEU cc_start: 0.9054 (tm) cc_final: 0.8710 (tt) REVERT: q 333 GLU cc_start: 0.9158 (tp30) cc_final: 0.8919 (mm-30) REVERT: q 360 TYR cc_start: 0.8665 (t80) cc_final: 0.8195 (t80) REVERT: q 387 ILE cc_start: 0.9298 (mm) cc_final: 0.8985 (mt) REVERT: p 67 SER cc_start: 0.9327 (OUTLIER) cc_final: 0.9035 (p) REVERT: p 186 MET cc_start: 0.9189 (ptm) cc_final: 0.8820 (ptt) REVERT: p 248 GLU cc_start: 0.9104 (tp30) cc_final: 0.8588 (mp0) REVERT: p 299 ARG cc_start: 0.8898 (mmm-85) cc_final: 0.8674 (mtm-85) REVERT: p 327 MET cc_start: 0.8921 (ptp) cc_final: 0.8684 (ptm) REVERT: p 334 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8329 (tm-30) REVERT: p 342 GLU cc_start: 0.8718 (mp0) cc_final: 0.8449 (pm20) REVERT: p 378 GLN cc_start: 0.9123 (mt0) cc_final: 0.8869 (mm-40) REVERT: p 396 MET cc_start: 0.9418 (tpp) cc_final: 0.9204 (tpp) REVERT: p 405 MET cc_start: 0.9106 (ttp) cc_final: 0.8829 (ttm) REVERT: o 33 ASP cc_start: 0.8787 (m-30) cc_final: 0.8560 (m-30) REVERT: o 115 LYS cc_start: 0.9069 (tmmt) cc_final: 0.8850 (ptmm) REVERT: o 143 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8716 (t) REVERT: o 210 ASP cc_start: 0.8236 (m-30) cc_final: 0.7772 (t0) REVERT: o 234 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7143 (mp0) REVERT: o 334 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8566 (tm-30) REVERT: o 348 LYS cc_start: 0.9256 (mtmm) cc_final: 0.8871 (ptpp) REVERT: o 396 MET cc_start: 0.9556 (tpp) cc_final: 0.9218 (tpp) REVERT: o 415 MET cc_start: 0.9258 (ttm) cc_final: 0.8944 (ptm) REVERT: n 19 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8576 (mm-30) REVERT: n 67 SER cc_start: 0.9294 (OUTLIER) cc_final: 0.8980 (p) REVERT: n 106 GLU cc_start: 0.7911 (pp20) cc_final: 0.7437 (pp20) REVERT: n 147 MET cc_start: 0.9559 (tpp) cc_final: 0.9128 (mmm) REVERT: n 186 MET cc_start: 0.8698 (ptm) cc_final: 0.8411 (ptp) REVERT: n 292 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8280 (p0) REVERT: n 342 GLU cc_start: 0.8468 (mp0) cc_final: 0.7809 (mp0) REVERT: n 411 ASP cc_start: 0.9283 (m-30) cc_final: 0.8797 (m-30) REVERT: m 21 MET cc_start: 0.8861 (ttm) cc_final: 0.8631 (ttt) REVERT: m 67 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8745 (p) REVERT: m 69 ASP cc_start: 0.8945 (t0) cc_final: 0.8655 (t70) REVERT: m 143 SER cc_start: 0.8965 (OUTLIER) cc_final: 0.8627 (p) REVERT: m 193 GLN cc_start: 0.8702 (tt0) cc_final: 0.8306 (tm-30) REVERT: m 362 ARG cc_start: 0.9195 (ttm110) cc_final: 0.8898 (mtp85) REVERT: m 374 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8026 (tm-30) REVERT: m 378 GLN cc_start: 0.9172 (mt0) cc_final: 0.8649 (mt0) REVERT: m 396 MET cc_start: 0.9156 (tpp) cc_final: 0.8849 (tpp) REVERT: m 400 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9155 (mm) REVERT: l 67 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8820 (p) REVERT: l 69 ASP cc_start: 0.8875 (t0) cc_final: 0.8612 (t0) REVERT: l 125 GLU cc_start: 0.8965 (mp0) cc_final: 0.8748 (mp0) REVERT: l 218 GLU cc_start: 0.8720 (tp30) cc_final: 0.8486 (tp30) REVERT: l 222 LEU cc_start: 0.9113 (mp) cc_final: 0.8673 (mm) REVERT: l 334 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8379 (tm-30) REVERT: l 342 GLU cc_start: 0.8414 (mp0) cc_final: 0.8205 (mt-10) REVERT: l 400 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9204 (mm) REVERT: k 67 SER cc_start: 0.9155 (OUTLIER) cc_final: 0.8540 (p) REVERT: k 69 ASP cc_start: 0.8940 (t0) cc_final: 0.8718 (t0) REVERT: k 218 GLU cc_start: 0.8989 (tp30) cc_final: 0.8502 (tt0) REVERT: k 248 GLU cc_start: 0.8996 (tp30) cc_final: 0.8769 (mm-30) REVERT: k 264 LEU cc_start: 0.8850 (tm) cc_final: 0.8550 (tt) REVERT: k 292 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8150 (p0) REVERT: k 299 ARG cc_start: 0.9161 (mmm-85) cc_final: 0.8932 (mtm-85) REVERT: k 348 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8726 (ptmm) REVERT: k 378 GLN cc_start: 0.8985 (mt0) cc_final: 0.8671 (mt0) REVERT: k 406 THR cc_start: 0.7390 (p) cc_final: 0.7172 (p) REVERT: j 1 MET cc_start: 0.7593 (ttp) cc_final: 0.7386 (ttt) REVERT: j 19 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8428 (mm-30) REVERT: j 67 SER cc_start: 0.9004 (OUTLIER) cc_final: 0.8400 (p) REVERT: j 218 GLU cc_start: 0.8868 (tp30) cc_final: 0.8562 (tt0) REVERT: j 334 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8219 (tm-30) REVERT: j 341 MET cc_start: 0.8881 (tmt) cc_final: 0.8611 (tmm) REVERT: j 411 ASP cc_start: 0.9072 (m-30) cc_final: 0.8760 (m-30) REVERT: i 19 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8292 (mm-30) REVERT: i 67 SER cc_start: 0.9120 (OUTLIER) cc_final: 0.8747 (p) REVERT: i 106 GLU cc_start: 0.7870 (pp20) cc_final: 0.7400 (pp20) REVERT: i 143 SER cc_start: 0.8864 (OUTLIER) cc_final: 0.8568 (t) REVERT: i 197 TYR cc_start: 0.9143 (t80) cc_final: 0.8928 (t80) REVERT: i 272 ARG cc_start: 0.8897 (tpp80) cc_final: 0.8526 (mmm-85) REVERT: i 352 LYS cc_start: 0.7649 (tppp) cc_final: 0.7403 (tptp) REVERT: i 374 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7645 (tm-30) REVERT: i 378 GLN cc_start: 0.8990 (mt0) cc_final: 0.8443 (mt0) REVERT: i 416 MET cc_start: 0.8885 (mmm) cc_final: 0.8681 (mmp) REVERT: h 292 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8457 (p0) REVERT: h 299 ARG cc_start: 0.9177 (mmm-85) cc_final: 0.8871 (mtm-85) REVERT: h 308 GLU cc_start: 0.9020 (tt0) cc_final: 0.8746 (tt0) REVERT: h 326 LYS cc_start: 0.8813 (mppt) cc_final: 0.8579 (ttmm) REVERT: h 333 GLU cc_start: 0.8719 (tp30) cc_final: 0.8509 (mm-30) REVERT: h 342 GLU cc_start: 0.8342 (mp0) cc_final: 0.7736 (mp0) REVERT: h 348 LYS cc_start: 0.9041 (mtmm) cc_final: 0.8668 (ptmm) REVERT: h 411 ASP cc_start: 0.8822 (m-30) cc_final: 0.8596 (m-30) REVERT: g 67 SER cc_start: 0.9273 (OUTLIER) cc_final: 0.8739 (p) REVERT: g 69 ASP cc_start: 0.8808 (t0) cc_final: 0.8488 (m-30) REVERT: g 218 GLU cc_start: 0.8893 (tp30) cc_final: 0.8602 (tt0) REVERT: g 224 LYS cc_start: 0.9264 (ttmm) cc_final: 0.9047 (tppt) REVERT: g 272 ARG cc_start: 0.8985 (tpp80) cc_final: 0.8772 (ttm-80) REVERT: g 292 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8648 (p0) REVERT: g 328 ASP cc_start: 0.8710 (m-30) cc_final: 0.8317 (m-30) REVERT: g 342 GLU cc_start: 0.8203 (mp0) cc_final: 0.7784 (mm-30) REVERT: g 411 ASP cc_start: 0.9153 (m-30) cc_final: 0.8735 (m-30) REVERT: f 67 SER cc_start: 0.9317 (OUTLIER) cc_final: 0.8871 (t) REVERT: e 67 SER cc_start: 0.9162 (OUTLIER) cc_final: 0.8663 (p) REVERT: e 69 ASP cc_start: 0.8952 (t0) cc_final: 0.8643 (t0) REVERT: e 70 SER cc_start: 0.9097 (t) cc_final: 0.8743 (m) REVERT: e 87 ARG cc_start: 0.9288 (mtm110) cc_final: 0.9035 (ttp80) REVERT: e 143 SER cc_start: 0.8871 (OUTLIER) cc_final: 0.8593 (t) REVERT: e 197 TYR cc_start: 0.9099 (t80) cc_final: 0.8899 (t80) REVERT: e 292 ASN cc_start: 0.9238 (OUTLIER) cc_final: 0.8808 (p0) REVERT: e 341 MET cc_start: 0.8633 (tmt) cc_final: 0.8369 (tmm) REVERT: e 405 MET cc_start: 0.8677 (ttp) cc_final: 0.8413 (ttm) REVERT: d 8 ASN cc_start: 0.9402 (t0) cc_final: 0.9086 (t0) REVERT: d 12 SER cc_start: 0.9378 (m) cc_final: 0.9056 (p) REVERT: d 21 MET cc_start: 0.9293 (ttm) cc_final: 0.8978 (ttt) REVERT: d 67 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8919 (t) REVERT: d 189 GLN cc_start: 0.9141 (mt0) cc_final: 0.8609 (mt0) REVERT: d 211 GLU cc_start: 0.8943 (tp30) cc_final: 0.8640 (tp30) REVERT: d 292 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8485 (p0) REVERT: d 327 MET cc_start: 0.8709 (ptp) cc_final: 0.8504 (ptm) REVERT: d 352 LYS cc_start: 0.8060 (tppp) cc_final: 0.7806 (tptp) REVERT: d 362 ARG cc_start: 0.9199 (ttm110) cc_final: 0.8997 (mtp85) REVERT: d 405 MET cc_start: 0.8263 (ttp) cc_final: 0.8028 (ttm) REVERT: d 406 THR cc_start: 0.7624 (p) cc_final: 0.6949 (p) REVERT: c 8 ASN cc_start: 0.9444 (t0) cc_final: 0.9219 (m-40) REVERT: c 12 SER cc_start: 0.9242 (m) cc_final: 0.8967 (p) REVERT: c 19 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8811 (mm-30) REVERT: c 67 SER cc_start: 0.9043 (OUTLIER) cc_final: 0.8476 (p) REVERT: c 186 MET cc_start: 0.8667 (ptm) cc_final: 0.8249 (ptt) REVERT: c 197 TYR cc_start: 0.9095 (t80) cc_final: 0.8833 (t80) REVERT: c 248 GLU cc_start: 0.9158 (tp30) cc_final: 0.8877 (mm-30) REVERT: c 272 ARG cc_start: 0.8932 (tpp80) cc_final: 0.8683 (ttm-80) REVERT: c 334 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8514 (tm-30) REVERT: c 397 GLU cc_start: 0.8502 (pp20) cc_final: 0.8267 (pp20) REVERT: c 411 ASP cc_start: 0.8996 (m-30) cc_final: 0.8291 (t70) REVERT: c 414 GLU cc_start: 0.8819 (pp20) cc_final: 0.8572 (pp20) REVERT: b 143 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8270 (p) REVERT: b 181 LYS cc_start: 0.9442 (mtpp) cc_final: 0.9212 (mmmt) REVERT: b 193 GLN cc_start: 0.8654 (tt0) cc_final: 0.8305 (tm-30) REVERT: b 218 GLU cc_start: 0.8978 (tp30) cc_final: 0.8372 (tp30) REVERT: b 219 MET cc_start: 0.9291 (mmm) cc_final: 0.9072 (mmm) REVERT: b 245 MET cc_start: 0.9303 (tpp) cc_final: 0.9052 (mmm) REVERT: b 292 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8411 (p0) REVERT: b 334 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8383 (tm-30) outliers start: 199 outliers final: 96 residues processed: 1544 average time/residue: 0.6148 time to fit residues: 1536.6051 Evaluate side-chains 1173 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1050 time to evaluate : 5.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 89 PHE Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 29 MET Chi-restraints excluded: chain r residue 89 PHE Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 292 ASN Chi-restraints excluded: chain q residue 29 MET Chi-restraints excluded: chain q residue 89 PHE Chi-restraints excluded: chain q residue 292 ASN Chi-restraints excluded: chain q residue 381 TRP Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 29 MET Chi-restraints excluded: chain p residue 60 ASP Chi-restraints excluded: chain p residue 67 SER Chi-restraints excluded: chain p residue 89 PHE Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 131 ILE Chi-restraints excluded: chain p residue 381 TRP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 89 PHE Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 131 ILE Chi-restraints excluded: chain o residue 143 SER Chi-restraints excluded: chain o residue 381 TRP Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 67 SER Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 131 ILE Chi-restraints excluded: chain n residue 292 ASN Chi-restraints excluded: chain n residue 381 TRP Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 143 SER Chi-restraints excluded: chain m residue 292 ASN Chi-restraints excluded: chain m residue 381 TRP Chi-restraints excluded: chain m residue 400 ILE Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 89 PHE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 292 ASN Chi-restraints excluded: chain l residue 381 TRP Chi-restraints excluded: chain l residue 400 ILE Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 67 SER Chi-restraints excluded: chain k residue 89 PHE Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 131 ILE Chi-restraints excluded: chain k residue 292 ASN Chi-restraints excluded: chain k residue 381 TRP Chi-restraints excluded: chain j residue 67 SER Chi-restraints excluded: chain j residue 89 PHE Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 131 ILE Chi-restraints excluded: chain j residue 292 ASN Chi-restraints excluded: chain j residue 381 TRP Chi-restraints excluded: chain j residue 400 ILE Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 67 SER Chi-restraints excluded: chain i residue 89 PHE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 143 SER Chi-restraints excluded: chain i residue 292 ASN Chi-restraints excluded: chain i residue 381 TRP Chi-restraints excluded: chain i residue 400 ILE Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 89 PHE Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 131 ILE Chi-restraints excluded: chain h residue 292 ASN Chi-restraints excluded: chain h residue 381 TRP Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 292 ASN Chi-restraints excluded: chain g residue 381 TRP Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 67 SER Chi-restraints excluded: chain f residue 89 PHE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 131 ILE Chi-restraints excluded: chain f residue 143 SER Chi-restraints excluded: chain f residue 292 ASN Chi-restraints excluded: chain f residue 381 TRP Chi-restraints excluded: chain f residue 400 ILE Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 67 SER Chi-restraints excluded: chain e residue 89 PHE Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 143 SER Chi-restraints excluded: chain e residue 292 ASN Chi-restraints excluded: chain e residue 381 TRP Chi-restraints excluded: chain e residue 400 ILE Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 29 MET Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 89 PHE Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 292 ASN Chi-restraints excluded: chain d residue 381 TRP Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 67 SER Chi-restraints excluded: chain c residue 89 PHE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 131 ILE Chi-restraints excluded: chain c residue 292 ASN Chi-restraints excluded: chain c residue 381 TRP Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 131 ILE Chi-restraints excluded: chain b residue 143 SER Chi-restraints excluded: chain b residue 292 ASN Chi-restraints excluded: chain b residue 381 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 623 optimal weight: 4.9990 chunk 559 optimal weight: 0.9980 chunk 310 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 377 optimal weight: 0.9980 chunk 298 optimal weight: 9.9990 chunk 578 optimal weight: 7.9990 chunk 223 optimal weight: 9.9990 chunk 351 optimal weight: 0.6980 chunk 430 optimal weight: 4.9990 chunk 670 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 220 GLN ** r 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 388 HIS ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 172 GLN ** p 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 374 GLN ** o 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 292 ASN ** n 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 90 ASN n 193 GLN n 275 ASN n 295 HIS ** m 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 275 ASN ** k 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 189 GLN h 220 GLN ** h 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 189 GLN ** g 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 193 GLN e 374 GLN d 220 GLN d 374 GLN c 42 HIS c 59 GLN ** c 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 60822 Z= 0.226 Angle : 0.628 7.583 82008 Z= 0.295 Chirality : 0.041 0.152 9324 Planarity : 0.004 0.040 10620 Dihedral : 7.394 172.829 8589 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 5.60 % Allowed : 30.06 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.35 (0.10), residues: 7506 helix: 1.57 (0.09), residues: 3456 sheet: 1.09 (0.15), residues: 1224 loop : 0.06 (0.11), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP a 381 HIS 0.008 0.001 HIS n 295 PHE 0.010 0.001 PHE d 412 TYR 0.019 0.002 TYR m 197 ARG 0.007 0.000 ARG o 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1430 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 363 poor density : 1067 time to evaluate : 5.546 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: a 29 MET cc_start: 0.7931 (ptp) cc_final: 0.7521 (ptp) REVERT: a 30 ARG cc_start: 0.7538 (mmm160) cc_final: 0.6849 (mtp85) REVERT: a 92 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8350 (mmt180) REVERT: a 110 TYR cc_start: 0.8252 (m-10) cc_final: 0.7973 (m-80) REVERT: a 197 TYR cc_start: 0.8977 (t80) cc_final: 0.8709 (t80) REVERT: a 218 GLU cc_start: 0.9339 (tp30) cc_final: 0.9018 (tp30) REVERT: a 265 ASP cc_start: 0.8369 (t70) cc_final: 0.8109 (p0) REVERT: a 274 TYR cc_start: 0.8913 (m-10) cc_final: 0.8707 (m-80) REVERT: a 374 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7931 (tm-30) REVERT: r 21 MET cc_start: 0.9156 (ttm) cc_final: 0.8777 (ttt) REVERT: r 85 GLN cc_start: 0.8683 (mp10) cc_final: 0.8186 (mp10) REVERT: r 132 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8553 (mt) REVERT: r 248 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8871 (mm-30) REVERT: r 259 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8383 (m-30) REVERT: r 328 ASP cc_start: 0.9112 (m-30) cc_final: 0.8860 (m-30) REVERT: r 396 MET cc_start: 0.9189 (tpt) cc_final: 0.8709 (tpp) REVERT: q 33 ASP cc_start: 0.9018 (m-30) cc_final: 0.8711 (m-30) REVERT: q 172 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8875 (tp40) REVERT: q 201 ASP cc_start: 0.8926 (p0) cc_final: 0.8623 (p0) REVERT: q 241 GLN cc_start: 0.8888 (pp30) cc_final: 0.8577 (pp30) REVERT: q 244 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8451 (mm-30) REVERT: q 248 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.8947 (mm-30) REVERT: q 264 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8732 (tt) REVERT: q 333 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8920 (mm-30) REVERT: q 360 TYR cc_start: 0.8825 (t80) cc_final: 0.8438 (t80) REVERT: q 412 PHE cc_start: 0.8902 (t80) cc_final: 0.8636 (t80) REVERT: p 5 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.9068 (pm20) REVERT: p 60 ASP cc_start: 0.8619 (m-30) cc_final: 0.8412 (m-30) REVERT: p 106 GLU cc_start: 0.7405 (pp20) cc_final: 0.6771 (pm20) REVERT: p 186 MET cc_start: 0.9233 (ptm) cc_final: 0.8973 (ptt) REVERT: p 248 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8703 (mp0) REVERT: p 259 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: p 334 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8265 (tm-30) REVERT: p 342 GLU cc_start: 0.8765 (mp0) cc_final: 0.8418 (mp0) REVERT: p 374 GLN cc_start: 0.8790 (tm130) cc_final: 0.8488 (tm-30) REVERT: p 378 GLN cc_start: 0.9291 (mt0) cc_final: 0.9040 (mm-40) REVERT: o 5 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8641 (pm20) REVERT: o 29 MET cc_start: 0.8487 (ptm) cc_final: 0.8156 (ptp) REVERT: o 33 ASP cc_start: 0.8725 (m-30) cc_final: 0.8481 (m-30) REVERT: o 110 TYR cc_start: 0.9012 (m-10) cc_final: 0.8811 (m-80) REVERT: o 115 LYS cc_start: 0.9127 (tmmt) cc_final: 0.8861 (ptmm) REVERT: o 210 ASP cc_start: 0.8339 (m-30) cc_final: 0.7810 (t0) REVERT: o 234 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7279 (mp0) REVERT: o 244 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8183 (mm-30) REVERT: o 248 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8556 (mp0) REVERT: o 334 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8611 (tm-30) REVERT: o 415 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8863 (ptm) REVERT: n 5 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8736 (pm20) REVERT: n 40 LYS cc_start: 0.9151 (ttpt) cc_final: 0.8837 (ttmm) REVERT: n 59 GLN cc_start: 0.8367 (tp-100) cc_final: 0.8145 (tp40) REVERT: n 147 MET cc_start: 0.9526 (tpp) cc_final: 0.8898 (mmm) REVERT: n 186 MET cc_start: 0.8779 (ptm) cc_final: 0.8441 (ptp) REVERT: n 326 LYS cc_start: 0.8632 (tptp) cc_final: 0.8236 (tptp) REVERT: n 342 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: n 411 ASP cc_start: 0.9130 (m-30) cc_final: 0.8891 (m-30) REVERT: m 5 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8972 (pm20) REVERT: m 21 MET cc_start: 0.8772 (ttm) cc_final: 0.8492 (ttt) REVERT: m 67 SER cc_start: 0.9102 (m) cc_final: 0.8769 (p) REVERT: m 69 ASP cc_start: 0.9001 (t0) cc_final: 0.8720 (t70) REVERT: m 226 GLU cc_start: 0.8425 (tp30) cc_final: 0.8059 (tt0) REVERT: m 259 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8692 (m-30) REVERT: m 342 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8646 (mt-10) REVERT: m 374 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8498 (tm-30) REVERT: m 405 MET cc_start: 0.9095 (ttp) cc_final: 0.8792 (ptp) REVERT: m 406 THR cc_start: 0.7801 (p) cc_final: 0.7539 (p) REVERT: m 411 ASP cc_start: 0.9317 (m-30) cc_final: 0.8649 (m-30) REVERT: l 5 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.9033 (pm20) REVERT: l 69 ASP cc_start: 0.8977 (t0) cc_final: 0.8730 (t0) REVERT: l 92 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7664 (pmm-80) REVERT: l 125 GLU cc_start: 0.9028 (mp0) cc_final: 0.8733 (mp0) REVERT: l 218 GLU cc_start: 0.8747 (tp30) cc_final: 0.8513 (tp30) REVERT: l 222 LEU cc_start: 0.9151 (mp) cc_final: 0.8767 (mm) REVERT: l 334 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8354 (tm-30) REVERT: l 342 GLU cc_start: 0.8489 (mp0) cc_final: 0.8252 (mt-10) REVERT: l 374 GLN cc_start: 0.8710 (tp40) cc_final: 0.8334 (tm-30) REVERT: l 416 MET cc_start: 0.9372 (mmp) cc_final: 0.9060 (mmp) REVERT: k 152 ASP cc_start: 0.7208 (t0) cc_final: 0.6624 (t0) REVERT: k 218 GLU cc_start: 0.8978 (tp30) cc_final: 0.8576 (tt0) REVERT: k 259 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8449 (m-30) REVERT: k 264 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8459 (tt) REVERT: k 374 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8178 (tm-30) REVERT: k 378 GLN cc_start: 0.9270 (mt0) cc_final: 0.8847 (mt0) REVERT: j 5 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8877 (pm20) REVERT: j 19 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8404 (mm-30) REVERT: j 67 SER cc_start: 0.9019 (m) cc_final: 0.8629 (p) REVERT: j 218 GLU cc_start: 0.8906 (tp30) cc_final: 0.8628 (tt0) REVERT: j 342 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: j 397 GLU cc_start: 0.8912 (pt0) cc_final: 0.8456 (pp20) REVERT: j 411 ASP cc_start: 0.9092 (m-30) cc_final: 0.8806 (m-30) REVERT: i 5 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8731 (pm20) REVERT: i 13 GLU cc_start: 0.8760 (pm20) cc_final: 0.8509 (pm20) REVERT: i 19 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8310 (mm-30) REVERT: i 67 SER cc_start: 0.9157 (m) cc_final: 0.8815 (p) REVERT: i 92 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7989 (pmm-80) REVERT: i 272 ARG cc_start: 0.8964 (tpp80) cc_final: 0.8689 (mmm-85) REVERT: i 342 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8184 (mt-10) REVERT: i 352 LYS cc_start: 0.7862 (tppp) cc_final: 0.7487 (tptp) REVERT: i 374 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7974 (tm-30) REVERT: i 378 GLN cc_start: 0.9061 (mt0) cc_final: 0.8433 (mt0) REVERT: i 416 MET cc_start: 0.8978 (mmm) cc_final: 0.8762 (mmp) REVERT: h 5 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8421 (pm20) REVERT: h 106 GLU cc_start: 0.8372 (pm20) cc_final: 0.8020 (pm20) REVERT: h 226 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: h 308 GLU cc_start: 0.9037 (tt0) cc_final: 0.8772 (tt0) REVERT: h 326 LYS cc_start: 0.8828 (mppt) cc_final: 0.8609 (ttmm) REVERT: h 333 GLU cc_start: 0.8742 (tp30) cc_final: 0.8523 (mm-30) REVERT: h 342 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: h 411 ASP cc_start: 0.8915 (m-30) cc_final: 0.8350 (m-30) REVERT: h 414 GLU cc_start: 0.8647 (pp20) cc_final: 0.8339 (pp20) REVERT: g 5 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8885 (pm20) REVERT: g 67 SER cc_start: 0.9234 (m) cc_final: 0.8857 (p) REVERT: g 92 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8005 (pmm-80) REVERT: g 106 GLU cc_start: 0.8157 (pp20) cc_final: 0.7877 (pp20) REVERT: g 292 ASN cc_start: 0.9030 (m110) cc_final: 0.8688 (p0) REVERT: g 327 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8506 (ptm) REVERT: e 30 ARG cc_start: 0.7801 (mmm-85) cc_final: 0.7522 (mmm-85) REVERT: e 58 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8899 (mt) REVERT: e 67 SER cc_start: 0.9115 (m) cc_final: 0.8846 (p) REVERT: e 92 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.8061 (pmm-80) REVERT: e 292 ASN cc_start: 0.9275 (m110) cc_final: 0.8852 (p0) REVERT: e 341 MET cc_start: 0.8688 (tmt) cc_final: 0.8355 (tmm) REVERT: e 347 ARG cc_start: 0.8285 (tpt-90) cc_final: 0.8070 (tpt-90) REVERT: d 8 ASN cc_start: 0.9393 (t0) cc_final: 0.9085 (t0) REVERT: d 12 SER cc_start: 0.9376 (m) cc_final: 0.9061 (p) REVERT: d 21 MET cc_start: 0.9237 (ttm) cc_final: 0.8986 (ttt) REVERT: d 211 GLU cc_start: 0.8918 (tp30) cc_final: 0.8658 (tp30) REVERT: d 264 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8494 (tt) REVERT: d 342 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7914 (mm-30) REVERT: d 352 LYS cc_start: 0.8211 (tppp) cc_final: 0.7829 (tptp) REVERT: d 362 ARG cc_start: 0.9201 (ttm110) cc_final: 0.8710 (ttm110) REVERT: c 8 ASN cc_start: 0.9472 (t0) cc_final: 0.9211 (m-40) REVERT: c 12 SER cc_start: 0.9267 (m) cc_final: 0.8960 (p) REVERT: c 19 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8782 (mm-30) REVERT: c 67 SER cc_start: 0.9017 (m) cc_final: 0.8644 (p) REVERT: c 197 TYR cc_start: 0.9133 (t80) cc_final: 0.8616 (t80) REVERT: c 244 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8084 (mm-30) REVERT: c 248 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8972 (mm-30) REVERT: c 272 ARG cc_start: 0.8933 (tpp80) cc_final: 0.8610 (ttm-80) REVERT: c 294 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9138 (tp) REVERT: c 334 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8513 (tm-30) REVERT: c 374 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7832 (tm-30) REVERT: c 396 MET cc_start: 0.9124 (tpp) cc_final: 0.8881 (tpp) REVERT: c 397 GLU cc_start: 0.8561 (pp20) cc_final: 0.8282 (pp20) REVERT: c 411 ASP cc_start: 0.9091 (m-30) cc_final: 0.8705 (m-30) REVERT: b 8 ASN cc_start: 0.9200 (t0) cc_final: 0.8819 (t0) REVERT: b 193 GLN cc_start: 0.8657 (tt0) cc_final: 0.8377 (tm-30) REVERT: b 218 GLU cc_start: 0.9000 (tp30) cc_final: 0.8599 (tp30) REVERT: b 219 MET cc_start: 0.9305 (mmm) cc_final: 0.9053 (mmm) REVERT: b 248 GLU cc_start: 0.9375 (OUTLIER) cc_final: 0.9134 (mm-30) REVERT: b 264 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8610 (tt) REVERT: b 326 LYS cc_start: 0.8872 (ttmm) cc_final: 0.8449 (tptp) REVERT: b 334 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8360 (tm-30) REVERT: b 352 LYS cc_start: 0.7838 (tppp) cc_final: 0.7340 (tptm) outliers start: 363 outliers final: 158 residues processed: 1328 average time/residue: 0.5896 time to fit residues: 1299.0721 Evaluate side-chains 1174 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 976 time to evaluate : 5.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 12 SER Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 89 PHE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 153 SER Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 390 MET Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 58 LEU Chi-restraints excluded: chain r residue 89 PHE Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 132 LEU Chi-restraints excluded: chain r residue 153 SER Chi-restraints excluded: chain r residue 216 VAL Chi-restraints excluded: chain r residue 248 GLU Chi-restraints excluded: chain r residue 259 ASP Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 58 LEU Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain q residue 89 PHE Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 137 THR Chi-restraints excluded: chain q residue 172 GLN Chi-restraints excluded: chain q residue 194 SER Chi-restraints excluded: chain q residue 242 VAL Chi-restraints excluded: chain q residue 248 GLU Chi-restraints excluded: chain q residue 264 LEU Chi-restraints excluded: chain q residue 333 GLU Chi-restraints excluded: chain p residue 5 GLU Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 58 LEU Chi-restraints excluded: chain p residue 89 PHE Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 242 VAL Chi-restraints excluded: chain p residue 248 GLU Chi-restraints excluded: chain p residue 259 ASP Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 58 LEU Chi-restraints excluded: chain o residue 89 PHE Chi-restraints excluded: chain o residue 92 ARG Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 216 VAL Chi-restraints excluded: chain o residue 248 GLU Chi-restraints excluded: chain o residue 264 LEU Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 390 MET Chi-restraints excluded: chain o residue 400 ILE Chi-restraints excluded: chain o residue 415 MET Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 29 MET Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 342 GLU Chi-restraints excluded: chain n residue 390 MET Chi-restraints excluded: chain n residue 400 ILE Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 5 GLU Chi-restraints excluded: chain m residue 6 LEU Chi-restraints excluded: chain m residue 49 ILE Chi-restraints excluded: chain m residue 60 ASP Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 259 ASP Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 5 GLU Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 58 LEU Chi-restraints excluded: chain l residue 60 ASP Chi-restraints excluded: chain l residue 89 PHE Chi-restraints excluded: chain l residue 92 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 132 LEU Chi-restraints excluded: chain l residue 216 VAL Chi-restraints excluded: chain l residue 242 VAL Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 89 PHE Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 216 VAL Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 259 ASP Chi-restraints excluded: chain k residue 264 LEU Chi-restraints excluded: chain j residue 5 GLU Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 49 ILE Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 89 PHE Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 242 VAL Chi-restraints excluded: chain j residue 342 GLU Chi-restraints excluded: chain j residue 383 LEU Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 5 GLU Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 89 PHE Chi-restraints excluded: chain i residue 92 ARG Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain i residue 216 VAL Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain i residue 417 LYS Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 5 GLU Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 49 ILE Chi-restraints excluded: chain h residue 52 ASP Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 89 PHE Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 216 VAL Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 342 GLU Chi-restraints excluded: chain h residue 354 VAL Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 5 GLU Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 52 ASP Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 327 MET Chi-restraints excluded: chain g residue 394 ASP Chi-restraints excluded: chain g residue 417 LYS Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 60 ASP Chi-restraints excluded: chain f residue 89 PHE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 52 ASP Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 89 PHE Chi-restraints excluded: chain e residue 92 ARG Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 216 VAL Chi-restraints excluded: chain e residue 354 VAL Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 60 ASP Chi-restraints excluded: chain d residue 89 PHE Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain d residue 241 GLN Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 264 LEU Chi-restraints excluded: chain d residue 342 GLU Chi-restraints excluded: chain d residue 354 VAL Chi-restraints excluded: chain d residue 400 ILE Chi-restraints excluded: chain d residue 415 MET Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 6 LEU Chi-restraints excluded: chain c residue 39 LEU Chi-restraints excluded: chain c residue 89 PHE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 248 GLU Chi-restraints excluded: chain c residue 294 LEU Chi-restraints excluded: chain c residue 383 LEU Chi-restraints excluded: chain c residue 400 ILE Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 101 ILE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 153 SER Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 248 GLU Chi-restraints excluded: chain b residue 264 LEU Chi-restraints excluded: chain b residue 394 ASP Chi-restraints excluded: chain b residue 397 GLU Chi-restraints excluded: chain b residue 410 ASP Chi-restraints excluded: chain b residue 415 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 372 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 557 optimal weight: 0.9980 chunk 456 optimal weight: 2.9990 chunk 184 optimal weight: 0.0770 chunk 671 optimal weight: 0.0270 chunk 725 optimal weight: 20.0000 chunk 597 optimal weight: 6.9990 chunk 665 optimal weight: 0.0370 chunk 228 optimal weight: 5.9990 chunk 538 optimal weight: 1.9990 overall best weight: 0.6276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: r 198 ASN r 220 GLN r 292 ASN r 378 GLN ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 220 GLN ** o 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 275 ASN ** n 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 295 HIS ** m 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 275 ASN k 90 ASN ** k 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 220 GLN ** h 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 32 GLN g 189 GLN g 193 GLN f 292 ASN f 374 GLN e 374 GLN d 90 ASN d 193 GLN d 275 ASN c 59 GLN c 374 GLN b 374 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 60822 Z= 0.147 Angle : 0.580 9.642 82008 Z= 0.272 Chirality : 0.040 0.159 9324 Planarity : 0.003 0.036 10620 Dihedral : 6.963 176.558 8454 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.60 % Allowed : 29.44 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.41 (0.10), residues: 7506 helix: 1.66 (0.09), residues: 3474 sheet: 1.14 (0.15), residues: 1224 loop : 0.02 (0.11), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP a 381 HIS 0.007 0.000 HIS n 295 PHE 0.015 0.001 PHE r 412 TYR 0.020 0.001 TYR n 197 ARG 0.007 0.000 ARG h 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1383 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1085 time to evaluate : 5.530 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: a 21 MET cc_start: 0.8450 (ttt) cc_final: 0.8030 (ttt) REVERT: a 29 MET cc_start: 0.8097 (ptp) cc_final: 0.7746 (ptp) REVERT: a 30 ARG cc_start: 0.7381 (mmm160) cc_final: 0.6944 (mtp85) REVERT: a 92 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8369 (mmt180) REVERT: a 110 TYR cc_start: 0.8219 (m-10) cc_final: 0.7942 (m-80) REVERT: a 132 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7862 (tp) REVERT: a 197 TYR cc_start: 0.8991 (t80) cc_final: 0.8741 (t80) REVERT: a 218 GLU cc_start: 0.9311 (tp30) cc_final: 0.9007 (tp30) REVERT: a 274 TYR cc_start: 0.8912 (m-10) cc_final: 0.8673 (m-80) REVERT: a 334 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8714 (mp0) REVERT: r 21 MET cc_start: 0.9092 (ttm) cc_final: 0.8805 (ttt) REVERT: r 85 GLN cc_start: 0.8704 (mp10) cc_final: 0.8165 (mp10) REVERT: r 132 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8587 (mt) REVERT: r 197 TYR cc_start: 0.8096 (t80) cc_final: 0.7799 (t80) REVERT: r 198 ASN cc_start: 0.9333 (OUTLIER) cc_final: 0.9104 (m110) REVERT: r 248 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8850 (mm-30) REVERT: r 328 ASP cc_start: 0.9160 (m-30) cc_final: 0.8817 (m-30) REVERT: r 390 MET cc_start: 0.8459 (pmm) cc_final: 0.8239 (pmm) REVERT: r 396 MET cc_start: 0.9241 (tpt) cc_final: 0.8778 (tpp) REVERT: q 29 MET cc_start: 0.8696 (ptm) cc_final: 0.8106 (ptp) REVERT: q 33 ASP cc_start: 0.8962 (m-30) cc_final: 0.8647 (m-30) REVERT: q 172 GLN cc_start: 0.9013 (tp40) cc_final: 0.8705 (tp40) REVERT: q 201 ASP cc_start: 0.8922 (p0) cc_final: 0.8625 (p0) REVERT: q 241 GLN cc_start: 0.8867 (pp30) cc_final: 0.8556 (pp30) REVERT: q 264 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8714 (tt) REVERT: q 333 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8920 (mm-30) REVERT: q 334 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8540 (tm-30) REVERT: q 360 TYR cc_start: 0.8903 (t80) cc_final: 0.8512 (t80) REVERT: p 60 ASP cc_start: 0.8635 (m-30) cc_final: 0.8428 (m-30) REVERT: p 172 GLN cc_start: 0.9224 (mm-40) cc_final: 0.8931 (mm-40) REVERT: p 186 MET cc_start: 0.9214 (ptm) cc_final: 0.8980 (ptt) REVERT: p 193 GLN cc_start: 0.9096 (tt0) cc_final: 0.8671 (tm-30) REVERT: p 244 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8270 (mm-30) REVERT: p 248 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8684 (mp0) REVERT: p 333 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8911 (mm-30) REVERT: p 334 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8271 (tm-30) REVERT: p 341 MET cc_start: 0.9071 (tmm) cc_final: 0.8838 (ppp) REVERT: p 342 GLU cc_start: 0.8786 (mp0) cc_final: 0.8414 (mp0) REVERT: o 5 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8638 (pm20) REVERT: o 30 ARG cc_start: 0.7749 (mmm-85) cc_final: 0.7518 (mmm-85) REVERT: o 33 ASP cc_start: 0.8693 (m-30) cc_final: 0.8491 (m-30) REVERT: o 105 LYS cc_start: 0.8563 (tmmt) cc_final: 0.8116 (tmmt) REVERT: o 115 LYS cc_start: 0.9141 (tmmt) cc_final: 0.8852 (ptmm) REVERT: o 197 TYR cc_start: 0.9493 (t80) cc_final: 0.9256 (t80) REVERT: o 210 ASP cc_start: 0.8309 (m-30) cc_final: 0.7729 (t0) REVERT: o 218 GLU cc_start: 0.9103 (tp30) cc_final: 0.8807 (tp30) REVERT: o 234 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7279 (mp0) REVERT: o 244 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8091 (mm-30) REVERT: o 248 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: o 274 TYR cc_start: 0.9235 (m-80) cc_final: 0.8878 (m-80) REVERT: o 333 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8363 (mp0) REVERT: o 334 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8608 (tm-30) REVERT: n 5 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8741 (pm20) REVERT: n 19 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8576 (mm-30) REVERT: n 40 LYS cc_start: 0.9133 (ttpt) cc_final: 0.8805 (ttmm) REVERT: n 59 GLN cc_start: 0.8419 (tp-100) cc_final: 0.8121 (tp-100) REVERT: n 147 MET cc_start: 0.9527 (tpp) cc_final: 0.8895 (mmm) REVERT: n 326 LYS cc_start: 0.8598 (tptp) cc_final: 0.8188 (tptp) REVERT: n 342 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: n 360 TYR cc_start: 0.9079 (t80) cc_final: 0.8868 (t80) REVERT: n 411 ASP cc_start: 0.9135 (m-30) cc_final: 0.8889 (m-30) REVERT: n 417 LYS cc_start: 0.9387 (pttt) cc_final: 0.9060 (tppt) REVERT: m 21 MET cc_start: 0.8751 (ttm) cc_final: 0.8468 (ttt) REVERT: m 67 SER cc_start: 0.9138 (m) cc_final: 0.8798 (p) REVERT: m 69 ASP cc_start: 0.8988 (t0) cc_final: 0.8709 (t70) REVERT: m 226 GLU cc_start: 0.8479 (tp30) cc_final: 0.8148 (tt0) REVERT: m 259 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8662 (m-30) REVERT: m 327 MET cc_start: 0.8793 (ptm) cc_final: 0.8510 (ttp) REVERT: m 406 THR cc_start: 0.7784 (p) cc_final: 0.7498 (p) REVERT: l 5 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.9008 (pm20) REVERT: l 69 ASP cc_start: 0.8952 (t0) cc_final: 0.8718 (t0) REVERT: l 92 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7629 (pmm-80) REVERT: l 125 GLU cc_start: 0.9021 (mp0) cc_final: 0.8803 (mp0) REVERT: l 218 GLU cc_start: 0.8741 (tp30) cc_final: 0.8503 (tp30) REVERT: l 222 LEU cc_start: 0.9177 (mp) cc_final: 0.8730 (mm) REVERT: l 342 GLU cc_start: 0.8487 (mp0) cc_final: 0.8250 (mt-10) REVERT: k 152 ASP cc_start: 0.7154 (t0) cc_final: 0.6687 (t70) REVERT: k 218 GLU cc_start: 0.8954 (tp30) cc_final: 0.8559 (tt0) REVERT: k 244 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8206 (mm-30) REVERT: k 259 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8442 (m-30) REVERT: k 264 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8483 (tt) REVERT: k 348 LYS cc_start: 0.8950 (mtmm) cc_final: 0.8703 (ptmm) REVERT: k 374 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8187 (tm-30) REVERT: k 378 GLN cc_start: 0.9285 (mt0) cc_final: 0.8903 (mt0) REVERT: j 19 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8375 (mm-30) REVERT: j 67 SER cc_start: 0.9001 (m) cc_final: 0.8590 (p) REVERT: j 218 GLU cc_start: 0.8908 (tp30) cc_final: 0.8644 (tt0) REVERT: j 326 LYS cc_start: 0.8322 (tmmt) cc_final: 0.8089 (tmmt) REVERT: j 397 GLU cc_start: 0.8851 (pt0) cc_final: 0.8513 (mt-10) REVERT: j 411 ASP cc_start: 0.9097 (m-30) cc_final: 0.8827 (m-30) REVERT: i 5 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8733 (pm20) REVERT: i 13 GLU cc_start: 0.8834 (pm20) cc_final: 0.8566 (pm20) REVERT: i 19 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8344 (mm-30) REVERT: i 67 SER cc_start: 0.9150 (m) cc_final: 0.8776 (p) REVERT: i 106 GLU cc_start: 0.7665 (pp20) cc_final: 0.7392 (pp20) REVERT: i 272 ARG cc_start: 0.8887 (tpp80) cc_final: 0.8656 (mmm-85) REVERT: i 352 LYS cc_start: 0.7935 (tppp) cc_final: 0.7682 (tptp) REVERT: i 374 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7857 (tm-30) REVERT: i 378 GLN cc_start: 0.9058 (mt0) cc_final: 0.8422 (mt0) REVERT: h 5 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8393 (pm20) REVERT: h 226 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: h 259 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8420 (m-30) REVERT: h 299 ARG cc_start: 0.9107 (mmm-85) cc_final: 0.8869 (mtm-85) REVERT: h 308 GLU cc_start: 0.9001 (tt0) cc_final: 0.8755 (tt0) REVERT: h 326 LYS cc_start: 0.8834 (mppt) cc_final: 0.8596 (ttmm) REVERT: h 333 GLU cc_start: 0.8740 (tp30) cc_final: 0.8526 (mm-30) REVERT: h 342 GLU cc_start: 0.8433 (mp0) cc_final: 0.7698 (mp0) REVERT: h 348 LYS cc_start: 0.9045 (mtmm) cc_final: 0.8664 (ptmm) REVERT: h 362 ARG cc_start: 0.9405 (ttm110) cc_final: 0.9167 (mtm-85) REVERT: h 411 ASP cc_start: 0.8904 (m-30) cc_final: 0.8548 (m-30) REVERT: g 5 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8869 (pm20) REVERT: g 8 ASN cc_start: 0.8963 (m-40) cc_final: 0.8762 (m-40) REVERT: g 67 SER cc_start: 0.9255 (m) cc_final: 0.8825 (p) REVERT: g 92 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7978 (pmm-80) REVERT: g 145 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8569 (mt) REVERT: g 272 ARG cc_start: 0.8961 (tpp80) cc_final: 0.8736 (ttm110) REVERT: g 292 ASN cc_start: 0.8968 (m110) cc_final: 0.8627 (p0) REVERT: g 327 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8348 (ptm) REVERT: g 342 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7782 (mm-30) REVERT: f 244 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8400 (mm-30) REVERT: e 58 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8899 (mt) REVERT: e 67 SER cc_start: 0.9144 (m) cc_final: 0.8845 (p) REVERT: e 292 ASN cc_start: 0.9213 (m110) cc_final: 0.8799 (p0) REVERT: e 333 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8524 (tp30) REVERT: e 341 MET cc_start: 0.8708 (tmt) cc_final: 0.8251 (tmm) REVERT: e 347 ARG cc_start: 0.8264 (tpt-90) cc_final: 0.8050 (tpt-90) REVERT: d 8 ASN cc_start: 0.9369 (t0) cc_final: 0.9069 (t0) REVERT: d 12 SER cc_start: 0.9327 (m) cc_final: 0.8995 (p) REVERT: d 21 MET cc_start: 0.9201 (ttm) cc_final: 0.8972 (ttt) REVERT: d 211 GLU cc_start: 0.8857 (tp30) cc_final: 0.8631 (tp30) REVERT: d 264 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8409 (tt) REVERT: d 329 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8588 (mm-30) REVERT: d 333 GLU cc_start: 0.9003 (tp30) cc_final: 0.8617 (tp30) REVERT: d 352 LYS cc_start: 0.8186 (tppp) cc_final: 0.7728 (tptp) REVERT: d 362 ARG cc_start: 0.9199 (ttm110) cc_final: 0.8956 (mtp85) REVERT: c 8 ASN cc_start: 0.9443 (t0) cc_final: 0.9212 (m-40) REVERT: c 12 SER cc_start: 0.9242 (m) cc_final: 0.8920 (p) REVERT: c 19 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8829 (mm-30) REVERT: c 67 SER cc_start: 0.9017 (m) cc_final: 0.8678 (p) REVERT: c 147 MET cc_start: 0.9321 (tpp) cc_final: 0.9115 (mmp) REVERT: c 197 TYR cc_start: 0.9117 (t80) cc_final: 0.8606 (t80) REVERT: c 244 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8249 (mm-30) REVERT: c 248 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8951 (mm-30) REVERT: c 334 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8540 (tm-30) REVERT: c 374 GLN cc_start: 0.8064 (tm130) cc_final: 0.7855 (tm-30) REVERT: c 411 ASP cc_start: 0.9048 (m-30) cc_final: 0.8700 (m-30) REVERT: b 92 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7378 (pmm-80) REVERT: b 193 GLN cc_start: 0.8686 (tt0) cc_final: 0.8370 (tm-30) REVERT: b 218 GLU cc_start: 0.9067 (tp30) cc_final: 0.8593 (tp30) REVERT: b 219 MET cc_start: 0.9299 (mmm) cc_final: 0.9009 (mmm) REVERT: b 248 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.9117 (mm-30) REVERT: b 259 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: b 264 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8603 (tt) REVERT: b 352 LYS cc_start: 0.7971 (tppp) cc_final: 0.7483 (tptm) REVERT: b 378 GLN cc_start: 0.9249 (mt0) cc_final: 0.9002 (mt0) outliers start: 298 outliers final: 155 residues processed: 1318 average time/residue: 0.5777 time to fit residues: 1292.1979 Evaluate side-chains 1169 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 980 time to evaluate : 5.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 12 SER Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 89 PHE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 153 SER Chi-restraints excluded: chain a residue 334 GLU Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 390 MET Chi-restraints excluded: chain a residue 401 ASN Chi-restraints excluded: chain a residue 415 MET Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 6 LEU Chi-restraints excluded: chain r residue 58 LEU Chi-restraints excluded: chain r residue 89 PHE Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 132 LEU Chi-restraints excluded: chain r residue 153 SER Chi-restraints excluded: chain r residue 198 ASN Chi-restraints excluded: chain r residue 216 VAL Chi-restraints excluded: chain r residue 248 GLU Chi-restraints excluded: chain r residue 292 ASN Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 58 LEU Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain q residue 89 PHE Chi-restraints excluded: chain q residue 137 THR Chi-restraints excluded: chain q residue 242 VAL Chi-restraints excluded: chain q residue 263 LEU Chi-restraints excluded: chain q residue 264 LEU Chi-restraints excluded: chain q residue 333 GLU Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 58 LEU Chi-restraints excluded: chain p residue 89 PHE Chi-restraints excluded: chain p residue 92 ARG Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 191 ILE Chi-restraints excluded: chain p residue 242 VAL Chi-restraints excluded: chain p residue 248 GLU Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain p residue 333 GLU Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 89 PHE Chi-restraints excluded: chain o residue 92 ARG Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 248 GLU Chi-restraints excluded: chain o residue 264 LEU Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 390 MET Chi-restraints excluded: chain o residue 400 ILE Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 92 ARG Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 226 GLU Chi-restraints excluded: chain n residue 342 GLU Chi-restraints excluded: chain n residue 390 MET Chi-restraints excluded: chain n residue 400 ILE Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 6 LEU Chi-restraints excluded: chain m residue 49 ILE Chi-restraints excluded: chain m residue 60 ASP Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 259 ASP Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 5 GLU Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 55 LEU Chi-restraints excluded: chain l residue 58 LEU Chi-restraints excluded: chain l residue 60 ASP Chi-restraints excluded: chain l residue 89 PHE Chi-restraints excluded: chain l residue 92 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 132 LEU Chi-restraints excluded: chain l residue 242 VAL Chi-restraints excluded: chain l residue 383 LEU Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain k residue 89 PHE Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 228 VAL Chi-restraints excluded: chain k residue 259 ASP Chi-restraints excluded: chain k residue 264 LEU Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 89 PHE Chi-restraints excluded: chain j residue 92 ARG Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 242 VAL Chi-restraints excluded: chain j residue 394 ASP Chi-restraints excluded: chain i residue 5 GLU Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 8 ASN Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 60 ASP Chi-restraints excluded: chain i residue 89 PHE Chi-restraints excluded: chain i residue 105 LYS Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 132 LEU Chi-restraints excluded: chain i residue 164 LEU Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain i residue 354 VAL Chi-restraints excluded: chain i residue 417 LYS Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 5 GLU Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 89 PHE Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 132 LEU Chi-restraints excluded: chain h residue 153 SER Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 259 ASP Chi-restraints excluded: chain h residue 354 VAL Chi-restraints excluded: chain h residue 383 LEU Chi-restraints excluded: chain g residue 5 GLU Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 52 ASP Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 327 MET Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain g residue 417 LYS Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 55 LEU Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 60 ASP Chi-restraints excluded: chain f residue 89 PHE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 153 SER Chi-restraints excluded: chain f residue 292 ASN Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 89 PHE Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain d residue 5 GLU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 60 ASP Chi-restraints excluded: chain d residue 89 PHE Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 194 SER Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain d residue 264 LEU Chi-restraints excluded: chain d residue 354 VAL Chi-restraints excluded: chain d residue 400 ILE Chi-restraints excluded: chain d residue 410 ASP Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 6 LEU Chi-restraints excluded: chain c residue 89 PHE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 248 GLU Chi-restraints excluded: chain c residue 383 LEU Chi-restraints excluded: chain c residue 400 ILE Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 92 ARG Chi-restraints excluded: chain b residue 101 ILE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 248 GLU Chi-restraints excluded: chain b residue 259 ASP Chi-restraints excluded: chain b residue 264 LEU Chi-restraints excluded: chain b residue 410 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 663 optimal weight: 0.0570 chunk 504 optimal weight: 0.8980 chunk 348 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 320 optimal weight: 1.9990 chunk 450 optimal weight: 5.9990 chunk 673 optimal weight: 10.0000 chunk 713 optimal weight: 6.9990 chunk 352 optimal weight: 0.6980 chunk 638 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 189 GLN r 59 GLN ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 275 ASN o 378 GLN ** n 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 193 GLN ** m 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 ASN ** k 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 189 GLN ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 220 GLN ** h 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 193 GLN f 374 GLN d 193 GLN c 59 GLN c 374 GLN c 378 GLN b 374 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 60822 Z= 0.175 Angle : 0.580 8.562 82008 Z= 0.272 Chirality : 0.041 0.181 9324 Planarity : 0.003 0.030 10620 Dihedral : 6.967 179.534 8451 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 4.77 % Allowed : 29.07 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.40 (0.10), residues: 7506 helix: 1.74 (0.09), residues: 3456 sheet: 0.89 (0.15), residues: 1332 loop : -0.01 (0.11), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP a 381 HIS 0.007 0.001 HIS n 295 PHE 0.022 0.001 PHE r 398 TYR 0.020 0.002 TYR r 332 ARG 0.006 0.000 ARG p 418 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1342 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 1033 time to evaluate : 5.591 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: a 21 MET cc_start: 0.8492 (ttt) cc_final: 0.8083 (ttt) REVERT: a 29 MET cc_start: 0.8167 (ptp) cc_final: 0.7857 (ptp) REVERT: a 30 ARG cc_start: 0.7327 (mmm160) cc_final: 0.7014 (mtp85) REVERT: a 92 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8416 (mmt180) REVERT: a 110 TYR cc_start: 0.8315 (m-10) cc_final: 0.8056 (m-80) REVERT: a 132 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7973 (tp) REVERT: a 218 GLU cc_start: 0.9328 (tp30) cc_final: 0.8859 (tp30) REVERT: a 222 LEU cc_start: 0.9620 (tp) cc_final: 0.9387 (tp) REVERT: a 274 TYR cc_start: 0.9027 (m-10) cc_final: 0.8772 (m-80) REVERT: r 21 MET cc_start: 0.9065 (ttm) cc_final: 0.8849 (ttt) REVERT: r 85 GLN cc_start: 0.8747 (mp10) cc_final: 0.8168 (mp10) REVERT: r 132 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8595 (mt) REVERT: r 248 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8827 (mm-30) REVERT: r 292 ASN cc_start: 0.9152 (m-40) cc_final: 0.8528 (p0) REVERT: r 328 ASP cc_start: 0.9187 (m-30) cc_final: 0.8872 (m-30) REVERT: r 390 MET cc_start: 0.8642 (pmm) cc_final: 0.8367 (pmm) REVERT: q 33 ASP cc_start: 0.8971 (m-30) cc_final: 0.8633 (m-30) REVERT: q 201 ASP cc_start: 0.8944 (p0) cc_final: 0.8648 (p0) REVERT: q 241 GLN cc_start: 0.8932 (pp30) cc_final: 0.8593 (pp30) REVERT: q 333 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8920 (mm-30) REVERT: q 334 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8510 (tm-30) REVERT: q 360 TYR cc_start: 0.8922 (t80) cc_final: 0.8580 (t80) REVERT: q 390 MET cc_start: 0.8701 (pmm) cc_final: 0.8458 (pmm) REVERT: p 60 ASP cc_start: 0.8648 (m-30) cc_final: 0.8437 (m-30) REVERT: p 186 MET cc_start: 0.9219 (ptm) cc_final: 0.8982 (ptt) REVERT: p 244 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8330 (mm-30) REVERT: p 248 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8739 (mp0) REVERT: p 333 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8910 (mm-30) REVERT: p 334 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8284 (tm-30) REVERT: p 342 GLU cc_start: 0.8786 (mp0) cc_final: 0.8429 (mp0) REVERT: p 362 ARG cc_start: 0.9109 (ttm110) cc_final: 0.8893 (ttp-110) REVERT: p 378 GLN cc_start: 0.9343 (mt0) cc_final: 0.9112 (mm-40) REVERT: p 390 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8806 (pmm) REVERT: o 5 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8639 (pm20) REVERT: o 105 LYS cc_start: 0.8535 (tmmt) cc_final: 0.8051 (tmmt) REVERT: o 115 LYS cc_start: 0.9171 (tmmt) cc_final: 0.8861 (ptmm) REVERT: o 197 TYR cc_start: 0.9517 (t80) cc_final: 0.9295 (t80) REVERT: o 218 GLU cc_start: 0.9143 (tp30) cc_final: 0.8800 (tp30) REVERT: o 234 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7304 (mp0) REVERT: o 244 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8067 (mm-30) REVERT: o 248 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8510 (mp0) REVERT: o 334 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8598 (tm-30) REVERT: n 5 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8739 (pm20) REVERT: n 19 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8584 (mm-30) REVERT: n 59 GLN cc_start: 0.8524 (tp-100) cc_final: 0.8212 (tp-100) REVERT: n 147 MET cc_start: 0.9514 (tpp) cc_final: 0.8895 (mmm) REVERT: n 326 LYS cc_start: 0.8603 (tptp) cc_final: 0.8173 (tptp) REVERT: n 342 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: n 360 TYR cc_start: 0.9113 (t80) cc_final: 0.8893 (t80) REVERT: n 411 ASP cc_start: 0.9170 (m-30) cc_final: 0.8939 (m-30) REVERT: n 417 LYS cc_start: 0.9413 (pttt) cc_final: 0.9070 (tppt) REVERT: m 67 SER cc_start: 0.9125 (m) cc_final: 0.8735 (p) REVERT: m 69 ASP cc_start: 0.9012 (t0) cc_final: 0.8760 (t70) REVERT: m 226 GLU cc_start: 0.8393 (tp30) cc_final: 0.8105 (tt0) REVERT: m 259 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8654 (m-30) REVERT: m 406 THR cc_start: 0.7803 (p) cc_final: 0.7553 (p) REVERT: m 414 GLU cc_start: 0.8742 (pp20) cc_final: 0.8523 (pp20) REVERT: l 69 ASP cc_start: 0.9001 (t0) cc_final: 0.8765 (t0) REVERT: l 92 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7584 (pmm-80) REVERT: l 125 GLU cc_start: 0.9017 (mp0) cc_final: 0.8768 (mp0) REVERT: l 218 GLU cc_start: 0.8756 (tp30) cc_final: 0.8485 (tp30) REVERT: l 222 LEU cc_start: 0.9206 (mp) cc_final: 0.8801 (mm) REVERT: l 234 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8410 (mt-10) REVERT: l 334 GLU cc_start: 0.8880 (tp30) cc_final: 0.8512 (tm-30) REVERT: l 342 GLU cc_start: 0.8504 (mp0) cc_final: 0.8248 (mt-10) REVERT: k 152 ASP cc_start: 0.7235 (t0) cc_final: 0.6746 (t70) REVERT: k 218 GLU cc_start: 0.8951 (tp30) cc_final: 0.8568 (tt0) REVERT: k 244 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8214 (mm-30) REVERT: k 259 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8488 (m-30) REVERT: k 264 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8471 (tt) REVERT: k 374 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8067 (tm-30) REVERT: k 378 GLN cc_start: 0.9297 (mt0) cc_final: 0.8805 (mt0) REVERT: j 19 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8436 (mm-30) REVERT: j 67 SER cc_start: 0.9017 (m) cc_final: 0.8577 (p) REVERT: j 218 GLU cc_start: 0.8905 (tp30) cc_final: 0.8644 (tt0) REVERT: j 342 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8174 (mp0) REVERT: j 397 GLU cc_start: 0.8831 (pt0) cc_final: 0.8545 (mt-10) REVERT: j 411 ASP cc_start: 0.9110 (m-30) cc_final: 0.8836 (m-30) REVERT: i 5 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8740 (pm20) REVERT: i 19 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8282 (mm-30) REVERT: i 67 SER cc_start: 0.9117 (m) cc_final: 0.8737 (p) REVERT: i 106 GLU cc_start: 0.7809 (pp20) cc_final: 0.7563 (pp20) REVERT: i 244 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8414 (mm-30) REVERT: i 352 LYS cc_start: 0.8159 (tppp) cc_final: 0.7875 (tptp) REVERT: i 374 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7981 (tm-30) REVERT: h 5 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8411 (pm20) REVERT: h 125 GLU cc_start: 0.8946 (mp0) cc_final: 0.8661 (mp0) REVERT: h 226 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: h 259 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8402 (m-30) REVERT: h 326 LYS cc_start: 0.8842 (mppt) cc_final: 0.8601 (ttmm) REVERT: h 333 GLU cc_start: 0.8739 (tp30) cc_final: 0.8522 (mm-30) REVERT: h 342 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: h 348 LYS cc_start: 0.8916 (mtmm) cc_final: 0.8684 (ptmm) REVERT: h 411 ASP cc_start: 0.8965 (m-30) cc_final: 0.8645 (m-30) REVERT: g 5 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8886 (pm20) REVERT: g 67 SER cc_start: 0.9238 (m) cc_final: 0.8813 (p) REVERT: g 92 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8011 (pmm-80) REVERT: g 145 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8629 (mt) REVERT: g 244 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8482 (mm-30) REVERT: g 272 ARG cc_start: 0.8961 (tpp80) cc_final: 0.8749 (ttm110) REVERT: g 292 ASN cc_start: 0.9003 (m110) cc_final: 0.8653 (p0) REVERT: g 327 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8254 (ptm) REVERT: g 342 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7928 (mm-30) REVERT: g 347 ARG cc_start: 0.8033 (tpt-90) cc_final: 0.7748 (tpt-90) REVERT: f 30 ARG cc_start: 0.7625 (mmm-85) cc_final: 0.7264 (mtm110) REVERT: f 207 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8294 (tt) REVERT: f 244 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8300 (mm-30) REVERT: f 374 GLN cc_start: 0.8511 (tp-100) cc_final: 0.8244 (tp40) REVERT: e 58 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8938 (mt) REVERT: e 67 SER cc_start: 0.9125 (m) cc_final: 0.8830 (p) REVERT: e 244 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8331 (mm-30) REVERT: e 292 ASN cc_start: 0.9218 (m110) cc_final: 0.8816 (p0) REVERT: e 326 LYS cc_start: 0.8495 (tppt) cc_final: 0.8291 (tppt) REVERT: e 333 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8566 (tp30) REVERT: e 341 MET cc_start: 0.8753 (tmt) cc_final: 0.8273 (tmm) REVERT: e 347 ARG cc_start: 0.8242 (tpt-90) cc_final: 0.7995 (tpt-90) REVERT: e 407 LYS cc_start: 0.8928 (mmmt) cc_final: 0.8530 (tptt) REVERT: d 8 ASN cc_start: 0.9392 (t0) cc_final: 0.9085 (t0) REVERT: d 12 SER cc_start: 0.9328 (m) cc_final: 0.8989 (p) REVERT: d 21 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8965 (ttt) REVERT: d 329 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8550 (mm-30) REVERT: d 333 GLU cc_start: 0.9037 (tp30) cc_final: 0.8657 (tp30) REVERT: d 342 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7928 (mm-30) REVERT: d 352 LYS cc_start: 0.8362 (tppp) cc_final: 0.8031 (tptp) REVERT: d 397 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8471 (mt-10) REVERT: c 8 ASN cc_start: 0.9456 (t0) cc_final: 0.9190 (m-40) REVERT: c 12 SER cc_start: 0.9262 (m) cc_final: 0.8950 (p) REVERT: c 19 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8814 (mm-30) REVERT: c 67 SER cc_start: 0.9039 (m) cc_final: 0.8695 (p) REVERT: c 147 MET cc_start: 0.9349 (tpp) cc_final: 0.9121 (mmp) REVERT: c 197 TYR cc_start: 0.9129 (t80) cc_final: 0.8638 (t80) REVERT: c 244 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8184 (mm-30) REVERT: c 248 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8950 (mm-30) REVERT: c 334 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8548 (tm-30) REVERT: c 411 ASP cc_start: 0.9074 (m-30) cc_final: 0.8770 (m-30) REVERT: c 416 MET cc_start: 0.8985 (mmp) cc_final: 0.8745 (mmp) REVERT: b 92 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7557 (pmm-80) REVERT: b 193 GLN cc_start: 0.8678 (tt0) cc_final: 0.8387 (tm-30) REVERT: b 218 GLU cc_start: 0.9088 (tp30) cc_final: 0.8619 (tp30) REVERT: b 219 MET cc_start: 0.9297 (mmm) cc_final: 0.8995 (mmm) REVERT: b 248 GLU cc_start: 0.9373 (OUTLIER) cc_final: 0.9146 (mm-30) REVERT: b 264 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8616 (tt) REVERT: b 326 LYS cc_start: 0.8884 (ttmm) cc_final: 0.8388 (tptp) REVERT: b 334 GLU cc_start: 0.8986 (tp30) cc_final: 0.8560 (tm-30) REVERT: b 342 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8636 (tt0) REVERT: b 374 GLN cc_start: 0.8715 (tp-100) cc_final: 0.8391 (tp40) REVERT: b 378 GLN cc_start: 0.9297 (mt0) cc_final: 0.8962 (mt0) outliers start: 309 outliers final: 179 residues processed: 1265 average time/residue: 0.5661 time to fit residues: 1197.5774 Evaluate side-chains 1194 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 981 time to evaluate : 5.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 12 SER Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 89 PHE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 327 MET Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 390 MET Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 6 LEU Chi-restraints excluded: chain r residue 58 LEU Chi-restraints excluded: chain r residue 89 PHE Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 132 LEU Chi-restraints excluded: chain r residue 153 SER Chi-restraints excluded: chain r residue 216 VAL Chi-restraints excluded: chain r residue 248 GLU Chi-restraints excluded: chain r residue 295 HIS Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 58 LEU Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain q residue 89 PHE Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 137 THR Chi-restraints excluded: chain q residue 191 ILE Chi-restraints excluded: chain q residue 333 GLU Chi-restraints excluded: chain q residue 354 VAL Chi-restraints excluded: chain q residue 394 ASP Chi-restraints excluded: chain q residue 410 ASP Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 58 LEU Chi-restraints excluded: chain p residue 89 PHE Chi-restraints excluded: chain p residue 92 ARG Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 164 LEU Chi-restraints excluded: chain p residue 191 ILE Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 242 VAL Chi-restraints excluded: chain p residue 248 GLU Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain p residue 333 GLU Chi-restraints excluded: chain p residue 390 MET Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain o residue 89 PHE Chi-restraints excluded: chain o residue 92 ARG Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 248 GLU Chi-restraints excluded: chain o residue 264 LEU Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 390 MET Chi-restraints excluded: chain o residue 400 ILE Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 92 ARG Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 226 GLU Chi-restraints excluded: chain n residue 321 ILE Chi-restraints excluded: chain n residue 342 GLU Chi-restraints excluded: chain n residue 390 MET Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 6 LEU Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 60 ASP Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 259 ASP Chi-restraints excluded: chain m residue 394 ASP Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 55 LEU Chi-restraints excluded: chain l residue 60 ASP Chi-restraints excluded: chain l residue 89 PHE Chi-restraints excluded: chain l residue 92 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 132 LEU Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 242 VAL Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain l residue 383 LEU Chi-restraints excluded: chain l residue 415 MET Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain k residue 89 PHE Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 216 VAL Chi-restraints excluded: chain k residue 228 VAL Chi-restraints excluded: chain k residue 259 ASP Chi-restraints excluded: chain k residue 264 LEU Chi-restraints excluded: chain k residue 354 VAL Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 55 LEU Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 89 PHE Chi-restraints excluded: chain j residue 92 ARG Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 342 GLU Chi-restraints excluded: chain j residue 394 ASP Chi-restraints excluded: chain j residue 405 MET Chi-restraints excluded: chain i residue 5 GLU Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 89 PHE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 132 LEU Chi-restraints excluded: chain i residue 216 VAL Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain i residue 417 LYS Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 5 GLU Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 52 ASP Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 89 PHE Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 132 LEU Chi-restraints excluded: chain h residue 153 SER Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 216 VAL Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 259 ASP Chi-restraints excluded: chain h residue 342 GLU Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 5 GLU Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 52 ASP Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 259 ASP Chi-restraints excluded: chain g residue 327 MET Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain g residue 417 LYS Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 55 LEU Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 60 ASP Chi-restraints excluded: chain f residue 89 PHE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 292 ASN Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 333 GLU Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 89 PHE Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 186 MET Chi-restraints excluded: chain e residue 354 VAL Chi-restraints excluded: chain e residue 400 ILE Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 5 GLU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 60 ASP Chi-restraints excluded: chain d residue 89 PHE Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 193 GLN Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain d residue 241 GLN Chi-restraints excluded: chain d residue 342 GLU Chi-restraints excluded: chain d residue 354 VAL Chi-restraints excluded: chain d residue 410 ASP Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 6 LEU Chi-restraints excluded: chain c residue 89 PHE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 248 GLU Chi-restraints excluded: chain c residue 378 GLN Chi-restraints excluded: chain c residue 383 LEU Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 92 ARG Chi-restraints excluded: chain b residue 101 ILE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 153 SER Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 248 GLU Chi-restraints excluded: chain b residue 264 LEU Chi-restraints excluded: chain b residue 394 ASP Chi-restraints excluded: chain b residue 410 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 594 optimal weight: 6.9990 chunk 404 optimal weight: 0.7980 chunk 10 optimal weight: 50.0000 chunk 531 optimal weight: 5.9990 chunk 294 optimal weight: 0.9990 chunk 608 optimal weight: 4.9990 chunk 493 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 364 optimal weight: 9.9990 chunk 640 optimal weight: 0.7980 chunk 180 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 374 GLN ** r 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 292 ASN ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 275 ASN ** p 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 374 GLN l 189 GLN ** l 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 189 GLN ** i 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 220 GLN ** h 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 90 ASN e 374 GLN ** c 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 60822 Z= 0.272 Angle : 0.612 8.558 82008 Z= 0.292 Chirality : 0.042 0.179 9324 Planarity : 0.004 0.044 10620 Dihedral : 7.066 179.696 8451 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 5.29 % Allowed : 28.40 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.41 (0.10), residues: 7506 helix: 1.64 (0.09), residues: 3456 sheet: 0.88 (0.15), residues: 1332 loop : 0.16 (0.12), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP a 381 HIS 0.008 0.001 HIS n 295 PHE 0.018 0.001 PHE r 398 TYR 0.020 0.002 TYR n 197 ARG 0.007 0.000 ARG o 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1351 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 343 poor density : 1008 time to evaluate : 5.548 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: a 21 MET cc_start: 0.8604 (ttt) cc_final: 0.8184 (ttt) REVERT: a 92 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8373 (mmt180) REVERT: a 110 TYR cc_start: 0.8662 (m-10) cc_final: 0.8454 (m-80) REVERT: a 132 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8250 (tp) REVERT: a 218 GLU cc_start: 0.9323 (tp30) cc_final: 0.8886 (tp30) REVERT: a 222 LEU cc_start: 0.9644 (tp) cc_final: 0.9420 (tp) REVERT: a 274 TYR cc_start: 0.9189 (m-10) cc_final: 0.8949 (m-80) REVERT: a 362 ARG cc_start: 0.9217 (ttm110) cc_final: 0.8810 (mtm-85) REVERT: r 21 MET cc_start: 0.9066 (ttm) cc_final: 0.8841 (ttt) REVERT: r 85 GLN cc_start: 0.8904 (mp10) cc_final: 0.8242 (mp10) REVERT: r 132 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8681 (mt) REVERT: r 248 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8831 (mm-30) REVERT: r 292 ASN cc_start: 0.9087 (m110) cc_final: 0.8558 (p0) REVERT: r 328 ASP cc_start: 0.9185 (m-30) cc_final: 0.8983 (m-30) REVERT: r 390 MET cc_start: 0.8750 (pmm) cc_final: 0.8452 (pmm) REVERT: q 33 ASP cc_start: 0.9000 (m-30) cc_final: 0.8610 (m-30) REVERT: q 186 MET cc_start: 0.8839 (ptp) cc_final: 0.8085 (ptt) REVERT: q 189 GLN cc_start: 0.9393 (mt0) cc_final: 0.8805 (mt0) REVERT: q 201 ASP cc_start: 0.8965 (p0) cc_final: 0.8763 (p0) REVERT: q 241 GLN cc_start: 0.9007 (pp30) cc_final: 0.8785 (pp30) REVERT: q 333 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8927 (mm-30) REVERT: q 334 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8546 (tm-30) REVERT: q 360 TYR cc_start: 0.8894 (t80) cc_final: 0.8588 (t80) REVERT: q 390 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8446 (pmm) REVERT: q 405 MET cc_start: 0.9274 (ptp) cc_final: 0.9043 (ptp) REVERT: q 412 PHE cc_start: 0.9167 (t80) cc_final: 0.8830 (t80) REVERT: q 415 MET cc_start: 0.8823 (ppp) cc_final: 0.8605 (ppp) REVERT: p 186 MET cc_start: 0.9249 (ptm) cc_final: 0.9016 (ptt) REVERT: p 244 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8323 (mm-30) REVERT: p 248 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8754 (mp0) REVERT: p 333 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8906 (mm-30) REVERT: p 334 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8340 (tp30) REVERT: p 342 GLU cc_start: 0.8832 (mp0) cc_final: 0.8411 (mp0) REVERT: o 5 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8729 (pm20) REVERT: o 105 LYS cc_start: 0.8485 (tmmt) cc_final: 0.8025 (tmmt) REVERT: o 115 LYS cc_start: 0.9229 (tmmt) cc_final: 0.8911 (ptmm) REVERT: o 197 TYR cc_start: 0.9510 (t80) cc_final: 0.9273 (t80) REVERT: o 218 GLU cc_start: 0.9142 (tp30) cc_final: 0.8818 (tp30) REVERT: o 234 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7460 (mp0) REVERT: o 244 GLU cc_start: 0.8564 (mm-30) cc_final: 0.7870 (mm-30) REVERT: o 248 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8360 (mp0) REVERT: o 259 ASP cc_start: 0.9155 (OUTLIER) cc_final: 0.8495 (m-30) REVERT: o 274 TYR cc_start: 0.9329 (m-80) cc_final: 0.8678 (m-80) REVERT: o 334 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8555 (tm-30) REVERT: n 5 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8717 (pm20) REVERT: n 147 MET cc_start: 0.9496 (tpp) cc_final: 0.8894 (mmm) REVERT: n 326 LYS cc_start: 0.8626 (tptp) cc_final: 0.8346 (tptp) REVERT: n 333 GLU cc_start: 0.9119 (tp30) cc_final: 0.8875 (tp30) REVERT: n 342 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: n 411 ASP cc_start: 0.9205 (m-30) cc_final: 0.8982 (m-30) REVERT: n 417 LYS cc_start: 0.9427 (pttt) cc_final: 0.9084 (tppt) REVERT: m 67 SER cc_start: 0.9016 (m) cc_final: 0.8638 (p) REVERT: m 69 ASP cc_start: 0.9068 (t0) cc_final: 0.8847 (t70) REVERT: m 226 GLU cc_start: 0.8258 (tp30) cc_final: 0.7875 (tt0) REVERT: m 259 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8643 (m-30) REVERT: m 390 MET cc_start: 0.9390 (ptp) cc_final: 0.9158 (ptp) REVERT: m 414 GLU cc_start: 0.8799 (pp20) cc_final: 0.8570 (pp20) REVERT: l 92 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7832 (pmm-80) REVERT: l 125 GLU cc_start: 0.9032 (mp0) cc_final: 0.8684 (mp0) REVERT: l 218 GLU cc_start: 0.8799 (tp30) cc_final: 0.8585 (tp30) REVERT: l 342 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8276 (mt-10) REVERT: k 152 ASP cc_start: 0.7491 (t0) cc_final: 0.6927 (t70) REVERT: k 218 GLU cc_start: 0.8917 (tp30) cc_final: 0.8574 (tt0) REVERT: k 259 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8542 (m-30) REVERT: k 374 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8049 (tm-30) REVERT: k 378 GLN cc_start: 0.9299 (mt0) cc_final: 0.8761 (mt0) REVERT: j 19 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8409 (mm-30) REVERT: j 100 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8954 (ptpp) REVERT: j 218 GLU cc_start: 0.8922 (tp30) cc_final: 0.8644 (tt0) REVERT: j 342 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: j 374 GLN cc_start: 0.8556 (tp40) cc_final: 0.7757 (tp40) REVERT: j 378 GLN cc_start: 0.9294 (mm-40) cc_final: 0.8764 (mm-40) REVERT: j 397 GLU cc_start: 0.8834 (pt0) cc_final: 0.8603 (mt-10) REVERT: j 411 ASP cc_start: 0.9143 (m-30) cc_final: 0.8859 (m-30) REVERT: i 5 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8794 (pm20) REVERT: i 19 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8223 (mm-30) REVERT: i 67 SER cc_start: 0.9012 (m) cc_final: 0.8648 (p) REVERT: i 106 GLU cc_start: 0.7818 (pp20) cc_final: 0.7448 (pp20) REVERT: i 244 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8320 (mm-30) REVERT: i 342 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8497 (mt-10) REVERT: i 351 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8169 (mt-10) REVERT: i 374 GLN cc_start: 0.8347 (tm-30) cc_final: 0.7661 (tm-30) REVERT: i 378 GLN cc_start: 0.9042 (mt0) cc_final: 0.8301 (mt0) REVERT: h 5 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8457 (pm20) REVERT: h 207 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8243 (tt) REVERT: h 226 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: h 259 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8390 (m-30) REVERT: h 292 ASN cc_start: 0.8874 (m110) cc_final: 0.8624 (p0) REVERT: h 326 LYS cc_start: 0.8864 (mppt) cc_final: 0.8623 (ttmm) REVERT: h 333 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8522 (mm-30) REVERT: h 342 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: h 411 ASP cc_start: 0.8977 (m-30) cc_final: 0.8635 (m-30) REVERT: g 5 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.8956 (pm20) REVERT: g 67 SER cc_start: 0.9107 (m) cc_final: 0.8687 (p) REVERT: g 92 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7943 (pmm-80) REVERT: g 145 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8715 (mt) REVERT: f 30 ARG cc_start: 0.7824 (mmm-85) cc_final: 0.7471 (mtm110) REVERT: f 244 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8341 (mm-30) REVERT: f 341 MET cc_start: 0.9118 (tmt) cc_final: 0.8621 (tmm) REVERT: e 58 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8958 (mt) REVERT: e 67 SER cc_start: 0.9057 (m) cc_final: 0.8763 (p) REVERT: e 244 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8285 (mm-30) REVERT: e 292 ASN cc_start: 0.9256 (m110) cc_final: 0.8846 (p0) REVERT: e 326 LYS cc_start: 0.8590 (tppt) cc_final: 0.8346 (tppt) REVERT: e 351 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8076 (mm-30) REVERT: e 407 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8520 (tptt) REVERT: d 8 ASN cc_start: 0.9409 (t0) cc_final: 0.9095 (t0) REVERT: d 12 SER cc_start: 0.9351 (m) cc_final: 0.9123 (t) REVERT: d 21 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8949 (ttt) REVERT: d 193 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8600 (pt0) REVERT: d 329 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8523 (mm-30) REVERT: d 333 GLU cc_start: 0.9072 (tp30) cc_final: 0.8611 (mm-30) REVERT: d 342 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8016 (mm-30) REVERT: d 374 GLN cc_start: 0.8562 (tp-100) cc_final: 0.8160 (tp-100) REVERT: d 378 GLN cc_start: 0.9370 (mm-40) cc_final: 0.9162 (mm-40) REVERT: d 397 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8430 (mt-10) REVERT: c 12 SER cc_start: 0.9332 (m) cc_final: 0.9043 (p) REVERT: c 19 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8808 (tp30) REVERT: c 67 SER cc_start: 0.9048 (m) cc_final: 0.8717 (p) REVERT: c 134 GLU cc_start: 0.9107 (mp0) cc_final: 0.8897 (mp0) REVERT: c 147 MET cc_start: 0.9360 (tpp) cc_final: 0.9137 (mmp) REVERT: c 197 TYR cc_start: 0.9121 (t80) cc_final: 0.8553 (t80) REVERT: c 244 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8146 (mm-30) REVERT: c 248 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8971 (mm-30) REVERT: c 334 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8503 (tm-30) REVERT: c 341 MET cc_start: 0.9068 (tmm) cc_final: 0.8827 (tmm) REVERT: c 411 ASP cc_start: 0.9106 (m-30) cc_final: 0.8827 (m-30) REVERT: b 92 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.8025 (pmm-80) REVERT: b 193 GLN cc_start: 0.8707 (tt0) cc_final: 0.8465 (tm-30) REVERT: b 218 GLU cc_start: 0.9101 (tp30) cc_final: 0.8689 (tp30) REVERT: b 219 MET cc_start: 0.9293 (mmm) cc_final: 0.9051 (mmm) REVERT: b 244 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8456 (mm-30) REVERT: b 248 GLU cc_start: 0.9393 (OUTLIER) cc_final: 0.9176 (mm-30) REVERT: b 259 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8244 (m-30) REVERT: b 264 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8634 (tt) REVERT: b 292 ASN cc_start: 0.8878 (m110) cc_final: 0.8645 (p0) REVERT: b 326 LYS cc_start: 0.8917 (ttmm) cc_final: 0.8425 (tptp) REVERT: b 334 GLU cc_start: 0.8968 (tp30) cc_final: 0.8524 (tm-30) REVERT: b 342 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8620 (tt0) REVERT: b 374 GLN cc_start: 0.8643 (tp-100) cc_final: 0.8255 (tp40) REVERT: b 378 GLN cc_start: 0.9268 (mt0) cc_final: 0.8719 (mt0) outliers start: 343 outliers final: 212 residues processed: 1264 average time/residue: 0.5830 time to fit residues: 1224.6118 Evaluate side-chains 1194 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 944 time to evaluate : 5.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 12 SER Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 89 PHE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 153 SER Chi-restraints excluded: chain a residue 264 LEU Chi-restraints excluded: chain a residue 327 MET Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 390 MET Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 401 ASN Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 58 LEU Chi-restraints excluded: chain r residue 89 PHE Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 132 LEU Chi-restraints excluded: chain r residue 153 SER Chi-restraints excluded: chain r residue 216 VAL Chi-restraints excluded: chain r residue 248 GLU Chi-restraints excluded: chain r residue 376 GLU Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 58 LEU Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain q residue 89 PHE Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 137 THR Chi-restraints excluded: chain q residue 162 LEU Chi-restraints excluded: chain q residue 191 ILE Chi-restraints excluded: chain q residue 242 VAL Chi-restraints excluded: chain q residue 333 GLU Chi-restraints excluded: chain q residue 354 VAL Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain q residue 390 MET Chi-restraints excluded: chain q residue 394 ASP Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 58 LEU Chi-restraints excluded: chain p residue 89 PHE Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 191 ILE Chi-restraints excluded: chain p residue 216 VAL Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 242 VAL Chi-restraints excluded: chain p residue 248 GLU Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain p residue 333 GLU Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 55 LEU Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain o residue 89 PHE Chi-restraints excluded: chain o residue 92 ARG Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 248 GLU Chi-restraints excluded: chain o residue 259 ASP Chi-restraints excluded: chain o residue 264 LEU Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 390 MET Chi-restraints excluded: chain o residue 400 ILE Chi-restraints excluded: chain o residue 411 ASP Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 92 ARG Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 186 MET Chi-restraints excluded: chain n residue 226 GLU Chi-restraints excluded: chain n residue 228 VAL Chi-restraints excluded: chain n residue 342 GLU Chi-restraints excluded: chain n residue 390 MET Chi-restraints excluded: chain n residue 410 ASP Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 6 LEU Chi-restraints excluded: chain m residue 40 LYS Chi-restraints excluded: chain m residue 49 ILE Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 60 ASP Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 164 LEU Chi-restraints excluded: chain m residue 259 ASP Chi-restraints excluded: chain m residue 394 ASP Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 55 LEU Chi-restraints excluded: chain l residue 60 ASP Chi-restraints excluded: chain l residue 89 PHE Chi-restraints excluded: chain l residue 92 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 132 LEU Chi-restraints excluded: chain l residue 216 VAL Chi-restraints excluded: chain l residue 242 VAL Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain l residue 342 GLU Chi-restraints excluded: chain l residue 383 LEU Chi-restraints excluded: chain l residue 394 ASP Chi-restraints excluded: chain l residue 415 MET Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 89 PHE Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 216 VAL Chi-restraints excluded: chain k residue 228 VAL Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 259 ASP Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 55 LEU Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 89 PHE Chi-restraints excluded: chain j residue 100 LYS Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 194 SER Chi-restraints excluded: chain j residue 242 VAL Chi-restraints excluded: chain j residue 342 GLU Chi-restraints excluded: chain j residue 394 ASP Chi-restraints excluded: chain j residue 405 MET Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 5 GLU Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 60 ASP Chi-restraints excluded: chain i residue 65 LEU Chi-restraints excluded: chain i residue 89 PHE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 132 LEU Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain i residue 216 VAL Chi-restraints excluded: chain i residue 228 VAL Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain i residue 354 VAL Chi-restraints excluded: chain i residue 417 LYS Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 5 GLU Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 52 ASP Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 89 PHE Chi-restraints excluded: chain h residue 92 ARG Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 132 LEU Chi-restraints excluded: chain h residue 153 SER Chi-restraints excluded: chain h residue 186 MET Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 207 LEU Chi-restraints excluded: chain h residue 216 VAL Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 259 ASP Chi-restraints excluded: chain h residue 333 GLU Chi-restraints excluded: chain h residue 342 GLU Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 5 GLU Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 52 ASP Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 259 ASP Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain g residue 394 ASP Chi-restraints excluded: chain g residue 417 LYS Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 55 LEU Chi-restraints excluded: chain f residue 60 ASP Chi-restraints excluded: chain f residue 89 PHE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 153 SER Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 415 MET Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 52 ASP Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 60 ASP Chi-restraints excluded: chain e residue 89 PHE Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 186 MET Chi-restraints excluded: chain e residue 216 VAL Chi-restraints excluded: chain e residue 354 VAL Chi-restraints excluded: chain e residue 394 ASP Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 60 ASP Chi-restraints excluded: chain d residue 89 PHE Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 193 GLN Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain d residue 241 GLN Chi-restraints excluded: chain d residue 342 GLU Chi-restraints excluded: chain d residue 354 VAL Chi-restraints excluded: chain d residue 383 LEU Chi-restraints excluded: chain d residue 410 ASP Chi-restraints excluded: chain d residue 415 MET Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 6 LEU Chi-restraints excluded: chain c residue 39 LEU Chi-restraints excluded: chain c residue 89 PHE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 248 GLU Chi-restraints excluded: chain c residue 354 VAL Chi-restraints excluded: chain c residue 383 LEU Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 92 ARG Chi-restraints excluded: chain b residue 101 ILE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 153 SER Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 248 GLU Chi-restraints excluded: chain b residue 259 ASP Chi-restraints excluded: chain b residue 264 LEU Chi-restraints excluded: chain b residue 354 VAL Chi-restraints excluded: chain b residue 394 ASP Chi-restraints excluded: chain b residue 410 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 240 optimal weight: 8.9990 chunk 642 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 418 optimal weight: 0.9990 chunk 176 optimal weight: 0.0670 chunk 714 optimal weight: 10.0000 chunk 592 optimal weight: 0.9980 chunk 330 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 236 optimal weight: 7.9990 chunk 374 optimal weight: 5.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 189 GLN r 198 ASN ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 378 GLN ** m 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 374 GLN ** k 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 189 GLN ** i 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 189 GLN h 25 ASN h 220 GLN ** h 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 41 GLN g 275 ASN f 90 ASN e 374 GLN d 193 GLN c 378 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 60822 Z= 0.180 Angle : 0.593 9.315 82008 Z= 0.278 Chirality : 0.041 0.172 9324 Planarity : 0.003 0.034 10620 Dihedral : 6.884 179.945 8451 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.43 % Allowed : 28.73 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.40 (0.10), residues: 7506 helix: 1.70 (0.09), residues: 3456 sheet: 0.87 (0.15), residues: 1332 loop : 0.05 (0.11), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP a 381 HIS 0.012 0.001 HIS n 295 PHE 0.025 0.001 PHE q 412 TYR 0.022 0.002 TYR p 197 ARG 0.007 0.000 ARG e 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1284 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 997 time to evaluate : 5.543 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: a 21 MET cc_start: 0.8713 (ttt) cc_final: 0.8245 (ttt) REVERT: a 92 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8457 (mmt180) REVERT: a 132 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8198 (tp) REVERT: a 218 GLU cc_start: 0.9316 (tp30) cc_final: 0.9061 (tp30) REVERT: a 274 TYR cc_start: 0.9180 (m-10) cc_final: 0.8954 (m-80) REVERT: a 341 MET cc_start: 0.9326 (tmm) cc_final: 0.9045 (tmm) REVERT: a 362 ARG cc_start: 0.9210 (ttm110) cc_final: 0.8807 (mtm-85) REVERT: a 374 GLN cc_start: 0.8514 (tp-100) cc_final: 0.8302 (tp-100) REVERT: r 21 MET cc_start: 0.9085 (ttm) cc_final: 0.8874 (ttt) REVERT: r 85 GLN cc_start: 0.8917 (mp10) cc_final: 0.8254 (mp10) REVERT: r 248 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.8811 (mm-30) REVERT: r 292 ASN cc_start: 0.9019 (m110) cc_final: 0.8508 (p0) REVERT: r 328 ASP cc_start: 0.9164 (m-30) cc_final: 0.8864 (m-30) REVERT: r 390 MET cc_start: 0.8796 (pmm) cc_final: 0.8546 (pmm) REVERT: q 33 ASP cc_start: 0.8996 (m-30) cc_final: 0.8614 (m-30) REVERT: q 201 ASP cc_start: 0.8934 (p0) cc_final: 0.8718 (p0) REVERT: q 253 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9351 (mm) REVERT: q 333 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8920 (mm-30) REVERT: q 334 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8533 (tm-30) REVERT: q 360 TYR cc_start: 0.8946 (t80) cc_final: 0.8737 (t80) REVERT: q 390 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8405 (pmm) REVERT: q 412 PHE cc_start: 0.8999 (t80) cc_final: 0.8641 (t80) REVERT: q 416 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7892 (tpt) REVERT: p 58 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9095 (mt) REVERT: p 59 GLN cc_start: 0.8594 (pm20) cc_final: 0.8282 (pm20) REVERT: p 186 MET cc_start: 0.9223 (ptm) cc_final: 0.9004 (ptt) REVERT: p 244 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8255 (mm-30) REVERT: p 248 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8751 (mp0) REVERT: p 333 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8886 (mm-30) REVERT: p 334 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8327 (tp30) REVERT: p 341 MET cc_start: 0.9377 (ppp) cc_final: 0.9164 (ppp) REVERT: p 378 GLN cc_start: 0.9386 (mt0) cc_final: 0.9069 (mm-40) REVERT: o 5 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8642 (pm20) REVERT: o 105 LYS cc_start: 0.8522 (tmmt) cc_final: 0.8098 (tmmt) REVERT: o 115 LYS cc_start: 0.9219 (tmmt) cc_final: 0.8898 (ptmm) REVERT: o 197 TYR cc_start: 0.9516 (t80) cc_final: 0.9297 (t80) REVERT: o 234 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7410 (mp0) REVERT: o 244 GLU cc_start: 0.8570 (mm-30) cc_final: 0.7803 (mm-30) REVERT: o 248 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8305 (mp0) REVERT: o 259 ASP cc_start: 0.9135 (OUTLIER) cc_final: 0.8487 (m-30) REVERT: o 334 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8517 (tm-30) REVERT: n 5 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8741 (pm20) REVERT: n 147 MET cc_start: 0.9458 (tpp) cc_final: 0.8877 (mmm) REVERT: n 326 LYS cc_start: 0.8563 (tptp) cc_final: 0.8322 (tptp) REVERT: n 333 GLU cc_start: 0.9118 (tp30) cc_final: 0.8859 (tp30) REVERT: n 342 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: n 411 ASP cc_start: 0.9196 (m-30) cc_final: 0.8983 (m-30) REVERT: n 417 LYS cc_start: 0.9410 (pttt) cc_final: 0.9070 (tppt) REVERT: m 21 MET cc_start: 0.8544 (ttt) cc_final: 0.8293 (ttt) REVERT: m 67 SER cc_start: 0.9069 (m) cc_final: 0.8661 (p) REVERT: m 69 ASP cc_start: 0.9069 (t0) cc_final: 0.8833 (t70) REVERT: m 226 GLU cc_start: 0.8332 (tp30) cc_final: 0.7961 (tt0) REVERT: m 244 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8321 (mm-30) REVERT: m 259 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8577 (m-30) REVERT: m 414 GLU cc_start: 0.8817 (pp20) cc_final: 0.8560 (pp20) REVERT: l 92 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7879 (pmm-80) REVERT: l 125 GLU cc_start: 0.9029 (mp0) cc_final: 0.8694 (mp0) REVERT: l 218 GLU cc_start: 0.8809 (tp30) cc_final: 0.8541 (tp30) REVERT: l 234 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8552 (mt-10) REVERT: l 244 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8290 (mm-30) REVERT: l 342 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8295 (mt-10) REVERT: l 378 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8939 (mm-40) REVERT: k 218 GLU cc_start: 0.8904 (tp30) cc_final: 0.8566 (tt0) REVERT: k 244 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8167 (mm-30) REVERT: k 259 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8531 (m-30) REVERT: k 264 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8494 (tt) REVERT: k 294 LEU cc_start: 0.9359 (tp) cc_final: 0.9158 (tt) REVERT: k 374 GLN cc_start: 0.8435 (tm-30) cc_final: 0.7768 (tm-30) REVERT: k 378 GLN cc_start: 0.9294 (mt0) cc_final: 0.8708 (mt0) REVERT: j 19 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8427 (mm-30) REVERT: j 218 GLU cc_start: 0.8892 (tp30) cc_final: 0.8631 (tt0) REVERT: j 219 MET cc_start: 0.9274 (tpp) cc_final: 0.9031 (tpp) REVERT: j 342 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: j 397 GLU cc_start: 0.8796 (pt0) cc_final: 0.8576 (mt-10) REVERT: j 411 ASP cc_start: 0.9119 (m-30) cc_final: 0.8882 (m-30) REVERT: i 5 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8813 (pm20) REVERT: i 19 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8227 (mm-30) REVERT: i 67 SER cc_start: 0.9082 (m) cc_final: 0.8686 (p) REVERT: i 106 GLU cc_start: 0.7771 (pp20) cc_final: 0.7371 (pp20) REVERT: i 244 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8286 (mm-30) REVERT: i 272 ARG cc_start: 0.9006 (mmm-85) cc_final: 0.8726 (mmm-85) REVERT: i 342 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8504 (mt-10) REVERT: i 351 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8180 (mt-10) REVERT: h 5 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8442 (pm20) REVERT: h 207 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8299 (tt) REVERT: h 226 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: h 259 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8391 (m-30) REVERT: h 326 LYS cc_start: 0.8870 (mppt) cc_final: 0.8615 (ttmm) REVERT: h 333 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8505 (mm-30) REVERT: h 342 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: h 411 ASP cc_start: 0.8976 (m-30) cc_final: 0.8644 (m-30) REVERT: g 5 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8959 (pm20) REVERT: g 92 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7885 (pmm-80) REVERT: g 145 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8724 (mt) REVERT: g 342 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7939 (mm-30) REVERT: g 374 GLN cc_start: 0.8528 (tp40) cc_final: 0.8213 (tp-100) REVERT: f 30 ARG cc_start: 0.7771 (mmm-85) cc_final: 0.7438 (mtm110) REVERT: f 244 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8278 (mm-30) REVERT: f 374 GLN cc_start: 0.8615 (tp40) cc_final: 0.8327 (tp-100) REVERT: e 58 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8945 (mt) REVERT: e 67 SER cc_start: 0.9075 (m) cc_final: 0.8753 (p) REVERT: e 244 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8264 (mm-30) REVERT: e 292 ASN cc_start: 0.9205 (m110) cc_final: 0.8799 (p0) REVERT: e 299 ARG cc_start: 0.8825 (mmm-85) cc_final: 0.8522 (mtp85) REVERT: e 326 LYS cc_start: 0.8547 (tppt) cc_final: 0.8282 (tppt) REVERT: e 351 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8066 (mm-30) REVERT: e 407 LYS cc_start: 0.8887 (mmmt) cc_final: 0.8478 (tptt) REVERT: d 8 ASN cc_start: 0.9402 (t0) cc_final: 0.9101 (t0) REVERT: d 12 SER cc_start: 0.9326 (m) cc_final: 0.9084 (t) REVERT: d 21 MET cc_start: 0.9187 (ttm) cc_final: 0.8967 (ttt) REVERT: d 329 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8512 (mm-30) REVERT: d 333 GLU cc_start: 0.9053 (tp30) cc_final: 0.8590 (mm-30) REVERT: d 397 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8411 (mt-10) REVERT: c 12 SER cc_start: 0.9323 (m) cc_final: 0.9043 (p) REVERT: c 19 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8794 (tp30) REVERT: c 67 SER cc_start: 0.9054 (m) cc_final: 0.8693 (p) REVERT: c 147 MET cc_start: 0.9367 (tpp) cc_final: 0.9152 (mmp) REVERT: c 197 TYR cc_start: 0.9111 (t80) cc_final: 0.8582 (t80) REVERT: c 244 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8154 (mm-30) REVERT: c 248 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8905 (mm-30) REVERT: c 334 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8567 (tp30) REVERT: c 341 MET cc_start: 0.9089 (tmm) cc_final: 0.8848 (tmm) REVERT: c 411 ASP cc_start: 0.9108 (m-30) cc_final: 0.8832 (m-30) REVERT: b 193 GLN cc_start: 0.8707 (tt0) cc_final: 0.8449 (tm-30) REVERT: b 218 GLU cc_start: 0.9093 (tp30) cc_final: 0.8687 (tp30) REVERT: b 248 GLU cc_start: 0.9357 (OUTLIER) cc_final: 0.9135 (mm-30) REVERT: b 259 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8241 (m-30) REVERT: b 264 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8663 (tt) REVERT: b 292 ASN cc_start: 0.8842 (m110) cc_final: 0.8627 (p0) REVERT: b 326 LYS cc_start: 0.8897 (ttmm) cc_final: 0.8387 (tptp) REVERT: b 334 GLU cc_start: 0.8961 (tp30) cc_final: 0.8523 (tm-30) REVERT: b 374 GLN cc_start: 0.8612 (tp-100) cc_final: 0.8157 (tp40) REVERT: b 378 GLN cc_start: 0.9249 (mt0) cc_final: 0.8670 (mt0) outliers start: 287 outliers final: 190 residues processed: 1205 average time/residue: 0.5730 time to fit residues: 1150.8929 Evaluate side-chains 1202 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 975 time to evaluate : 5.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 89 PHE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 153 SER Chi-restraints excluded: chain a residue 264 LEU Chi-restraints excluded: chain a residue 327 MET Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 390 MET Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 401 ASN Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 216 VAL Chi-restraints excluded: chain r residue 248 GLU Chi-restraints excluded: chain r residue 295 HIS Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 58 LEU Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain q residue 89 PHE Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 137 THR Chi-restraints excluded: chain q residue 191 ILE Chi-restraints excluded: chain q residue 242 VAL Chi-restraints excluded: chain q residue 253 LEU Chi-restraints excluded: chain q residue 333 GLU Chi-restraints excluded: chain q residue 354 VAL Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain q residue 390 MET Chi-restraints excluded: chain q residue 410 ASP Chi-restraints excluded: chain q residue 411 ASP Chi-restraints excluded: chain q residue 416 MET Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 58 LEU Chi-restraints excluded: chain p residue 89 PHE Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 191 ILE Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 242 VAL Chi-restraints excluded: chain p residue 248 GLU Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain p residue 333 GLU Chi-restraints excluded: chain p residue 394 ASP Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain o residue 89 PHE Chi-restraints excluded: chain o residue 92 ARG Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 186 MET Chi-restraints excluded: chain o residue 248 GLU Chi-restraints excluded: chain o residue 259 ASP Chi-restraints excluded: chain o residue 264 LEU Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 390 MET Chi-restraints excluded: chain o residue 400 ILE Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 186 MET Chi-restraints excluded: chain n residue 228 VAL Chi-restraints excluded: chain n residue 321 ILE Chi-restraints excluded: chain n residue 342 GLU Chi-restraints excluded: chain n residue 390 MET Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 6 LEU Chi-restraints excluded: chain m residue 49 ILE Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 60 ASP Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 164 LEU Chi-restraints excluded: chain m residue 259 ASP Chi-restraints excluded: chain m residue 394 ASP Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 55 LEU Chi-restraints excluded: chain l residue 60 ASP Chi-restraints excluded: chain l residue 92 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 132 LEU Chi-restraints excluded: chain l residue 162 LEU Chi-restraints excluded: chain l residue 216 VAL Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain l residue 342 GLU Chi-restraints excluded: chain l residue 383 LEU Chi-restraints excluded: chain l residue 394 ASP Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 89 PHE Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 228 VAL Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 259 ASP Chi-restraints excluded: chain k residue 264 LEU Chi-restraints excluded: chain k residue 354 VAL Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 55 LEU Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 89 PHE Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 194 SER Chi-restraints excluded: chain j residue 241 GLN Chi-restraints excluded: chain j residue 242 VAL Chi-restraints excluded: chain j residue 342 GLU Chi-restraints excluded: chain j residue 354 VAL Chi-restraints excluded: chain j residue 394 ASP Chi-restraints excluded: chain j residue 405 MET Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 5 GLU Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 89 PHE Chi-restraints excluded: chain i residue 105 LYS Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 132 LEU Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain i residue 417 LYS Chi-restraints excluded: chain h residue 5 GLU Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 52 ASP Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 89 PHE Chi-restraints excluded: chain h residue 92 ARG Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 132 LEU Chi-restraints excluded: chain h residue 153 SER Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 207 LEU Chi-restraints excluded: chain h residue 216 VAL Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 259 ASP Chi-restraints excluded: chain h residue 333 GLU Chi-restraints excluded: chain h residue 342 GLU Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 5 GLU Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 52 ASP Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 259 ASP Chi-restraints excluded: chain g residue 342 GLU Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain g residue 394 ASP Chi-restraints excluded: chain g residue 417 LYS Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 55 LEU Chi-restraints excluded: chain f residue 60 ASP Chi-restraints excluded: chain f residue 89 PHE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 153 SER Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 52 ASP Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 60 ASP Chi-restraints excluded: chain e residue 89 PHE Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 186 MET Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 354 VAL Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 29 MET Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 60 ASP Chi-restraints excluded: chain d residue 89 PHE Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain d residue 241 GLN Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 383 LEU Chi-restraints excluded: chain d residue 410 ASP Chi-restraints excluded: chain d residue 415 MET Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 6 LEU Chi-restraints excluded: chain c residue 39 LEU Chi-restraints excluded: chain c residue 89 PHE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 132 LEU Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 248 GLU Chi-restraints excluded: chain c residue 378 GLN Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 101 ILE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 153 SER Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 248 GLU Chi-restraints excluded: chain b residue 259 ASP Chi-restraints excluded: chain b residue 264 LEU Chi-restraints excluded: chain b residue 394 ASP Chi-restraints excluded: chain b residue 410 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 688 optimal weight: 0.0980 chunk 80 optimal weight: 10.0000 chunk 406 optimal weight: 0.8980 chunk 521 optimal weight: 4.9990 chunk 404 optimal weight: 6.9990 chunk 601 optimal weight: 3.9990 chunk 398 optimal weight: 1.9990 chunk 711 optimal weight: 10.0000 chunk 445 optimal weight: 5.9990 chunk 433 optimal weight: 0.9980 chunk 328 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 189 GLN ** r 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 189 GLN ** p 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 193 GLN ** k 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 193 GLN ** i 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 189 GLN i 374 GLN h 220 GLN g 41 GLN g 374 GLN e 374 GLN d 193 GLN c 378 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 60822 Z= 0.193 Angle : 0.601 10.222 82008 Z= 0.282 Chirality : 0.041 0.234 9324 Planarity : 0.003 0.038 10620 Dihedral : 6.759 178.879 8445 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.51 % Allowed : 28.55 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.36 (0.10), residues: 7506 helix: 1.70 (0.09), residues: 3474 sheet: 0.82 (0.16), residues: 1170 loop : 0.04 (0.11), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP a 381 HIS 0.011 0.001 HIS n 295 PHE 0.024 0.001 PHE q 412 TYR 0.022 0.002 TYR p 197 ARG 0.007 0.000 ARG g 418 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1293 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1001 time to evaluate : 5.788 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: a 21 MET cc_start: 0.8711 (ttt) cc_final: 0.8213 (ttt) REVERT: a 92 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8458 (mmt180) REVERT: a 110 TYR cc_start: 0.8679 (m-80) cc_final: 0.8472 (m-80) REVERT: a 132 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8260 (tp) REVERT: a 197 TYR cc_start: 0.8941 (t80) cc_final: 0.8724 (t80) REVERT: a 218 GLU cc_start: 0.9294 (tp30) cc_final: 0.8827 (tp30) REVERT: a 274 TYR cc_start: 0.9204 (m-10) cc_final: 0.8992 (m-80) REVERT: a 341 MET cc_start: 0.9318 (tmm) cc_final: 0.9026 (tmm) REVERT: a 362 ARG cc_start: 0.9205 (ttm110) cc_final: 0.8790 (mtm-85) REVERT: a 374 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8351 (tp-100) REVERT: a 411 ASP cc_start: 0.9332 (m-30) cc_final: 0.8831 (m-30) REVERT: r 21 MET cc_start: 0.9088 (ttm) cc_final: 0.8808 (ttt) REVERT: r 244 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8744 (mm-30) REVERT: r 248 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8818 (mm-30) REVERT: r 292 ASN cc_start: 0.9006 (m110) cc_final: 0.8509 (p0) REVERT: r 328 ASP cc_start: 0.9185 (m-30) cc_final: 0.8926 (m-30) REVERT: r 390 MET cc_start: 0.8788 (pmm) cc_final: 0.8474 (pmm) REVERT: q 33 ASP cc_start: 0.9000 (m-30) cc_final: 0.8615 (m-30) REVERT: q 186 MET cc_start: 0.8744 (ptp) cc_final: 0.7825 (ppp) REVERT: q 201 ASP cc_start: 0.8938 (p0) cc_final: 0.8715 (p0) REVERT: q 241 GLN cc_start: 0.8972 (pp30) cc_final: 0.8753 (pp30) REVERT: q 253 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9366 (mm) REVERT: q 333 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8945 (mm-30) REVERT: q 334 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8510 (tm-30) REVERT: q 390 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8449 (pmm) REVERT: q 401 ASN cc_start: 0.9534 (t0) cc_final: 0.9216 (t0) REVERT: p 58 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9125 (mt) REVERT: p 59 GLN cc_start: 0.8557 (pm20) cc_final: 0.8236 (pm20) REVERT: p 186 MET cc_start: 0.9257 (ptm) cc_final: 0.9006 (ptp) REVERT: p 244 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8269 (mm-30) REVERT: p 248 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8761 (mp0) REVERT: p 259 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: p 333 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8871 (mm-30) REVERT: p 334 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8335 (tp30) REVERT: p 341 MET cc_start: 0.9353 (ppp) cc_final: 0.9148 (ppp) REVERT: o 5 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8650 (pm20) REVERT: o 105 LYS cc_start: 0.8542 (tmmt) cc_final: 0.8141 (tmmt) REVERT: o 115 LYS cc_start: 0.9214 (tmmt) cc_final: 0.8902 (ptmm) REVERT: o 197 TYR cc_start: 0.9522 (t80) cc_final: 0.9313 (t80) REVERT: o 218 GLU cc_start: 0.9028 (tp30) cc_final: 0.8766 (tp30) REVERT: o 234 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7431 (mp0) REVERT: o 244 GLU cc_start: 0.8565 (mm-30) cc_final: 0.7844 (mm-30) REVERT: o 248 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8326 (mp0) REVERT: o 259 ASP cc_start: 0.9118 (OUTLIER) cc_final: 0.8484 (m-30) REVERT: n 5 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8736 (pm20) REVERT: n 147 MET cc_start: 0.9449 (tpp) cc_final: 0.8878 (mmm) REVERT: n 326 LYS cc_start: 0.8545 (tptp) cc_final: 0.8295 (tptp) REVERT: n 333 GLU cc_start: 0.9110 (tp30) cc_final: 0.8902 (tp30) REVERT: n 342 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8295 (mp0) REVERT: n 383 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9282 (tm) REVERT: n 405 MET cc_start: 0.9197 (ptm) cc_final: 0.8993 (ptm) REVERT: n 417 LYS cc_start: 0.9386 (pttt) cc_final: 0.9051 (tppt) REVERT: m 21 MET cc_start: 0.8525 (ttt) cc_final: 0.8266 (ttt) REVERT: m 67 SER cc_start: 0.9057 (m) cc_final: 0.8655 (p) REVERT: m 69 ASP cc_start: 0.9088 (t0) cc_final: 0.8877 (t70) REVERT: m 193 GLN cc_start: 0.8791 (tt0) cc_final: 0.8418 (tm-30) REVERT: m 226 GLU cc_start: 0.8367 (tp30) cc_final: 0.7987 (tt0) REVERT: m 244 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8335 (mm-30) REVERT: m 259 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8563 (m-30) REVERT: m 327 MET cc_start: 0.8534 (ttp) cc_final: 0.8210 (tmm) REVERT: m 414 GLU cc_start: 0.8839 (pp20) cc_final: 0.8565 (pp20) REVERT: l 92 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7896 (pmm-80) REVERT: l 125 GLU cc_start: 0.9028 (mp0) cc_final: 0.8694 (mp0) REVERT: l 218 GLU cc_start: 0.8817 (tp30) cc_final: 0.8537 (tp30) REVERT: l 244 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8391 (mm-30) REVERT: l 342 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8304 (mt-10) REVERT: l 416 MET cc_start: 0.9357 (mmm) cc_final: 0.9139 (mmp) REVERT: k 218 GLU cc_start: 0.8875 (tp30) cc_final: 0.8541 (tt0) REVERT: k 259 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8544 (m-30) REVERT: k 264 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8500 (tt) REVERT: k 374 GLN cc_start: 0.8422 (tm-30) cc_final: 0.7727 (tm-30) REVERT: k 378 GLN cc_start: 0.9318 (mt0) cc_final: 0.8723 (mt0) REVERT: j 19 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8440 (mm-30) REVERT: j 218 GLU cc_start: 0.8888 (tp30) cc_final: 0.8624 (tt0) REVERT: j 219 MET cc_start: 0.9264 (tpp) cc_final: 0.9023 (tpp) REVERT: j 342 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: j 374 GLN cc_start: 0.8519 (tp40) cc_final: 0.8317 (tp40) REVERT: j 397 GLU cc_start: 0.8800 (pt0) cc_final: 0.8563 (mt-10) REVERT: i 5 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8823 (pm20) REVERT: i 19 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8190 (mm-30) REVERT: i 30 ARG cc_start: 0.7849 (mmm-85) cc_final: 0.7476 (mtm180) REVERT: i 67 SER cc_start: 0.9068 (m) cc_final: 0.8683 (p) REVERT: i 106 GLU cc_start: 0.7734 (pp20) cc_final: 0.7383 (pp20) REVERT: i 244 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8266 (mm-30) REVERT: i 272 ARG cc_start: 0.9015 (mmm-85) cc_final: 0.8747 (mmm-85) REVERT: i 342 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8505 (mt-10) REVERT: i 351 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8243 (mt-10) REVERT: i 374 GLN cc_start: 0.8624 (tp-100) cc_final: 0.8262 (tp40) REVERT: i 378 GLN cc_start: 0.9042 (mt0) cc_final: 0.8665 (mt0) REVERT: h 5 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8447 (pm20) REVERT: h 207 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8288 (tt) REVERT: h 226 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: h 259 ASP cc_start: 0.8800 (OUTLIER) cc_final: 0.8385 (m-30) REVERT: h 326 LYS cc_start: 0.8864 (mppt) cc_final: 0.8604 (ttmm) REVERT: h 342 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: h 374 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8129 (tp-100) REVERT: h 411 ASP cc_start: 0.8998 (m-30) cc_final: 0.8574 (m-30) REVERT: g 5 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8971 (pm20) REVERT: g 92 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7928 (pmm-80) REVERT: g 145 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8712 (mt) REVERT: g 342 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: f 30 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7443 (mtm110) REVERT: f 92 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8066 (pmm-80) REVERT: f 244 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8429 (mm-30) REVERT: e 30 ARG cc_start: 0.8198 (mmm-85) cc_final: 0.7791 (mtp-110) REVERT: e 58 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8936 (mt) REVERT: e 67 SER cc_start: 0.9058 (m) cc_final: 0.8740 (p) REVERT: e 292 ASN cc_start: 0.9192 (m110) cc_final: 0.8794 (p0) REVERT: e 299 ARG cc_start: 0.8797 (mmm-85) cc_final: 0.8486 (mtp85) REVERT: e 351 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8148 (mm-30) REVERT: e 407 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8481 (tptt) REVERT: d 8 ASN cc_start: 0.9404 (t0) cc_final: 0.9105 (t0) REVERT: d 12 SER cc_start: 0.9321 (m) cc_final: 0.9075 (t) REVERT: d 21 MET cc_start: 0.9174 (ttm) cc_final: 0.8960 (ttt) REVERT: d 329 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8499 (mm-30) REVERT: d 333 GLU cc_start: 0.9053 (tp30) cc_final: 0.8613 (mm-30) REVERT: d 342 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8015 (mm-30) REVERT: d 397 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8417 (mt-10) REVERT: c 12 SER cc_start: 0.9323 (m) cc_final: 0.9050 (p) REVERT: c 19 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8795 (tp30) REVERT: c 67 SER cc_start: 0.9058 (m) cc_final: 0.8701 (p) REVERT: c 147 MET cc_start: 0.9384 (tpp) cc_final: 0.9040 (mmp) REVERT: c 197 TYR cc_start: 0.9107 (t80) cc_final: 0.8601 (t80) REVERT: c 244 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8111 (mm-30) REVERT: c 248 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8905 (mm-30) REVERT: c 341 MET cc_start: 0.9095 (tmm) cc_final: 0.8857 (tmm) REVERT: c 411 ASP cc_start: 0.9151 (m-30) cc_final: 0.8860 (m-30) REVERT: b 92 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7778 (pmm-80) REVERT: b 193 GLN cc_start: 0.8712 (tt0) cc_final: 0.8479 (tm-30) REVERT: b 218 GLU cc_start: 0.9094 (tp30) cc_final: 0.8701 (tp30) REVERT: b 248 GLU cc_start: 0.9357 (OUTLIER) cc_final: 0.9149 (mm-30) REVERT: b 259 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8235 (m-30) REVERT: b 292 ASN cc_start: 0.8873 (m110) cc_final: 0.8657 (p0) REVERT: b 326 LYS cc_start: 0.8900 (ttmm) cc_final: 0.8381 (tptp) REVERT: b 334 GLU cc_start: 0.8956 (tp30) cc_final: 0.8511 (tm-30) REVERT: b 374 GLN cc_start: 0.8598 (tp-100) cc_final: 0.8179 (tp40) REVERT: b 378 GLN cc_start: 0.9251 (mm-40) cc_final: 0.8672 (mt0) outliers start: 292 outliers final: 201 residues processed: 1207 average time/residue: 0.5824 time to fit residues: 1172.1826 Evaluate side-chains 1217 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 977 time to evaluate : 5.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 89 PHE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 153 SER Chi-restraints excluded: chain a residue 264 LEU Chi-restraints excluded: chain a residue 327 MET Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 390 MET Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 401 ASN Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 216 VAL Chi-restraints excluded: chain r residue 248 GLU Chi-restraints excluded: chain r residue 295 HIS Chi-restraints excluded: chain r residue 398 PHE Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain q residue 89 PHE Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 137 THR Chi-restraints excluded: chain q residue 164 LEU Chi-restraints excluded: chain q residue 194 SER Chi-restraints excluded: chain q residue 242 VAL Chi-restraints excluded: chain q residue 253 LEU Chi-restraints excluded: chain q residue 333 GLU Chi-restraints excluded: chain q residue 354 VAL Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain q residue 390 MET Chi-restraints excluded: chain q residue 410 ASP Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 58 LEU Chi-restraints excluded: chain p residue 60 ASP Chi-restraints excluded: chain p residue 89 PHE Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 248 GLU Chi-restraints excluded: chain p residue 259 ASP Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain p residue 333 GLU Chi-restraints excluded: chain p residue 394 ASP Chi-restraints excluded: chain o residue 1 MET Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 55 LEU Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain o residue 89 PHE Chi-restraints excluded: chain o residue 92 ARG Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 186 MET Chi-restraints excluded: chain o residue 216 VAL Chi-restraints excluded: chain o residue 248 GLU Chi-restraints excluded: chain o residue 259 ASP Chi-restraints excluded: chain o residue 264 LEU Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 390 MET Chi-restraints excluded: chain o residue 400 ILE Chi-restraints excluded: chain o residue 411 ASP Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 186 MET Chi-restraints excluded: chain n residue 342 GLU Chi-restraints excluded: chain n residue 383 LEU Chi-restraints excluded: chain n residue 390 MET Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 6 LEU Chi-restraints excluded: chain m residue 49 ILE Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 60 ASP Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 164 LEU Chi-restraints excluded: chain m residue 259 ASP Chi-restraints excluded: chain m residue 394 ASP Chi-restraints excluded: chain m residue 410 ASP Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 55 LEU Chi-restraints excluded: chain l residue 60 ASP Chi-restraints excluded: chain l residue 89 PHE Chi-restraints excluded: chain l residue 92 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 132 LEU Chi-restraints excluded: chain l residue 216 VAL Chi-restraints excluded: chain l residue 222 LEU Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain l residue 342 GLU Chi-restraints excluded: chain l residue 354 VAL Chi-restraints excluded: chain l residue 383 LEU Chi-restraints excluded: chain l residue 394 ASP Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 228 VAL Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 259 ASP Chi-restraints excluded: chain k residue 264 LEU Chi-restraints excluded: chain k residue 415 MET Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 55 LEU Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 89 PHE Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 193 GLN Chi-restraints excluded: chain j residue 194 SER Chi-restraints excluded: chain j residue 241 GLN Chi-restraints excluded: chain j residue 242 VAL Chi-restraints excluded: chain j residue 342 GLU Chi-restraints excluded: chain j residue 354 VAL Chi-restraints excluded: chain j residue 394 ASP Chi-restraints excluded: chain j residue 405 MET Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 5 GLU Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 60 ASP Chi-restraints excluded: chain i residue 89 PHE Chi-restraints excluded: chain i residue 105 LYS Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 132 LEU Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain i residue 417 LYS Chi-restraints excluded: chain h residue 5 GLU Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 52 ASP Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 89 PHE Chi-restraints excluded: chain h residue 92 ARG Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 132 LEU Chi-restraints excluded: chain h residue 153 SER Chi-restraints excluded: chain h residue 186 MET Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 207 LEU Chi-restraints excluded: chain h residue 216 VAL Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 259 ASP Chi-restraints excluded: chain h residue 342 GLU Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 5 GLU Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 52 ASP Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 259 ASP Chi-restraints excluded: chain g residue 292 ASN Chi-restraints excluded: chain g residue 342 GLU Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain g residue 394 ASP Chi-restraints excluded: chain g residue 417 LYS Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 55 LEU Chi-restraints excluded: chain f residue 60 ASP Chi-restraints excluded: chain f residue 89 PHE Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 153 SER Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 52 ASP Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 60 ASP Chi-restraints excluded: chain e residue 89 PHE Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 186 MET Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 354 VAL Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 29 MET Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 60 ASP Chi-restraints excluded: chain d residue 89 PHE Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 193 GLN Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain d residue 241 GLN Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 342 GLU Chi-restraints excluded: chain d residue 383 LEU Chi-restraints excluded: chain d residue 410 ASP Chi-restraints excluded: chain d residue 415 MET Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 6 LEU Chi-restraints excluded: chain c residue 39 LEU Chi-restraints excluded: chain c residue 89 PHE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 248 GLU Chi-restraints excluded: chain c residue 354 VAL Chi-restraints excluded: chain c residue 378 GLN Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 92 ARG Chi-restraints excluded: chain b residue 101 ILE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 153 SER Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 248 GLU Chi-restraints excluded: chain b residue 259 ASP Chi-restraints excluded: chain b residue 394 ASP Chi-restraints excluded: chain b residue 410 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 440 optimal weight: 1.9990 chunk 284 optimal weight: 3.9990 chunk 424 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 452 optimal weight: 0.8980 chunk 484 optimal weight: 3.9990 chunk 351 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 559 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 295 HIS ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 275 ASN ** n 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 374 GLN j 189 GLN j 193 GLN j 374 GLN ** i 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 220 GLN g 41 GLN e 374 GLN d 193 GLN c 378 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 60822 Z= 0.292 Angle : 0.639 10.863 82008 Z= 0.304 Chirality : 0.042 0.205 9324 Planarity : 0.004 0.043 10620 Dihedral : 6.850 179.757 8442 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.40 % Allowed : 28.60 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.32 (0.10), residues: 7506 helix: 1.65 (0.09), residues: 3456 sheet: 0.74 (0.16), residues: 1170 loop : 0.09 (0.11), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP a 381 HIS 0.011 0.001 HIS a 295 PHE 0.014 0.001 PHE q 413 TYR 0.026 0.002 TYR r 332 ARG 0.009 0.000 ARG j 149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1250 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 965 time to evaluate : 5.515 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: a 21 MET cc_start: 0.8786 (ttt) cc_final: 0.8264 (ttt) REVERT: a 92 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8442 (mmt180) REVERT: a 132 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8398 (tp) REVERT: a 197 TYR cc_start: 0.8996 (t80) cc_final: 0.8794 (t80) REVERT: a 218 GLU cc_start: 0.9303 (tp30) cc_final: 0.8842 (tp30) REVERT: a 362 ARG cc_start: 0.9200 (ttm110) cc_final: 0.8724 (mtm-85) REVERT: a 374 GLN cc_start: 0.8616 (tp-100) cc_final: 0.8398 (tp-100) REVERT: a 411 ASP cc_start: 0.9282 (m-30) cc_final: 0.8819 (m-30) REVERT: r 21 MET cc_start: 0.9137 (ttm) cc_final: 0.8803 (ttt) REVERT: r 248 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8808 (mm-30) REVERT: r 328 ASP cc_start: 0.9180 (m-30) cc_final: 0.8866 (m-30) REVERT: r 390 MET cc_start: 0.8829 (pmm) cc_final: 0.8509 (pmm) REVERT: q 33 ASP cc_start: 0.9037 (m-30) cc_final: 0.8785 (m-30) REVERT: q 241 GLN cc_start: 0.9029 (pp30) cc_final: 0.8805 (pp30) REVERT: q 253 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9379 (mm) REVERT: q 333 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8889 (mm-30) REVERT: q 390 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8489 (pmm) REVERT: q 401 ASN cc_start: 0.9550 (t0) cc_final: 0.9250 (t0) REVERT: p 30 ARG cc_start: 0.8526 (mmm-85) cc_final: 0.8060 (mtp-110) REVERT: p 59 GLN cc_start: 0.8584 (pm20) cc_final: 0.8280 (pm20) REVERT: p 186 MET cc_start: 0.9231 (ptm) cc_final: 0.9022 (ptp) REVERT: p 244 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8243 (mm-30) REVERT: p 248 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8767 (mp0) REVERT: p 259 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8075 (m-30) REVERT: p 334 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8557 (tp30) REVERT: p 341 MET cc_start: 0.9346 (ppp) cc_final: 0.9140 (ppp) REVERT: p 394 ASP cc_start: 0.9399 (OUTLIER) cc_final: 0.9166 (t0) REVERT: o 5 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8731 (pm20) REVERT: o 105 LYS cc_start: 0.8503 (tmmt) cc_final: 0.8077 (tmmt) REVERT: o 115 LYS cc_start: 0.9246 (tmmt) cc_final: 0.8931 (ptmm) REVERT: o 197 TYR cc_start: 0.9514 (t80) cc_final: 0.9298 (t80) REVERT: o 234 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7488 (mp0) REVERT: o 244 GLU cc_start: 0.8595 (mm-30) cc_final: 0.7847 (mm-30) REVERT: o 248 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8396 (mp0) REVERT: o 259 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8483 (m-30) REVERT: o 333 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8448 (mp0) REVERT: n 5 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8757 (pm20) REVERT: n 59 GLN cc_start: 0.8865 (tp-100) cc_final: 0.8480 (tp-100) REVERT: n 147 MET cc_start: 0.9434 (tpp) cc_final: 0.8878 (mmm) REVERT: n 326 LYS cc_start: 0.8640 (tptp) cc_final: 0.8364 (tptp) REVERT: n 342 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: n 383 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9282 (tm) REVERT: n 405 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8934 (ptp) REVERT: n 415 MET cc_start: 0.9222 (ttm) cc_final: 0.8933 (ttt) REVERT: n 417 LYS cc_start: 0.9403 (pttt) cc_final: 0.9060 (tppt) REVERT: m 67 SER cc_start: 0.8972 (m) cc_final: 0.8574 (p) REVERT: m 226 GLU cc_start: 0.8315 (tp30) cc_final: 0.7900 (tt0) REVERT: m 259 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8577 (m-30) REVERT: m 411 ASP cc_start: 0.9247 (m-30) cc_final: 0.8817 (m-30) REVERT: m 414 GLU cc_start: 0.8875 (pp20) cc_final: 0.8600 (pp20) REVERT: l 92 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7897 (pmm-80) REVERT: l 125 GLU cc_start: 0.9067 (mp0) cc_final: 0.8665 (mp0) REVERT: l 218 GLU cc_start: 0.8861 (tp30) cc_final: 0.8583 (tp30) REVERT: l 341 MET cc_start: 0.9041 (tmt) cc_final: 0.8733 (tmt) REVERT: l 342 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8327 (mt-10) REVERT: l 378 GLN cc_start: 0.9255 (mm-40) cc_final: 0.9033 (mm-40) REVERT: k 218 GLU cc_start: 0.8818 (tp30) cc_final: 0.8518 (tt0) REVERT: k 244 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8247 (mm-30) REVERT: k 259 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8552 (m-30) REVERT: k 374 GLN cc_start: 0.8516 (tm-30) cc_final: 0.7907 (tm-30) REVERT: k 378 GLN cc_start: 0.9319 (mt0) cc_final: 0.8900 (mt0) REVERT: j 218 GLU cc_start: 0.8901 (tp30) cc_final: 0.8620 (tt0) REVERT: j 326 LYS cc_start: 0.8311 (tmmt) cc_final: 0.8004 (ttpp) REVERT: j 342 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: j 374 GLN cc_start: 0.8596 (tp-100) cc_final: 0.8335 (tp40) REVERT: i 5 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8816 (pm20) REVERT: i 19 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8180 (mm-30) REVERT: i 30 ARG cc_start: 0.7885 (mmm-85) cc_final: 0.7512 (mtm180) REVERT: i 67 SER cc_start: 0.8985 (m) cc_final: 0.8625 (p) REVERT: i 244 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8231 (mm-30) REVERT: i 342 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8511 (mt-10) REVERT: i 351 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8321 (mt-10) REVERT: i 374 GLN cc_start: 0.8297 (tp-100) cc_final: 0.7924 (tp40) REVERT: i 390 MET cc_start: 0.9311 (ptp) cc_final: 0.8541 (pmm) REVERT: h 5 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8473 (pm20) REVERT: h 125 GLU cc_start: 0.8901 (mp0) cc_final: 0.8633 (mp0) REVERT: h 207 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8235 (tt) REVERT: h 226 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: h 259 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8381 (m-30) REVERT: h 292 ASN cc_start: 0.8916 (m110) cc_final: 0.8693 (p0) REVERT: h 326 LYS cc_start: 0.8891 (mppt) cc_final: 0.8634 (ttmm) REVERT: h 342 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: h 411 ASP cc_start: 0.8994 (m-30) cc_final: 0.8682 (m-30) REVERT: g 5 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8999 (pm20) REVERT: g 92 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7915 (pmm-80) REVERT: g 145 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8776 (mt) REVERT: f 30 ARG cc_start: 0.7877 (mmm-85) cc_final: 0.7552 (mtm110) REVERT: e 30 ARG cc_start: 0.8289 (mmm-85) cc_final: 0.7931 (mtp-110) REVERT: e 58 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8978 (mt) REVERT: e 292 ASN cc_start: 0.9218 (m110) cc_final: 0.8805 (p0) REVERT: e 351 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8051 (mm-30) REVERT: e 407 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8472 (tptt) REVERT: d 8 ASN cc_start: 0.9421 (t0) cc_final: 0.9099 (t0) REVERT: d 12 SER cc_start: 0.9354 (m) cc_final: 0.9119 (t) REVERT: d 21 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8954 (ttt) REVERT: d 219 MET cc_start: 0.9022 (mmm) cc_final: 0.8806 (mmt) REVERT: d 292 ASN cc_start: 0.9018 (m110) cc_final: 0.8669 (p0) REVERT: d 333 GLU cc_start: 0.9088 (tp30) cc_final: 0.8816 (tp30) REVERT: d 342 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8089 (mm-30) REVERT: d 397 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8430 (mt-10) REVERT: c 12 SER cc_start: 0.9365 (m) cc_final: 0.9140 (p) REVERT: c 19 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8794 (tp30) REVERT: c 67 SER cc_start: 0.9005 (m) cc_final: 0.8670 (p) REVERT: c 147 MET cc_start: 0.9387 (tpp) cc_final: 0.9041 (mmp) REVERT: c 197 TYR cc_start: 0.9105 (t80) cc_final: 0.8550 (t80) REVERT: c 248 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8951 (mm-30) REVERT: c 341 MET cc_start: 0.9119 (tmm) cc_final: 0.8875 (tmm) REVERT: c 411 ASP cc_start: 0.9162 (m-30) cc_final: 0.8873 (m-30) REVERT: b 92 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7914 (pmm-80) REVERT: b 193 GLN cc_start: 0.8719 (tt0) cc_final: 0.8490 (tm-30) REVERT: b 218 GLU cc_start: 0.9095 (tp30) cc_final: 0.8704 (tp30) REVERT: b 259 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8230 (m-30) REVERT: b 292 ASN cc_start: 0.8934 (m110) cc_final: 0.8693 (p0) REVERT: b 326 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8405 (tptp) REVERT: b 334 GLU cc_start: 0.8946 (tp30) cc_final: 0.8656 (tp30) REVERT: b 374 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8241 (tp40) outliers start: 285 outliers final: 198 residues processed: 1172 average time/residue: 0.5729 time to fit residues: 1118.3988 Evaluate side-chains 1165 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 931 time to evaluate : 5.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 89 PHE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 153 SER Chi-restraints excluded: chain a residue 264 LEU Chi-restraints excluded: chain a residue 295 HIS Chi-restraints excluded: chain a residue 327 MET Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 401 ASN Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 153 SER Chi-restraints excluded: chain r residue 216 VAL Chi-restraints excluded: chain r residue 248 GLU Chi-restraints excluded: chain r residue 295 HIS Chi-restraints excluded: chain r residue 376 GLU Chi-restraints excluded: chain r residue 398 PHE Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain q residue 89 PHE Chi-restraints excluded: chain q residue 92 ARG Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 137 THR Chi-restraints excluded: chain q residue 194 SER Chi-restraints excluded: chain q residue 253 LEU Chi-restraints excluded: chain q residue 333 GLU Chi-restraints excluded: chain q residue 354 VAL Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain q residue 390 MET Chi-restraints excluded: chain q residue 394 ASP Chi-restraints excluded: chain q residue 410 ASP Chi-restraints excluded: chain q residue 411 ASP Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 60 ASP Chi-restraints excluded: chain p residue 89 PHE Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 248 GLU Chi-restraints excluded: chain p residue 259 ASP Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain p residue 394 ASP Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 55 LEU Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain o residue 89 PHE Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 186 MET Chi-restraints excluded: chain o residue 216 VAL Chi-restraints excluded: chain o residue 248 GLU Chi-restraints excluded: chain o residue 259 ASP Chi-restraints excluded: chain o residue 264 LEU Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 390 MET Chi-restraints excluded: chain o residue 411 ASP Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 186 MET Chi-restraints excluded: chain n residue 216 VAL Chi-restraints excluded: chain n residue 321 ILE Chi-restraints excluded: chain n residue 342 GLU Chi-restraints excluded: chain n residue 383 LEU Chi-restraints excluded: chain n residue 390 MET Chi-restraints excluded: chain n residue 405 MET Chi-restraints excluded: chain n residue 411 ASP Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 6 LEU Chi-restraints excluded: chain m residue 49 ILE Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 60 ASP Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 162 LEU Chi-restraints excluded: chain m residue 164 LEU Chi-restraints excluded: chain m residue 259 ASP Chi-restraints excluded: chain m residue 394 ASP Chi-restraints excluded: chain m residue 410 ASP Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 55 LEU Chi-restraints excluded: chain l residue 58 LEU Chi-restraints excluded: chain l residue 60 ASP Chi-restraints excluded: chain l residue 92 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 132 LEU Chi-restraints excluded: chain l residue 216 VAL Chi-restraints excluded: chain l residue 222 LEU Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain l residue 342 GLU Chi-restraints excluded: chain l residue 354 VAL Chi-restraints excluded: chain l residue 383 LEU Chi-restraints excluded: chain l residue 394 ASP Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 228 VAL Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 259 ASP Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 55 LEU Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 89 PHE Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 193 GLN Chi-restraints excluded: chain j residue 241 GLN Chi-restraints excluded: chain j residue 242 VAL Chi-restraints excluded: chain j residue 342 GLU Chi-restraints excluded: chain j residue 394 ASP Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 5 GLU Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 60 ASP Chi-restraints excluded: chain i residue 89 PHE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 132 LEU Chi-restraints excluded: chain i residue 216 VAL Chi-restraints excluded: chain i residue 228 VAL Chi-restraints excluded: chain i residue 241 GLN Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain i residue 294 LEU Chi-restraints excluded: chain i residue 417 LYS Chi-restraints excluded: chain h residue 5 GLU Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 52 ASP Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 89 PHE Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 132 LEU Chi-restraints excluded: chain h residue 153 SER Chi-restraints excluded: chain h residue 186 MET Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 207 LEU Chi-restraints excluded: chain h residue 216 VAL Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 259 ASP Chi-restraints excluded: chain h residue 342 GLU Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 5 GLU Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 52 ASP Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 259 ASP Chi-restraints excluded: chain g residue 292 ASN Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain g residue 394 ASP Chi-restraints excluded: chain g residue 417 LYS Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 60 ASP Chi-restraints excluded: chain f residue 89 PHE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 153 SER Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 52 ASP Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 60 ASP Chi-restraints excluded: chain e residue 89 PHE Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 186 MET Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 354 VAL Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 60 ASP Chi-restraints excluded: chain d residue 89 PHE Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain d residue 241 GLN Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 342 GLU Chi-restraints excluded: chain d residue 383 LEU Chi-restraints excluded: chain d residue 410 ASP Chi-restraints excluded: chain d residue 415 MET Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 6 LEU Chi-restraints excluded: chain c residue 39 LEU Chi-restraints excluded: chain c residue 89 PHE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 248 GLU Chi-restraints excluded: chain c residue 378 GLN Chi-restraints excluded: chain c residue 383 LEU Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 92 ARG Chi-restraints excluded: chain b residue 101 ILE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 153 SER Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 259 ASP Chi-restraints excluded: chain b residue 394 ASP Chi-restraints excluded: chain b residue 410 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 647 optimal weight: 4.9990 chunk 681 optimal weight: 0.9990 chunk 621 optimal weight: 0.9990 chunk 662 optimal weight: 9.9990 chunk 398 optimal weight: 1.9990 chunk 288 optimal weight: 0.4980 chunk 520 optimal weight: 20.0000 chunk 203 optimal weight: 6.9990 chunk 598 optimal weight: 0.9980 chunk 626 optimal weight: 2.9990 chunk 660 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 189 GLN ** r 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 292 ASN ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 220 GLN ** p 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 275 ASN ** n 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 241 GLN ** m 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 189 GLN ** i 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 220 GLN h 374 GLN e 374 GLN d 193 GLN c 378 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 60822 Z= 0.176 Angle : 0.629 11.522 82008 Z= 0.296 Chirality : 0.041 0.205 9324 Planarity : 0.003 0.033 10620 Dihedral : 6.583 179.280 8441 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.49 % Allowed : 29.48 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.36 (0.10), residues: 7506 helix: 1.73 (0.09), residues: 3438 sheet: 0.80 (0.16), residues: 1170 loop : 0.03 (0.11), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP a 381 HIS 0.012 0.001 HIS n 295 PHE 0.014 0.001 PHE q 413 TYR 0.022 0.002 TYR a 80 ARG 0.009 0.000 ARG m 418 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 995 time to evaluate : 5.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 MET cc_start: 0.8770 (ttt) cc_final: 0.8199 (ttt) REVERT: a 92 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8463 (mmt180) REVERT: a 132 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8305 (tm) REVERT: a 197 TYR cc_start: 0.9003 (t80) cc_final: 0.8780 (t80) REVERT: a 218 GLU cc_start: 0.9283 (tp30) cc_final: 0.8841 (tp30) REVERT: a 362 ARG cc_start: 0.9206 (ttm110) cc_final: 0.8935 (mtm-85) REVERT: a 374 GLN cc_start: 0.8598 (tp-100) cc_final: 0.8316 (tp-100) REVERT: a 388 HIS cc_start: 0.9452 (t70) cc_final: 0.9154 (t70) REVERT: a 411 ASP cc_start: 0.9315 (m-30) cc_final: 0.8903 (m-30) REVERT: r 21 MET cc_start: 0.9138 (ttm) cc_final: 0.8800 (ttt) REVERT: r 186 MET cc_start: 0.8605 (ptt) cc_final: 0.7965 (pmm) REVERT: r 244 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8701 (mm-30) REVERT: r 248 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8783 (mm-30) REVERT: r 292 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8437 (p0) REVERT: r 298 LYS cc_start: 0.9094 (mmmm) cc_final: 0.8528 (tmtt) REVERT: r 328 ASP cc_start: 0.9201 (m-30) cc_final: 0.8945 (m-30) REVERT: r 390 MET cc_start: 0.8825 (pmm) cc_final: 0.8536 (pmm) REVERT: q 33 ASP cc_start: 0.8954 (m-30) cc_final: 0.8544 (m-30) REVERT: q 253 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9372 (mm) REVERT: q 333 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8898 (mm-30) REVERT: q 390 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8466 (pmm) REVERT: q 401 ASN cc_start: 0.9529 (t0) cc_final: 0.9217 (t0) REVERT: p 30 ARG cc_start: 0.8469 (mmm-85) cc_final: 0.7965 (mtp-110) REVERT: p 59 GLN cc_start: 0.8560 (pm20) cc_final: 0.8231 (pm20) REVERT: p 186 MET cc_start: 0.9193 (ptm) cc_final: 0.8954 (ptm) REVERT: p 189 GLN cc_start: 0.9336 (mt0) cc_final: 0.9082 (mt0) REVERT: p 244 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8235 (mm-30) REVERT: p 248 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8757 (mp0) REVERT: p 259 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8068 (m-30) REVERT: p 378 GLN cc_start: 0.8838 (mp10) cc_final: 0.8558 (pm20) REVERT: p 390 MET cc_start: 0.9102 (pmm) cc_final: 0.8779 (pmm) REVERT: p 394 ASP cc_start: 0.9299 (OUTLIER) cc_final: 0.8684 (t0) REVERT: o 5 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8648 (pm20) REVERT: o 105 LYS cc_start: 0.8576 (tmmt) cc_final: 0.8265 (tmmt) REVERT: o 115 LYS cc_start: 0.9226 (tmmt) cc_final: 0.8938 (ptmm) REVERT: o 197 TYR cc_start: 0.9505 (t80) cc_final: 0.9285 (t80) REVERT: o 234 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7435 (mp0) REVERT: o 244 GLU cc_start: 0.8557 (mm-30) cc_final: 0.7824 (mm-30) REVERT: o 248 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8312 (mp0) REVERT: o 259 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.8482 (m-30) REVERT: o 333 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8423 (mp0) REVERT: n 5 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8817 (pm20) REVERT: n 147 MET cc_start: 0.9413 (tpp) cc_final: 0.8860 (mmm) REVERT: n 326 LYS cc_start: 0.8503 (tptp) cc_final: 0.8253 (tptp) REVERT: n 342 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: n 383 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9284 (tm) REVERT: n 405 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8947 (ptp) REVERT: n 415 MET cc_start: 0.9215 (ttm) cc_final: 0.8922 (ttt) REVERT: n 417 LYS cc_start: 0.9391 (pttt) cc_final: 0.9038 (tppt) REVERT: m 67 SER cc_start: 0.9051 (m) cc_final: 0.8637 (p) REVERT: m 226 GLU cc_start: 0.8373 (tp30) cc_final: 0.7968 (tt0) REVERT: m 244 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8374 (mm-30) REVERT: m 259 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8554 (m-30) REVERT: m 411 ASP cc_start: 0.9249 (m-30) cc_final: 0.8775 (m-30) REVERT: m 414 GLU cc_start: 0.8866 (pp20) cc_final: 0.8594 (pp20) REVERT: l 92 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7903 (pmm-80) REVERT: l 125 GLU cc_start: 0.9055 (mp0) cc_final: 0.8664 (mp0) REVERT: l 144 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8286 (ttt90) REVERT: l 218 GLU cc_start: 0.8825 (tp30) cc_final: 0.8533 (tp30) REVERT: l 342 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8296 (mt-10) REVERT: l 378 GLN cc_start: 0.9234 (mm-40) cc_final: 0.9006 (mm-40) REVERT: l 416 MET cc_start: 0.9314 (mmm) cc_final: 0.9104 (mmp) REVERT: k 218 GLU cc_start: 0.8814 (tp30) cc_final: 0.8523 (tt0) REVERT: k 244 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8195 (mm-30) REVERT: k 259 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8544 (m-30) REVERT: k 374 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7652 (tm-30) REVERT: k 378 GLN cc_start: 0.9320 (mt0) cc_final: 0.8760 (mt0) REVERT: j 218 GLU cc_start: 0.8890 (tp30) cc_final: 0.8631 (tt0) REVERT: j 219 MET cc_start: 0.9263 (tpp) cc_final: 0.9018 (tpp) REVERT: j 342 GLU cc_start: 0.8492 (mp0) cc_final: 0.7834 (mp0) REVERT: j 397 GLU cc_start: 0.8809 (pt0) cc_final: 0.8565 (mt-10) REVERT: i 19 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8135 (mm-30) REVERT: i 30 ARG cc_start: 0.7817 (mmm-85) cc_final: 0.7478 (mtm180) REVERT: i 67 SER cc_start: 0.9060 (m) cc_final: 0.8670 (p) REVERT: i 197 TYR cc_start: 0.9234 (t80) cc_final: 0.8843 (t80) REVERT: i 244 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8219 (mm-30) REVERT: i 272 ARG cc_start: 0.8999 (mmm-85) cc_final: 0.8735 (mmm-85) REVERT: i 342 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8524 (mt-10) REVERT: i 374 GLN cc_start: 0.8334 (tp-100) cc_final: 0.8025 (tp40) REVERT: i 397 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8289 (mp0) REVERT: h 5 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8476 (pm20) REVERT: h 19 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8555 (mm-30) REVERT: h 207 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8307 (tt) REVERT: h 226 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: h 259 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8397 (m-30) REVERT: h 326 LYS cc_start: 0.8906 (mppt) cc_final: 0.8652 (ttmm) REVERT: h 342 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: h 411 ASP cc_start: 0.8964 (m-30) cc_final: 0.8623 (m-30) REVERT: g 5 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8995 (pm20) REVERT: g 92 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7859 (pmm-80) REVERT: g 145 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8734 (mt) REVERT: g 342 GLU cc_start: 0.8539 (mt-10) cc_final: 0.7990 (mm-30) REVERT: f 30 ARG cc_start: 0.7822 (mmm-85) cc_final: 0.7496 (mtm110) REVERT: f 244 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8434 (mm-30) REVERT: e 30 ARG cc_start: 0.8295 (mmm-85) cc_final: 0.7925 (mtp-110) REVERT: e 58 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8948 (mt) REVERT: e 292 ASN cc_start: 0.9183 (m110) cc_final: 0.8803 (p0) REVERT: e 299 ARG cc_start: 0.8760 (mmm-85) cc_final: 0.8458 (mtp85) REVERT: e 334 GLU cc_start: 0.9118 (tp30) cc_final: 0.8637 (mp0) REVERT: e 351 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8114 (mm-30) REVERT: e 407 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8447 (tptt) REVERT: d 8 ASN cc_start: 0.9409 (t0) cc_final: 0.9111 (t0) REVERT: d 12 SER cc_start: 0.9324 (m) cc_final: 0.9077 (t) REVERT: d 21 MET cc_start: 0.9193 (ttm) cc_final: 0.8926 (ttt) REVERT: d 333 GLU cc_start: 0.9077 (tp30) cc_final: 0.8787 (tp30) REVERT: d 351 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8468 (mm-30) REVERT: d 397 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8423 (mt-10) REVERT: c 12 SER cc_start: 0.9361 (m) cc_final: 0.9099 (p) REVERT: c 19 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8786 (tp30) REVERT: c 67 SER cc_start: 0.9029 (m) cc_final: 0.8662 (p) REVERT: c 244 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8115 (mm-30) REVERT: c 248 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8904 (mm-30) REVERT: c 341 MET cc_start: 0.9126 (tmm) cc_final: 0.8900 (tmm) REVERT: c 411 ASP cc_start: 0.9154 (m-30) cc_final: 0.8873 (m-30) REVERT: b 92 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7815 (pmm-80) REVERT: b 193 GLN cc_start: 0.8733 (tt0) cc_final: 0.8484 (tm-30) REVERT: b 218 GLU cc_start: 0.9078 (tp30) cc_final: 0.8685 (tp30) REVERT: b 259 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8234 (m-30) REVERT: b 292 ASN cc_start: 0.8887 (m110) cc_final: 0.8666 (p0) REVERT: b 326 LYS cc_start: 0.8891 (ttmm) cc_final: 0.8400 (tptp) REVERT: b 334 GLU cc_start: 0.8945 (tp30) cc_final: 0.8646 (tp30) REVERT: b 342 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8694 (tt0) REVERT: b 351 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8386 (mt-10) REVERT: b 374 GLN cc_start: 0.8521 (tp-100) cc_final: 0.8031 (tp40) outliers start: 226 outliers final: 175 residues processed: 1159 average time/residue: 0.5662 time to fit residues: 1096.0610 Evaluate side-chains 1174 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 965 time to evaluate : 5.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 12 SER Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 89 PHE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 153 SER Chi-restraints excluded: chain a residue 327 MET Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 216 VAL Chi-restraints excluded: chain r residue 248 GLU Chi-restraints excluded: chain r residue 292 ASN Chi-restraints excluded: chain r residue 295 HIS Chi-restraints excluded: chain r residue 376 GLU Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain q residue 89 PHE Chi-restraints excluded: chain q residue 92 ARG Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 137 THR Chi-restraints excluded: chain q residue 164 LEU Chi-restraints excluded: chain q residue 194 SER Chi-restraints excluded: chain q residue 253 LEU Chi-restraints excluded: chain q residue 333 GLU Chi-restraints excluded: chain q residue 354 VAL Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain q residue 390 MET Chi-restraints excluded: chain q residue 410 ASP Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 60 ASP Chi-restraints excluded: chain p residue 89 PHE Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 248 GLU Chi-restraints excluded: chain p residue 259 ASP Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain p residue 394 ASP Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 55 LEU Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain o residue 89 PHE Chi-restraints excluded: chain o residue 92 ARG Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 186 MET Chi-restraints excluded: chain o residue 248 GLU Chi-restraints excluded: chain o residue 259 ASP Chi-restraints excluded: chain o residue 264 LEU Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 390 MET Chi-restraints excluded: chain o residue 411 ASP Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 186 MET Chi-restraints excluded: chain n residue 241 GLN Chi-restraints excluded: chain n residue 321 ILE Chi-restraints excluded: chain n residue 342 GLU Chi-restraints excluded: chain n residue 383 LEU Chi-restraints excluded: chain n residue 390 MET Chi-restraints excluded: chain n residue 405 MET Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 6 LEU Chi-restraints excluded: chain m residue 49 ILE Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 60 ASP Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 162 LEU Chi-restraints excluded: chain m residue 164 LEU Chi-restraints excluded: chain m residue 259 ASP Chi-restraints excluded: chain m residue 394 ASP Chi-restraints excluded: chain m residue 410 ASP Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 55 LEU Chi-restraints excluded: chain l residue 58 LEU Chi-restraints excluded: chain l residue 60 ASP Chi-restraints excluded: chain l residue 92 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 132 LEU Chi-restraints excluded: chain l residue 144 ARG Chi-restraints excluded: chain l residue 216 VAL Chi-restraints excluded: chain l residue 222 LEU Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain l residue 342 GLU Chi-restraints excluded: chain l residue 383 LEU Chi-restraints excluded: chain l residue 394 ASP Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 259 ASP Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 55 LEU Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 89 PHE Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 242 VAL Chi-restraints excluded: chain j residue 394 ASP Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 60 ASP Chi-restraints excluded: chain i residue 65 LEU Chi-restraints excluded: chain i residue 89 PHE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 132 LEU Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain i residue 417 LYS Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 5 GLU Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 89 PHE Chi-restraints excluded: chain h residue 92 ARG Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 132 LEU Chi-restraints excluded: chain h residue 153 SER Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 207 LEU Chi-restraints excluded: chain h residue 216 VAL Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 259 ASP Chi-restraints excluded: chain h residue 342 GLU Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 5 GLU Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 52 ASP Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 259 ASP Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain g residue 394 ASP Chi-restraints excluded: chain g residue 417 LYS Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 60 ASP Chi-restraints excluded: chain f residue 89 PHE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain f residue 153 SER Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 52 ASP Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 60 ASP Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 60 ASP Chi-restraints excluded: chain d residue 89 PHE Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 193 GLN Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 383 LEU Chi-restraints excluded: chain d residue 410 ASP Chi-restraints excluded: chain d residue 415 MET Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 6 LEU Chi-restraints excluded: chain c residue 39 LEU Chi-restraints excluded: chain c residue 89 PHE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 132 LEU Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 248 GLU Chi-restraints excluded: chain c residue 378 GLN Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 92 ARG Chi-restraints excluded: chain b residue 101 ILE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 153 SER Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 259 ASP Chi-restraints excluded: chain b residue 410 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 435 optimal weight: 0.9990 chunk 700 optimal weight: 1.9990 chunk 427 optimal weight: 0.9990 chunk 332 optimal weight: 0.0980 chunk 487 optimal weight: 5.9990 chunk 735 optimal weight: 1.9990 chunk 676 optimal weight: 4.9990 chunk 585 optimal weight: 0.0970 chunk 60 optimal weight: 8.9990 chunk 452 optimal weight: 0.9980 chunk 358 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 295 HIS r 292 ASN ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 220 GLN ** p 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 275 ASN ** n 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 241 GLN ** m 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 189 GLN ** e 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 60822 Z= 0.163 Angle : 0.635 12.217 82008 Z= 0.299 Chirality : 0.041 0.204 9324 Planarity : 0.003 0.030 10620 Dihedral : 6.328 177.887 8439 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.12 % Allowed : 29.92 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.39 (0.10), residues: 7506 helix: 1.74 (0.09), residues: 3438 sheet: 0.87 (0.16), residues: 1170 loop : 0.03 (0.11), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP a 381 HIS 0.012 0.001 HIS a 295 PHE 0.010 0.001 PHE q 412 TYR 0.022 0.001 TYR a 80 ARG 0.009 0.000 ARG m 418 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1201 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 999 time to evaluate : 5.594 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: a 21 MET cc_start: 0.8724 (ttt) cc_final: 0.8197 (ttt) REVERT: a 92 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8464 (mmt180) REVERT: a 132 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8322 (tm) REVERT: a 197 TYR cc_start: 0.9021 (t80) cc_final: 0.8802 (t80) REVERT: a 218 GLU cc_start: 0.9280 (tp30) cc_final: 0.8850 (tp30) REVERT: a 341 MET cc_start: 0.9317 (tmm) cc_final: 0.9030 (tmm) REVERT: a 362 ARG cc_start: 0.9213 (ttm110) cc_final: 0.8794 (mtm-85) REVERT: a 374 GLN cc_start: 0.8606 (tp-100) cc_final: 0.8322 (tp-100) REVERT: a 388 HIS cc_start: 0.9429 (t70) cc_final: 0.9160 (t-90) REVERT: a 411 ASP cc_start: 0.9275 (m-30) cc_final: 0.8871 (m-30) REVERT: r 21 MET cc_start: 0.9138 (ttm) cc_final: 0.8799 (ttt) REVERT: r 244 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8693 (mm-30) REVERT: r 248 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8774 (mm-30) REVERT: r 292 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8476 (p0) REVERT: r 298 LYS cc_start: 0.9090 (mmmm) cc_final: 0.8519 (tmtt) REVERT: r 328 ASP cc_start: 0.9218 (m-30) cc_final: 0.8842 (m-30) REVERT: r 390 MET cc_start: 0.8828 (pmm) cc_final: 0.8580 (pmm) REVERT: q 33 ASP cc_start: 0.8967 (m-30) cc_final: 0.8544 (m-30) REVERT: q 134 GLU cc_start: 0.8611 (mp0) cc_final: 0.8394 (mp0) REVERT: q 186 MET cc_start: 0.8211 (ptt) cc_final: 0.7986 (ppp) REVERT: q 253 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9361 (mm) REVERT: q 360 TYR cc_start: 0.9173 (t80) cc_final: 0.8844 (t80) REVERT: q 390 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8457 (pmm) REVERT: p 30 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.7892 (mtp-110) REVERT: p 59 GLN cc_start: 0.8526 (pm20) cc_final: 0.8176 (pm20) REVERT: p 186 MET cc_start: 0.9169 (ptm) cc_final: 0.8881 (ptp) REVERT: p 189 GLN cc_start: 0.9311 (mt0) cc_final: 0.9041 (mt0) REVERT: p 244 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8269 (mm-30) REVERT: p 248 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8761 (mp0) REVERT: p 259 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: p 334 GLU cc_start: 0.8771 (tp30) cc_final: 0.8427 (tp30) REVERT: p 401 ASN cc_start: 0.9042 (t0) cc_final: 0.8830 (t0) REVERT: o 5 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8655 (pm20) REVERT: o 105 LYS cc_start: 0.8560 (tmmt) cc_final: 0.8184 (tmmt) REVERT: o 115 LYS cc_start: 0.9199 (tmmt) cc_final: 0.8910 (ptmm) REVERT: o 147 MET cc_start: 0.9446 (tpp) cc_final: 0.8951 (mmm) REVERT: o 218 GLU cc_start: 0.9026 (tp30) cc_final: 0.8807 (tp30) REVERT: o 234 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7373 (mp0) REVERT: o 244 GLU cc_start: 0.8547 (mm-30) cc_final: 0.7835 (mm-30) REVERT: o 248 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8305 (mp0) REVERT: o 259 ASP cc_start: 0.9081 (OUTLIER) cc_final: 0.8459 (m-30) REVERT: o 327 MET cc_start: 0.8763 (ptm) cc_final: 0.8553 (ttp) REVERT: o 329 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8345 (mm-30) REVERT: o 333 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8344 (mp0) REVERT: n 5 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8795 (pm20) REVERT: n 40 LYS cc_start: 0.9101 (ttpt) cc_final: 0.8747 (ttmm) REVERT: n 147 MET cc_start: 0.9406 (tpp) cc_final: 0.8857 (mmm) REVERT: n 326 LYS cc_start: 0.8431 (tptp) cc_final: 0.8209 (tptp) REVERT: n 342 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8228 (mp0) REVERT: n 383 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9288 (tm) REVERT: n 405 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8844 (ptp) REVERT: n 415 MET cc_start: 0.9206 (ttm) cc_final: 0.8904 (ttt) REVERT: n 417 LYS cc_start: 0.9386 (pttt) cc_final: 0.9024 (tppt) REVERT: m 67 SER cc_start: 0.9072 (m) cc_final: 0.8653 (p) REVERT: m 226 GLU cc_start: 0.8423 (tp30) cc_final: 0.8023 (tt0) REVERT: m 244 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8320 (mm-30) REVERT: m 259 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8543 (m-30) REVERT: m 327 MET cc_start: 0.8497 (ttp) cc_final: 0.8199 (tmm) REVERT: m 411 ASP cc_start: 0.9228 (m-30) cc_final: 0.8759 (m-30) REVERT: m 414 GLU cc_start: 0.8867 (pp20) cc_final: 0.8582 (pp20) REVERT: l 59 GLN cc_start: 0.9325 (mp10) cc_final: 0.9068 (mp10) REVERT: l 92 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7917 (pmm-80) REVERT: l 125 GLU cc_start: 0.9052 (mp0) cc_final: 0.8676 (mp0) REVERT: l 218 GLU cc_start: 0.8817 (tp30) cc_final: 0.8514 (tp30) REVERT: l 378 GLN cc_start: 0.9241 (mm-40) cc_final: 0.9036 (mm-40) REVERT: l 416 MET cc_start: 0.9323 (mmm) cc_final: 0.9102 (mmp) REVERT: k 218 GLU cc_start: 0.8815 (tp30) cc_final: 0.8514 (tt0) REVERT: k 244 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8243 (mm-30) REVERT: k 259 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8513 (m-30) REVERT: k 374 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7643 (tm-30) REVERT: k 378 GLN cc_start: 0.9314 (mt0) cc_final: 0.8766 (mt0) REVERT: j 19 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8515 (mm-30) REVERT: j 218 GLU cc_start: 0.8908 (tp30) cc_final: 0.8646 (tt0) REVERT: j 219 MET cc_start: 0.9251 (tpp) cc_final: 0.9010 (tpp) REVERT: j 244 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8413 (mm-30) REVERT: j 342 GLU cc_start: 0.8472 (mp0) cc_final: 0.7836 (mp0) REVERT: j 374 GLN cc_start: 0.8420 (tp40) cc_final: 0.7633 (tp40) REVERT: j 378 GLN cc_start: 0.9327 (mm-40) cc_final: 0.8847 (mm-40) REVERT: j 397 GLU cc_start: 0.8816 (pt0) cc_final: 0.8562 (mt-10) REVERT: i 19 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8144 (mm-30) REVERT: i 30 ARG cc_start: 0.7802 (mmm-85) cc_final: 0.7480 (mtm180) REVERT: i 67 SER cc_start: 0.9077 (m) cc_final: 0.8678 (p) REVERT: i 197 TYR cc_start: 0.9253 (t80) cc_final: 0.8934 (t80) REVERT: i 244 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8248 (mm-30) REVERT: i 272 ARG cc_start: 0.9000 (mmm-85) cc_final: 0.8736 (mmm-85) REVERT: i 342 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8504 (mt-10) REVERT: i 347 ARG cc_start: 0.8560 (tpt-90) cc_final: 0.8154 (tpt-90) REVERT: i 374 GLN cc_start: 0.8223 (tp-100) cc_final: 0.7664 (tp40) REVERT: i 378 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8545 (mm-40) REVERT: i 397 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8319 (mp0) REVERT: h 5 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8468 (pm20) REVERT: h 19 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8551 (mm-30) REVERT: h 125 GLU cc_start: 0.8915 (mp0) cc_final: 0.8651 (mp0) REVERT: h 207 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8333 (tt) REVERT: h 226 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: h 259 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8394 (m-30) REVERT: h 326 LYS cc_start: 0.8893 (mppt) cc_final: 0.8634 (ttmm) REVERT: h 342 GLU cc_start: 0.8515 (mp0) cc_final: 0.7724 (mp0) REVERT: h 374 GLN cc_start: 0.8390 (tp-100) cc_final: 0.8172 (tp-100) REVERT: h 411 ASP cc_start: 0.8963 (m-30) cc_final: 0.8680 (m-30) REVERT: g 1 MET cc_start: 0.7403 (ttt) cc_final: 0.7120 (tpp) REVERT: g 5 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8995 (pm20) REVERT: g 92 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7829 (pmm-80) REVERT: g 145 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8702 (mt) REVERT: g 342 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7972 (mm-30) REVERT: f 30 ARG cc_start: 0.7757 (mmm-85) cc_final: 0.7431 (mtm110) REVERT: f 211 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8259 (mm-30) REVERT: f 244 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8417 (mm-30) REVERT: f 374 GLN cc_start: 0.8598 (tp40) cc_final: 0.8275 (tp40) REVERT: f 378 GLN cc_start: 0.9368 (mm-40) cc_final: 0.9103 (mm-40) REVERT: e 30 ARG cc_start: 0.8290 (mmm-85) cc_final: 0.7926 (mtp-110) REVERT: e 58 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8929 (mt) REVERT: e 292 ASN cc_start: 0.9177 (m110) cc_final: 0.8817 (p0) REVERT: e 299 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.8453 (mtp85) REVERT: e 334 GLU cc_start: 0.9137 (tp30) cc_final: 0.8623 (mp0) REVERT: e 342 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8346 (mm-30) REVERT: e 351 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8107 (mm-30) REVERT: e 407 LYS cc_start: 0.8882 (mmmt) cc_final: 0.8469 (tptt) REVERT: d 8 ASN cc_start: 0.9400 (t0) cc_final: 0.9115 (t0) REVERT: d 12 SER cc_start: 0.9272 (m) cc_final: 0.9013 (t) REVERT: d 21 MET cc_start: 0.9195 (ttm) cc_final: 0.8921 (ttt) REVERT: d 333 GLU cc_start: 0.9056 (tp30) cc_final: 0.8773 (tp30) REVERT: d 397 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8446 (mt-10) REVERT: c 12 SER cc_start: 0.9348 (m) cc_final: 0.9080 (p) REVERT: c 19 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8778 (tp30) REVERT: c 67 SER cc_start: 0.9039 (m) cc_final: 0.8659 (p) REVERT: c 197 TYR cc_start: 0.9052 (t80) cc_final: 0.8629 (t80) REVERT: c 244 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8130 (mm-30) REVERT: c 248 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8901 (mm-30) REVERT: c 341 MET cc_start: 0.9094 (tmm) cc_final: 0.8863 (tmm) REVERT: c 411 ASP cc_start: 0.9140 (m-30) cc_final: 0.8811 (m-30) REVERT: b 92 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7797 (pmm-80) REVERT: b 193 GLN cc_start: 0.8740 (tt0) cc_final: 0.8487 (tm-30) REVERT: b 218 GLU cc_start: 0.9089 (tp30) cc_final: 0.8681 (tp30) REVERT: b 259 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: b 326 LYS cc_start: 0.8891 (ttmm) cc_final: 0.8367 (tptp) REVERT: b 329 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8590 (mm-30) REVERT: b 334 GLU cc_start: 0.8954 (tp30) cc_final: 0.8653 (tp30) REVERT: b 342 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8702 (tt0) REVERT: b 351 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8362 (mt-10) REVERT: b 374 GLN cc_start: 0.8509 (tp-100) cc_final: 0.7941 (tm-30) outliers start: 202 outliers final: 145 residues processed: 1148 average time/residue: 0.5668 time to fit residues: 1089.3352 Evaluate side-chains 1141 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 967 time to evaluate : 5.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 89 PHE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 295 HIS Chi-restraints excluded: chain a residue 327 MET Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 216 VAL Chi-restraints excluded: chain r residue 248 GLU Chi-restraints excluded: chain r residue 292 ASN Chi-restraints excluded: chain r residue 295 HIS Chi-restraints excluded: chain r residue 374 GLN Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 60 ASP Chi-restraints excluded: chain q residue 89 PHE Chi-restraints excluded: chain q residue 92 ARG Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 137 THR Chi-restraints excluded: chain q residue 164 LEU Chi-restraints excluded: chain q residue 194 SER Chi-restraints excluded: chain q residue 253 LEU Chi-restraints excluded: chain q residue 333 GLU Chi-restraints excluded: chain q residue 354 VAL Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain q residue 390 MET Chi-restraints excluded: chain q residue 410 ASP Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 248 GLU Chi-restraints excluded: chain p residue 259 ASP Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain o residue 5 GLU Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain o residue 92 ARG Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 186 MET Chi-restraints excluded: chain o residue 248 GLU Chi-restraints excluded: chain o residue 259 ASP Chi-restraints excluded: chain o residue 264 LEU Chi-restraints excluded: chain o residue 390 MET Chi-restraints excluded: chain o residue 411 ASP Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 39 LEU Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 186 MET Chi-restraints excluded: chain n residue 241 GLN Chi-restraints excluded: chain n residue 321 ILE Chi-restraints excluded: chain n residue 342 GLU Chi-restraints excluded: chain n residue 383 LEU Chi-restraints excluded: chain n residue 390 MET Chi-restraints excluded: chain n residue 405 MET Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 6 LEU Chi-restraints excluded: chain m residue 49 ILE Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 164 LEU Chi-restraints excluded: chain m residue 259 ASP Chi-restraints excluded: chain m residue 394 ASP Chi-restraints excluded: chain m residue 410 ASP Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 55 LEU Chi-restraints excluded: chain l residue 60 ASP Chi-restraints excluded: chain l residue 89 PHE Chi-restraints excluded: chain l residue 92 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 132 LEU Chi-restraints excluded: chain l residue 222 LEU Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain l residue 394 ASP Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 259 ASP Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 55 LEU Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 89 PHE Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 242 VAL Chi-restraints excluded: chain j residue 394 ASP Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 132 LEU Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 5 GLU Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 132 LEU Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 207 LEU Chi-restraints excluded: chain h residue 216 VAL Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 259 ASP Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 5 GLU Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 52 ASP Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain g residue 417 LYS Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 153 SER Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 52 ASP Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 60 ASP Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 60 ASP Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 193 GLN Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 383 LEU Chi-restraints excluded: chain d residue 410 ASP Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 6 LEU Chi-restraints excluded: chain c residue 39 LEU Chi-restraints excluded: chain c residue 89 PHE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 248 GLU Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 92 ARG Chi-restraints excluded: chain b residue 101 ILE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 259 ASP Chi-restraints excluded: chain b residue 410 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 465 optimal weight: 5.9990 chunk 623 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 539 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 586 optimal weight: 0.9990 chunk 245 optimal weight: 6.9990 chunk 602 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 295 HIS ** r 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 292 ASN ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 220 GLN p 374 GLN ** n 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 59 GLN ** m 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 198 ASN ** k 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 193 GLN j 374 GLN ** i 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 189 GLN h 220 GLN d 193 GLN c 378 GLN b 90 ASN ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.072168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.055274 restraints weight = 151572.451| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.07 r_work: 0.2594 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 60822 Z= 0.224 Angle : 0.653 12.016 82008 Z= 0.307 Chirality : 0.042 0.198 9324 Planarity : 0.003 0.031 10620 Dihedral : 6.226 176.833 8425 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.04 % Allowed : 30.25 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.38 (0.10), residues: 7506 helix: 1.74 (0.09), residues: 3438 sheet: 0.83 (0.16), residues: 1170 loop : 0.04 (0.11), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP a 381 HIS 0.012 0.001 HIS n 295 PHE 0.024 0.001 PHE q 412 TYR 0.021 0.002 TYR e 332 ARG 0.009 0.000 ARG g 418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17373.40 seconds wall clock time: 303 minutes 40.66 seconds (18220.66 seconds total)