Starting phenix.real_space_refine on Sat Apr 6 21:18:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3p_18132/04_2024/8q3p_18132_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3p_18132/04_2024/8q3p_18132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3p_18132/04_2024/8q3p_18132.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3p_18132/04_2024/8q3p_18132.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3p_18132/04_2024/8q3p_18132_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3p_18132/04_2024/8q3p_18132_updated.pdb" } resolution = 3.5 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= 0.015 sd= 0.066 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 GLU 19": "OE1" <-> "OE2" Residue "a PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 52": "OD1" <-> "OD2" Residue "a ASP 60": "OD1" <-> "OD2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "a GLU 218": "OE1" <-> "OE2" Residue "a GLU 244": "OE1" <-> "OE2" Residue "a ASP 259": "OD1" <-> "OD2" Residue "a TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 334": "OE1" <-> "OE2" Residue "a GLU 342": "OE1" <-> "OE2" Residue "a GLU 375": "OE1" <-> "OE2" Residue "a PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 19": "OE1" <-> "OE2" Residue "r PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 52": "OD1" <-> "OD2" Residue "r ASP 60": "OD1" <-> "OD2" Residue "r GLU 155": "OE1" <-> "OE2" Residue "r GLU 218": "OE1" <-> "OE2" Residue "r GLU 244": "OE1" <-> "OE2" Residue "r ASP 259": "OD1" <-> "OD2" Residue "r TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 334": "OE1" <-> "OE2" Residue "r GLU 342": "OE1" <-> "OE2" Residue "r GLU 375": "OE1" <-> "OE2" Residue "r PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 19": "OE1" <-> "OE2" Residue "q PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 52": "OD1" <-> "OD2" Residue "q ASP 60": "OD1" <-> "OD2" Residue "q GLU 155": "OE1" <-> "OE2" Residue "q GLU 218": "OE1" <-> "OE2" Residue "q GLU 244": "OE1" <-> "OE2" Residue "q ASP 259": "OD1" <-> "OD2" Residue "q TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 334": "OE1" <-> "OE2" Residue "q GLU 342": "OE1" <-> "OE2" Residue "q GLU 375": "OE1" <-> "OE2" Residue "q PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 19": "OE1" <-> "OE2" Residue "p PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 52": "OD1" <-> "OD2" Residue "p ASP 60": "OD1" <-> "OD2" Residue "p GLU 155": "OE1" <-> "OE2" Residue "p GLU 218": "OE1" <-> "OE2" Residue "p GLU 244": "OE1" <-> "OE2" Residue "p ASP 259": "OD1" <-> "OD2" Residue "p TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 334": "OE1" <-> "OE2" Residue "p GLU 342": "OE1" <-> "OE2" Residue "p GLU 375": "OE1" <-> "OE2" Residue "p PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 19": "OE1" <-> "OE2" Residue "o PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 52": "OD1" <-> "OD2" Residue "o ASP 60": "OD1" <-> "OD2" Residue "o GLU 155": "OE1" <-> "OE2" Residue "o GLU 218": "OE1" <-> "OE2" Residue "o GLU 244": "OE1" <-> "OE2" Residue "o ASP 259": "OD1" <-> "OD2" Residue "o TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 334": "OE1" <-> "OE2" Residue "o GLU 342": "OE1" <-> "OE2" Residue "o GLU 375": "OE1" <-> "OE2" Residue "o PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 19": "OE1" <-> "OE2" Residue "n PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 52": "OD1" <-> "OD2" Residue "n ASP 60": "OD1" <-> "OD2" Residue "n GLU 155": "OE1" <-> "OE2" Residue "n GLU 218": "OE1" <-> "OE2" Residue "n GLU 244": "OE1" <-> "OE2" Residue "n ASP 259": "OD1" <-> "OD2" Residue "n TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 334": "OE1" <-> "OE2" Residue "n GLU 342": "OE1" <-> "OE2" Residue "n GLU 375": "OE1" <-> "OE2" Residue "n PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 19": "OE1" <-> "OE2" Residue "m PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 52": "OD1" <-> "OD2" Residue "m ASP 60": "OD1" <-> "OD2" Residue "m GLU 155": "OE1" <-> "OE2" Residue "m GLU 218": "OE1" <-> "OE2" Residue "m GLU 244": "OE1" <-> "OE2" Residue "m ASP 259": "OD1" <-> "OD2" Residue "m TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 334": "OE1" <-> "OE2" Residue "m GLU 342": "OE1" <-> "OE2" Residue "m GLU 375": "OE1" <-> "OE2" Residue "m PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 19": "OE1" <-> "OE2" Residue "l PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 52": "OD1" <-> "OD2" Residue "l ASP 60": "OD1" <-> "OD2" Residue "l GLU 155": "OE1" <-> "OE2" Residue "l GLU 218": "OE1" <-> "OE2" Residue "l GLU 244": "OE1" <-> "OE2" Residue "l ASP 259": "OD1" <-> "OD2" Residue "l TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 334": "OE1" <-> "OE2" Residue "l GLU 342": "OE1" <-> "OE2" Residue "l GLU 375": "OE1" <-> "OE2" Residue "l PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 19": "OE1" <-> "OE2" Residue "k PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 52": "OD1" <-> "OD2" Residue "k ASP 60": "OD1" <-> "OD2" Residue "k GLU 155": "OE1" <-> "OE2" Residue "k GLU 218": "OE1" <-> "OE2" Residue "k GLU 244": "OE1" <-> "OE2" Residue "k ASP 259": "OD1" <-> "OD2" Residue "k TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 334": "OE1" <-> "OE2" Residue "k GLU 342": "OE1" <-> "OE2" Residue "k GLU 375": "OE1" <-> "OE2" Residue "k PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 19": "OE1" <-> "OE2" Residue "j PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 52": "OD1" <-> "OD2" Residue "j ASP 60": "OD1" <-> "OD2" Residue "j GLU 155": "OE1" <-> "OE2" Residue "j GLU 218": "OE1" <-> "OE2" Residue "j GLU 244": "OE1" <-> "OE2" Residue "j ASP 259": "OD1" <-> "OD2" Residue "j TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 334": "OE1" <-> "OE2" Residue "j GLU 342": "OE1" <-> "OE2" Residue "j GLU 375": "OE1" <-> "OE2" Residue "j PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 19": "OE1" <-> "OE2" Residue "b PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 52": "OD1" <-> "OD2" Residue "b ASP 60": "OD1" <-> "OD2" Residue "b GLU 155": "OE1" <-> "OE2" Residue "b GLU 218": "OE1" <-> "OE2" Residue "b GLU 244": "OE1" <-> "OE2" Residue "b ASP 259": "OD1" <-> "OD2" Residue "b TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 334": "OE1" <-> "OE2" Residue "b GLU 342": "OE1" <-> "OE2" Residue "b GLU 375": "OE1" <-> "OE2" Residue "b PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 19": "OE1" <-> "OE2" Residue "c PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 52": "OD1" <-> "OD2" Residue "c ASP 60": "OD1" <-> "OD2" Residue "c GLU 155": "OE1" <-> "OE2" Residue "c GLU 218": "OE1" <-> "OE2" Residue "c GLU 244": "OE1" <-> "OE2" Residue "c ASP 259": "OD1" <-> "OD2" Residue "c TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 334": "OE1" <-> "OE2" Residue "c GLU 342": "OE1" <-> "OE2" Residue "c GLU 375": "OE1" <-> "OE2" Residue "c PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 19": "OE1" <-> "OE2" Residue "d PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 52": "OD1" <-> "OD2" Residue "d ASP 60": "OD1" <-> "OD2" Residue "d GLU 155": "OE1" <-> "OE2" Residue "d GLU 218": "OE1" <-> "OE2" Residue "d GLU 244": "OE1" <-> "OE2" Residue "d ASP 259": "OD1" <-> "OD2" Residue "d TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 334": "OE1" <-> "OE2" Residue "d GLU 342": "OE1" <-> "OE2" Residue "d GLU 375": "OE1" <-> "OE2" Residue "d PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 19": "OE1" <-> "OE2" Residue "e PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 52": "OD1" <-> "OD2" Residue "e ASP 60": "OD1" <-> "OD2" Residue "e GLU 155": "OE1" <-> "OE2" Residue "e GLU 218": "OE1" <-> "OE2" Residue "e GLU 244": "OE1" <-> "OE2" Residue "e ASP 259": "OD1" <-> "OD2" Residue "e TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 334": "OE1" <-> "OE2" Residue "e GLU 342": "OE1" <-> "OE2" Residue "e GLU 375": "OE1" <-> "OE2" Residue "e PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 19": "OE1" <-> "OE2" Residue "f PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 52": "OD1" <-> "OD2" Residue "f ASP 60": "OD1" <-> "OD2" Residue "f GLU 155": "OE1" <-> "OE2" Residue "f GLU 218": "OE1" <-> "OE2" Residue "f GLU 244": "OE1" <-> "OE2" Residue "f ASP 259": "OD1" <-> "OD2" Residue "f TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 334": "OE1" <-> "OE2" Residue "f GLU 342": "OE1" <-> "OE2" Residue "f GLU 375": "OE1" <-> "OE2" Residue "f PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 19": "OE1" <-> "OE2" Residue "g PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 52": "OD1" <-> "OD2" Residue "g ASP 60": "OD1" <-> "OD2" Residue "g GLU 155": "OE1" <-> "OE2" Residue "g GLU 218": "OE1" <-> "OE2" Residue "g GLU 244": "OE1" <-> "OE2" Residue "g ASP 259": "OD1" <-> "OD2" Residue "g TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 334": "OE1" <-> "OE2" Residue "g GLU 342": "OE1" <-> "OE2" Residue "g GLU 375": "OE1" <-> "OE2" Residue "g PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 19": "OE1" <-> "OE2" Residue "h PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 52": "OD1" <-> "OD2" Residue "h ASP 60": "OD1" <-> "OD2" Residue "h GLU 155": "OE1" <-> "OE2" Residue "h GLU 218": "OE1" <-> "OE2" Residue "h GLU 244": "OE1" <-> "OE2" Residue "h ASP 259": "OD1" <-> "OD2" Residue "h TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 334": "OE1" <-> "OE2" Residue "h GLU 342": "OE1" <-> "OE2" Residue "h GLU 375": "OE1" <-> "OE2" Residue "h PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 19": "OE1" <-> "OE2" Residue "i PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 52": "OD1" <-> "OD2" Residue "i ASP 60": "OD1" <-> "OD2" Residue "i GLU 155": "OE1" <-> "OE2" Residue "i GLU 218": "OE1" <-> "OE2" Residue "i GLU 244": "OE1" <-> "OE2" Residue "i ASP 259": "OD1" <-> "OD2" Residue "i TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 334": "OE1" <-> "OE2" Residue "i GLU 342": "OE1" <-> "OE2" Residue "i GLU 375": "OE1" <-> "OE2" Residue "i PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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} 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: "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: "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: "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: "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: "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: "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} Time building chain proxies: 22.67, per 1000 atoms: 0.38 Number of scatterers: 59922 At special positions: 0 Unit cell: (139.776, 140.608, 277.056, 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: 18.82 Conformation dependent library (CDL) restraints added in 7.9 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: 306 helices and 36 sheets defined 42.0% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.70 Creating SS restraints... Processing helix chain 'a' and resid 3 through 8 Processing helix chain 'a' and resid 11 through 21 removed outlier: 3.871A pdb=" N THR a 16 " --> pdb=" O SER a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 31 through 44 Processing helix chain 'a' and resid 83 through 88 Processing helix chain 'a' and resid 124 through 128 Processing helix chain 'a' and resid 158 through 165 removed outlier: 3.625A pdb=" N LEU a 164 " --> pdb=" O ARG a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 198 Processing helix chain 'a' and resid 213 through 222 removed outlier: 3.718A pdb=" N GLU a 218 " --> pdb=" O GLU a 214 " (cutoff:3.500A) Processing helix chain 'a' and resid 236 through 256 removed outlier: 3.573A 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 286 through 288 No H-bonds generated for 'chain 'a' and resid 286 through 288' Processing helix chain 'a' and resid 291 through 302 removed outlier: 4.027A 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 336 removed outlier: 3.899A pdb=" N VAL a 330 " --> pdb=" O LYS a 326 " (cutoff:3.500A) Processing helix chain 'a' and resid 347 through 352 Processing helix chain 'a' and resid 374 through 388 removed outlier: 4.525A pdb=" N GLN a 378 " --> pdb=" O GLN a 374 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS a 379 " --> pdb=" O GLU a 375 " (cutoff:3.500A) Processing helix chain 'a' and resid 392 through 405 Processing helix chain 'a' and resid 409 through 416 Processing helix chain 'r' and resid 3 through 8 Processing helix chain 'r' and resid 11 through 21 removed outlier: 3.872A pdb=" N THR r 16 " --> pdb=" O SER r 12 " (cutoff:3.500A) Processing helix chain 'r' and resid 31 through 44 Processing helix chain 'r' and resid 83 through 88 Processing helix chain 'r' and resid 124 through 128 Processing helix chain 'r' and resid 158 through 165 removed outlier: 3.624A pdb=" N LEU r 164 " --> pdb=" O ARG r 160 " (cutoff:3.500A) Processing helix chain 'r' and resid 184 through 198 Processing helix chain 'r' and resid 213 through 222 removed outlier: 3.718A pdb=" N GLU r 218 " --> pdb=" O GLU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 236 through 256 removed outlier: 3.574A 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 286 through 288 No H-bonds generated for 'chain 'r' and resid 286 through 288' Processing helix chain 'r' and resid 291 through 302 removed outlier: 4.027A 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 336 removed outlier: 3.900A pdb=" N VAL r 330 " --> pdb=" O LYS r 326 " (cutoff:3.500A) Processing helix chain 'r' and resid 347 through 352 Processing helix chain 'r' and resid 374 through 388 removed outlier: 4.525A pdb=" N GLN r 378 " --> pdb=" O GLN r 374 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS r 379 " --> pdb=" O GLU r 375 " (cutoff:3.500A) Processing helix chain 'r' and resid 392 through 405 Processing helix chain 'r' and resid 409 through 416 Processing helix chain 'q' and resid 3 through 8 Processing helix chain 'q' and resid 11 through 21 removed outlier: 3.873A pdb=" N THR q 16 " --> pdb=" O SER q 12 " (cutoff:3.500A) Processing helix chain 'q' and resid 31 through 44 Processing helix chain 'q' and resid 83 through 88 Processing helix chain 'q' and resid 124 through 128 Processing helix chain 'q' and resid 158 through 165 removed outlier: 3.624A pdb=" N LEU q 164 " --> pdb=" O ARG q 160 " (cutoff:3.500A) Processing helix chain 'q' and resid 184 through 198 Processing helix chain 'q' and resid 213 through 222 removed outlier: 3.719A pdb=" N GLU q 218 " --> pdb=" O GLU q 214 " (cutoff:3.500A) Processing helix chain 'q' and resid 236 through 256 removed outlier: 3.573A 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 286 through 288 No H-bonds generated for 'chain 'q' and resid 286 through 288' Processing helix chain 'q' and resid 291 through 302 removed outlier: 4.027A 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 336 removed outlier: 3.899A pdb=" N VAL q 330 " --> pdb=" O LYS q 326 " (cutoff:3.500A) Processing helix chain 'q' and resid 347 through 352 Processing helix chain 'q' and resid 374 through 388 removed outlier: 4.525A pdb=" N GLN q 378 " --> pdb=" O GLN q 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS q 379 " --> pdb=" O GLU q 375 " (cutoff:3.500A) Processing helix chain 'q' and resid 392 through 405 Processing helix chain 'q' and resid 409 through 416 Processing helix chain 'p' and resid 3 through 8 Processing helix chain 'p' and resid 11 through 21 removed outlier: 3.872A pdb=" N THR p 16 " --> pdb=" O SER p 12 " (cutoff:3.500A) Processing helix chain 'p' and resid 31 through 44 Processing helix chain 'p' and resid 83 through 88 Processing helix chain 'p' and resid 124 through 128 Processing helix chain 'p' and resid 158 through 165 removed outlier: 3.624A pdb=" N LEU p 164 " --> pdb=" O ARG p 160 " (cutoff:3.500A) Processing helix chain 'p' and resid 184 through 198 Processing helix chain 'p' and resid 213 through 222 removed outlier: 3.719A pdb=" N GLU p 218 " --> pdb=" O GLU p 214 " (cutoff:3.500A) Processing helix chain 'p' and resid 236 through 256 removed outlier: 3.573A 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 286 through 288 No H-bonds generated for 'chain 'p' and resid 286 through 288' Processing helix chain 'p' and resid 291 through 302 removed outlier: 4.027A 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 336 removed outlier: 3.899A pdb=" N VAL p 330 " --> pdb=" O LYS p 326 " (cutoff:3.500A) Processing helix chain 'p' and resid 347 through 352 Processing helix chain 'p' and resid 374 through 388 removed outlier: 4.525A pdb=" N GLN p 378 " --> pdb=" O GLN p 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS p 379 " --> pdb=" O GLU p 375 " (cutoff:3.500A) Processing helix chain 'p' and resid 392 through 405 Processing helix chain 'p' and resid 409 through 416 Processing helix chain 'o' and resid 3 through 8 Processing helix chain 'o' and resid 11 through 21 removed outlier: 3.872A pdb=" N THR o 16 " --> pdb=" O SER o 12 " (cutoff:3.500A) Processing helix chain 'o' and resid 31 through 44 Processing helix chain 'o' and resid 83 through 88 Processing helix chain 'o' and resid 124 through 128 Processing helix chain 'o' and resid 158 through 165 removed outlier: 3.625A pdb=" N LEU o 164 " --> pdb=" O ARG o 160 " (cutoff:3.500A) Processing helix chain 'o' and resid 184 through 198 Processing helix chain 'o' and resid 213 through 222 removed outlier: 3.718A pdb=" N GLU o 218 " --> pdb=" O GLU o 214 " (cutoff:3.500A) Processing helix chain 'o' and resid 236 through 256 removed outlier: 3.574A 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 286 through 288 No H-bonds generated for 'chain 'o' and resid 286 through 288' Processing helix chain 'o' and resid 291 through 302 removed outlier: 4.027A 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 336 removed outlier: 3.900A pdb=" N VAL o 330 " --> pdb=" O LYS o 326 " (cutoff:3.500A) Processing helix chain 'o' and resid 347 through 352 Processing helix chain 'o' and resid 374 through 388 removed outlier: 4.526A pdb=" N GLN o 378 " --> pdb=" O GLN o 374 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS o 379 " --> pdb=" O GLU o 375 " (cutoff:3.500A) Processing helix chain 'o' and resid 392 through 405 Processing helix chain 'o' and resid 409 through 416 Processing helix chain 'n' and resid 3 through 8 Processing helix chain 'n' and resid 11 through 21 removed outlier: 3.872A pdb=" N THR n 16 " --> pdb=" O SER n 12 " (cutoff:3.500A) Processing helix chain 'n' and resid 31 through 44 Processing helix chain 'n' and resid 83 through 88 Processing helix chain 'n' and resid 124 through 128 Processing helix chain 'n' and resid 158 through 165 removed outlier: 3.624A pdb=" N LEU n 164 " --> pdb=" O ARG n 160 " (cutoff:3.500A) Processing helix chain 'n' and resid 184 through 198 Processing helix chain 'n' and resid 213 through 222 removed outlier: 3.719A pdb=" N GLU n 218 " --> pdb=" O GLU n 214 " (cutoff:3.500A) Processing helix chain 'n' and resid 236 through 256 removed outlier: 3.573A 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 286 through 288 No H-bonds generated for 'chain 'n' and resid 286 through 288' Processing helix chain 'n' and resid 291 through 302 removed outlier: 4.027A 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 336 removed outlier: 3.900A pdb=" N VAL n 330 " --> pdb=" O LYS n 326 " (cutoff:3.500A) Processing helix chain 'n' and resid 347 through 352 Processing helix chain 'n' and resid 374 through 388 removed outlier: 4.525A pdb=" N GLN n 378 " --> pdb=" O GLN n 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS n 379 " --> pdb=" O GLU n 375 " (cutoff:3.500A) Processing helix chain 'n' and resid 392 through 405 Processing helix chain 'n' and resid 409 through 416 Processing helix chain 'm' and resid 3 through 8 Processing helix chain 'm' and resid 11 through 21 removed outlier: 3.871A pdb=" N THR m 16 " --> pdb=" O SER m 12 " (cutoff:3.500A) Processing helix chain 'm' and resid 31 through 44 Processing helix chain 'm' and resid 83 through 88 Processing helix chain 'm' and resid 124 through 128 Processing helix chain 'm' and resid 158 through 165 removed outlier: 3.625A pdb=" N LEU m 164 " --> pdb=" O ARG m 160 " (cutoff:3.500A) Processing helix chain 'm' and resid 184 through 198 Processing helix chain 'm' and resid 213 through 222 removed outlier: 3.719A pdb=" N GLU m 218 " --> pdb=" O GLU m 214 " (cutoff:3.500A) Processing helix chain 'm' and resid 236 through 256 removed outlier: 3.573A 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 286 through 288 No H-bonds generated for 'chain 'm' and resid 286 through 288' Processing helix chain 'm' and resid 291 through 302 removed outlier: 4.027A 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 336 removed outlier: 3.900A pdb=" N VAL m 330 " --> pdb=" O LYS m 326 " (cutoff:3.500A) Processing helix chain 'm' and resid 347 through 352 Processing helix chain 'm' and resid 374 through 388 removed outlier: 4.526A pdb=" N GLN m 378 " --> pdb=" O GLN m 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS m 379 " --> pdb=" O GLU m 375 " (cutoff:3.500A) Processing helix chain 'm' and resid 392 through 405 Processing helix chain 'm' and resid 409 through 416 Processing helix chain 'l' and resid 3 through 8 Processing helix chain 'l' and resid 11 through 21 removed outlier: 3.871A pdb=" N THR l 16 " --> pdb=" O SER l 12 " (cutoff:3.500A) Processing helix chain 'l' and resid 31 through 44 Processing helix chain 'l' and resid 83 through 88 Processing helix chain 'l' and resid 124 through 128 Processing helix chain 'l' and resid 158 through 165 removed outlier: 3.624A pdb=" N LEU l 164 " --> pdb=" O ARG l 160 " (cutoff:3.500A) Processing helix chain 'l' and resid 184 through 198 Processing helix chain 'l' and resid 213 through 222 removed outlier: 3.719A pdb=" N GLU l 218 " --> pdb=" O GLU l 214 " (cutoff:3.500A) Processing helix chain 'l' and resid 236 through 256 removed outlier: 3.573A 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 286 through 288 No H-bonds generated for 'chain 'l' and resid 286 through 288' Processing helix chain 'l' and resid 291 through 302 removed outlier: 4.027A 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 336 removed outlier: 3.900A pdb=" N VAL l 330 " --> pdb=" O LYS l 326 " (cutoff:3.500A) Processing helix chain 'l' and resid 347 through 352 Processing helix chain 'l' and resid 374 through 388 removed outlier: 4.526A pdb=" N GLN l 378 " --> pdb=" O GLN l 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS l 379 " --> pdb=" O GLU l 375 " (cutoff:3.500A) Processing helix chain 'l' and resid 392 through 405 Processing helix chain 'l' and resid 409 through 416 Processing helix chain 'k' and resid 3 through 8 Processing helix chain 'k' and resid 11 through 21 removed outlier: 3.871A pdb=" N THR k 16 " --> pdb=" O SER k 12 " (cutoff:3.500A) Processing helix chain 'k' and resid 31 through 44 Processing helix chain 'k' and resid 83 through 88 Processing helix chain 'k' and resid 124 through 128 Processing helix chain 'k' and resid 158 through 165 removed outlier: 3.625A pdb=" N LEU k 164 " --> pdb=" O ARG k 160 " (cutoff:3.500A) Processing helix chain 'k' and resid 184 through 198 Processing helix chain 'k' and resid 213 through 222 removed outlier: 3.718A pdb=" N GLU k 218 " --> pdb=" O GLU k 214 " (cutoff:3.500A) Processing helix chain 'k' and resid 236 through 256 removed outlier: 3.572A 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 286 through 288 No H-bonds generated for 'chain 'k' and resid 286 through 288' Processing helix chain 'k' and resid 291 through 302 removed outlier: 4.028A 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 336 removed outlier: 3.899A pdb=" N VAL k 330 " --> pdb=" O LYS k 326 " (cutoff:3.500A) Processing helix chain 'k' and resid 347 through 352 Processing helix chain 'k' and resid 374 through 388 removed outlier: 4.526A pdb=" N GLN k 378 " --> pdb=" O GLN k 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS k 379 " --> pdb=" O GLU k 375 " (cutoff:3.500A) Processing helix chain 'k' and resid 392 through 405 Processing helix chain 'k' and resid 409 through 416 Processing helix chain 'j' and resid 3 through 8 Processing helix chain 'j' and resid 11 through 21 removed outlier: 3.872A pdb=" N THR j 16 " --> pdb=" O SER j 12 " (cutoff:3.500A) Processing helix chain 'j' and resid 31 through 44 Processing helix chain 'j' and resid 83 through 88 Processing helix chain 'j' and resid 124 through 128 Processing helix chain 'j' and resid 158 through 165 removed outlier: 3.624A pdb=" N LEU j 164 " --> pdb=" O ARG j 160 " (cutoff:3.500A) Processing helix chain 'j' and resid 184 through 198 Processing helix chain 'j' and resid 213 through 222 removed outlier: 3.718A pdb=" N GLU j 218 " --> pdb=" O GLU j 214 " (cutoff:3.500A) Processing helix chain 'j' and resid 236 through 256 removed outlier: 3.573A 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 286 through 288 No H-bonds generated for 'chain 'j' and resid 286 through 288' Processing helix chain 'j' and resid 291 through 302 removed outlier: 4.027A 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 336 removed outlier: 3.900A pdb=" N VAL j 330 " --> pdb=" O LYS j 326 " (cutoff:3.500A) Processing helix chain 'j' and resid 347 through 352 Processing helix chain 'j' and resid 374 through 388 removed outlier: 4.525A pdb=" N GLN j 378 " --> pdb=" O GLN j 374 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS j 379 " --> pdb=" O GLU j 375 " (cutoff:3.500A) Processing helix chain 'j' and resid 392 through 405 Processing helix chain 'j' and resid 409 through 416 Processing helix chain 'b' and resid 3 through 8 Processing helix chain 'b' and resid 11 through 21 removed outlier: 3.871A pdb=" N THR b 16 " --> pdb=" O SER b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 44 Processing helix chain 'b' and resid 83 through 88 Processing helix chain 'b' and resid 124 through 128 Processing helix chain 'b' and resid 158 through 165 removed outlier: 3.625A pdb=" N LEU b 164 " --> pdb=" O ARG b 160 " (cutoff:3.500A) Processing helix chain 'b' and resid 184 through 198 Processing helix chain 'b' and resid 213 through 222 removed outlier: 3.718A pdb=" N GLU b 218 " --> pdb=" O GLU b 214 " (cutoff:3.500A) Processing helix chain 'b' and resid 236 through 256 removed outlier: 3.573A 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 286 through 288 No H-bonds generated for 'chain 'b' and resid 286 through 288' Processing helix chain 'b' and resid 291 through 302 removed outlier: 4.027A 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 336 removed outlier: 3.899A pdb=" N VAL b 330 " --> pdb=" O LYS b 326 " (cutoff:3.500A) Processing helix chain 'b' and resid 347 through 352 Processing helix chain 'b' and resid 374 through 388 removed outlier: 4.525A pdb=" N GLN b 378 " --> pdb=" O GLN b 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS b 379 " --> pdb=" O GLU b 375 " (cutoff:3.500A) Processing helix chain 'b' and resid 392 through 405 Processing helix chain 'b' and resid 409 through 416 Processing helix chain 'c' and resid 3 through 8 Processing helix chain 'c' and resid 11 through 21 removed outlier: 3.872A pdb=" N THR c 16 " --> pdb=" O SER c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 31 through 44 Processing helix chain 'c' and resid 83 through 88 Processing helix chain 'c' and resid 124 through 128 Processing helix chain 'c' and resid 158 through 165 removed outlier: 3.625A pdb=" N LEU c 164 " --> pdb=" O ARG c 160 " (cutoff:3.500A) Processing helix chain 'c' and resid 184 through 198 Processing helix chain 'c' and resid 213 through 222 removed outlier: 3.718A pdb=" N GLU c 218 " --> pdb=" O GLU c 214 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 256 removed outlier: 3.573A 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 286 through 288 No H-bonds generated for 'chain 'c' and resid 286 through 288' Processing helix chain 'c' and resid 291 through 302 removed outlier: 4.027A 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 336 removed outlier: 3.900A pdb=" N VAL c 330 " --> pdb=" O LYS c 326 " (cutoff:3.500A) Processing helix chain 'c' and resid 347 through 352 Processing helix chain 'c' and resid 374 through 388 removed outlier: 4.525A pdb=" N GLN c 378 " --> pdb=" O GLN c 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS c 379 " --> pdb=" O GLU c 375 " (cutoff:3.500A) Processing helix chain 'c' and resid 392 through 405 Processing helix chain 'c' and resid 409 through 416 Processing helix chain 'd' and resid 3 through 8 Processing helix chain 'd' and resid 11 through 21 removed outlier: 3.872A pdb=" N THR d 16 " --> pdb=" O SER d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 31 through 44 Processing helix chain 'd' and resid 83 through 88 Processing helix chain 'd' and resid 124 through 128 Processing helix chain 'd' and resid 158 through 165 removed outlier: 3.624A pdb=" N LEU d 164 " --> pdb=" O ARG d 160 " (cutoff:3.500A) Processing helix chain 'd' and resid 184 through 198 Processing helix chain 'd' and resid 213 through 222 removed outlier: 3.719A pdb=" N GLU d 218 " --> pdb=" O GLU d 214 " (cutoff:3.500A) Processing helix chain 'd' and resid 236 through 256 removed outlier: 3.573A 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 286 through 288 No H-bonds generated for 'chain 'd' and resid 286 through 288' Processing helix chain 'd' and resid 291 through 302 removed outlier: 4.028A 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 336 removed outlier: 3.900A pdb=" N VAL d 330 " --> pdb=" O LYS d 326 " (cutoff:3.500A) Processing helix chain 'd' and resid 347 through 352 Processing helix chain 'd' and resid 374 through 388 removed outlier: 4.525A pdb=" N GLN d 378 " --> pdb=" O GLN d 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS d 379 " --> pdb=" O GLU d 375 " (cutoff:3.500A) Processing helix chain 'd' and resid 392 through 405 Processing helix chain 'd' and resid 409 through 416 Processing helix chain 'e' and resid 3 through 8 Processing helix chain 'e' and resid 11 through 21 removed outlier: 3.872A pdb=" N THR e 16 " --> pdb=" O SER e 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 31 through 44 Processing helix chain 'e' and resid 83 through 88 Processing helix chain 'e' and resid 124 through 128 Processing helix chain 'e' and resid 158 through 165 removed outlier: 3.624A pdb=" N LEU e 164 " --> pdb=" O ARG e 160 " (cutoff:3.500A) Processing helix chain 'e' and resid 184 through 198 Processing helix chain 'e' and resid 213 through 222 removed outlier: 3.719A pdb=" N GLU e 218 " --> pdb=" O GLU e 214 " (cutoff:3.500A) Processing helix chain 'e' and resid 236 through 256 removed outlier: 3.573A 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 286 through 288 No H-bonds generated for 'chain 'e' and resid 286 through 288' Processing helix chain 'e' and resid 291 through 302 removed outlier: 4.028A 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 336 removed outlier: 3.899A pdb=" N VAL e 330 " --> pdb=" O LYS e 326 " (cutoff:3.500A) Processing helix chain 'e' and resid 347 through 352 Processing helix chain 'e' and resid 374 through 388 removed outlier: 4.525A pdb=" N GLN e 378 " --> pdb=" O GLN e 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS e 379 " --> pdb=" O GLU e 375 " (cutoff:3.500A) Processing helix chain 'e' and resid 392 through 405 Processing helix chain 'e' and resid 409 through 416 Processing helix chain 'f' and resid 3 through 8 Processing helix chain 'f' and resid 11 through 21 removed outlier: 3.871A pdb=" N THR f 16 " --> pdb=" O SER f 12 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 44 Processing helix chain 'f' and resid 83 through 88 Processing helix chain 'f' and resid 124 through 128 Processing helix chain 'f' and resid 158 through 165 removed outlier: 3.625A pdb=" N LEU f 164 " --> pdb=" O ARG f 160 " (cutoff:3.500A) Processing helix chain 'f' and resid 184 through 198 Processing helix chain 'f' and resid 213 through 222 removed outlier: 3.719A pdb=" N GLU f 218 " --> pdb=" O GLU f 214 " (cutoff:3.500A) Processing helix chain 'f' and resid 236 through 256 removed outlier: 3.573A 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 286 through 288 No H-bonds generated for 'chain 'f' and resid 286 through 288' Processing helix chain 'f' and resid 291 through 302 removed outlier: 4.027A 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 336 removed outlier: 3.899A pdb=" N VAL f 330 " --> pdb=" O LYS f 326 " (cutoff:3.500A) Processing helix chain 'f' and resid 347 through 352 Processing helix chain 'f' and resid 374 through 388 removed outlier: 4.525A pdb=" N GLN f 378 " --> pdb=" O GLN f 374 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS f 379 " --> pdb=" O GLU f 375 " (cutoff:3.500A) Processing helix chain 'f' and resid 392 through 405 Processing helix chain 'f' and resid 409 through 416 Processing helix chain 'g' and resid 3 through 8 Processing helix chain 'g' and resid 11 through 21 removed outlier: 3.871A pdb=" N THR g 16 " --> pdb=" O SER g 12 " (cutoff:3.500A) Processing helix chain 'g' and resid 31 through 44 Processing helix chain 'g' and resid 83 through 88 Processing helix chain 'g' and resid 124 through 128 Processing helix chain 'g' and resid 158 through 165 removed outlier: 3.624A pdb=" N LEU g 164 " --> pdb=" O ARG g 160 " (cutoff:3.500A) Processing helix chain 'g' and resid 184 through 198 Processing helix chain 'g' and resid 213 through 222 removed outlier: 3.718A pdb=" N GLU g 218 " --> pdb=" O GLU g 214 " (cutoff:3.500A) Processing helix chain 'g' and resid 236 through 256 removed outlier: 3.574A 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 286 through 288 No H-bonds generated for 'chain 'g' and resid 286 through 288' Processing helix chain 'g' and resid 291 through 302 removed outlier: 4.027A 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 336 removed outlier: 3.900A pdb=" N VAL g 330 " --> pdb=" O LYS g 326 " (cutoff:3.500A) Processing helix chain 'g' and resid 347 through 352 Processing helix chain 'g' and resid 374 through 388 removed outlier: 4.526A pdb=" N GLN g 378 " --> pdb=" O GLN g 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS g 379 " --> pdb=" O GLU g 375 " (cutoff:3.500A) Processing helix chain 'g' and resid 392 through 405 Processing helix chain 'g' and resid 409 through 416 Processing helix chain 'h' and resid 3 through 8 Processing helix chain 'h' and resid 11 through 21 removed outlier: 3.871A pdb=" N THR h 16 " --> pdb=" O SER h 12 " (cutoff:3.500A) Processing helix chain 'h' and resid 31 through 44 Processing helix chain 'h' and resid 83 through 88 Processing helix chain 'h' and resid 124 through 128 Processing helix chain 'h' and resid 158 through 165 removed outlier: 3.625A pdb=" N LEU h 164 " --> pdb=" O ARG h 160 " (cutoff:3.500A) Processing helix chain 'h' and resid 184 through 198 Processing helix chain 'h' and resid 213 through 222 removed outlier: 3.719A pdb=" N GLU h 218 " --> pdb=" O GLU h 214 " (cutoff:3.500A) Processing helix chain 'h' and resid 236 through 256 removed outlier: 3.573A 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 286 through 288 No H-bonds generated for 'chain 'h' and resid 286 through 288' Processing helix chain 'h' and resid 291 through 302 removed outlier: 4.028A 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 336 removed outlier: 3.899A pdb=" N VAL h 330 " --> pdb=" O LYS h 326 " (cutoff:3.500A) Processing helix chain 'h' and resid 347 through 352 Processing helix chain 'h' and resid 374 through 388 removed outlier: 4.526A pdb=" N GLN h 378 " --> pdb=" O GLN h 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS h 379 " --> pdb=" O GLU h 375 " (cutoff:3.500A) Processing helix chain 'h' and resid 392 through 405 Processing helix chain 'h' and resid 409 through 416 Processing helix chain 'i' and resid 3 through 8 Processing helix chain 'i' and resid 11 through 21 removed outlier: 3.871A pdb=" N THR i 16 " --> pdb=" O SER i 12 " (cutoff:3.500A) Processing helix chain 'i' and resid 31 through 44 Processing helix chain 'i' and resid 83 through 88 Processing helix chain 'i' and resid 124 through 128 Processing helix chain 'i' and resid 158 through 165 removed outlier: 3.624A pdb=" N LEU i 164 " --> pdb=" O ARG i 160 " (cutoff:3.500A) Processing helix chain 'i' and resid 184 through 198 Processing helix chain 'i' and resid 213 through 222 removed outlier: 3.719A pdb=" N GLU i 218 " --> pdb=" O GLU i 214 " (cutoff:3.500A) Processing helix chain 'i' and resid 236 through 256 removed outlier: 3.573A 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 286 through 288 No H-bonds generated for 'chain 'i' and resid 286 through 288' Processing helix chain 'i' and resid 291 through 302 removed outlier: 4.027A 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 336 removed outlier: 3.900A pdb=" N VAL i 330 " --> pdb=" O LYS i 326 " (cutoff:3.500A) Processing helix chain 'i' and resid 347 through 352 Processing helix chain 'i' and resid 374 through 388 removed outlier: 4.526A pdb=" N GLN i 378 " --> pdb=" O GLN i 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS i 379 " --> pdb=" O GLU i 375 " (cutoff:3.500A) Processing helix chain 'i' and resid 392 through 405 Processing helix chain 'i' and resid 409 through 416 Processing sheet with id= A, first strand: chain 'a' and resid 79 through 81 removed outlier: 3.836A pdb=" N ILE a 79 " --> pdb=" O LEU a 65 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE a 49 " --> pdb=" O ILE a 101 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS a 100 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 5.360A 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: 6.595A pdb=" N LEU a 175 " --> pdb=" O LEU a 343 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE a 176 " --> pdb=" O ILE a 315 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA a 317 " --> pdb=" O ILE a 176 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA a 178 " --> pdb=" O ALA a 317 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA a 319 " --> pdb=" O ALA a 178 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL a 260 " --> pdb=" O THR a 314 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE a 316 " --> pdb=" O VAL a 260 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE a 262 " --> pdb=" O ILE a 316 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N THR a 318 " --> pdb=" O ILE a 262 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU a 264 " --> pdb=" O THR a 318 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N LEU a 320 " --> pdb=" O LEU a 264 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL a 203 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU a 263 " --> pdb=" O VAL a 203 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET a 205 " --> pdb=" O LEU a 263 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU a 226 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N LEU a 208 " --> pdb=" O GLU a 226 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL a 228 " --> pdb=" O LEU a 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'r' and resid 79 through 81 removed outlier: 3.836A pdb=" N ILE r 79 " --> pdb=" O LEU r 65 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE r 49 " --> pdb=" O ILE r 101 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS r 100 " --> pdb=" O VAL r 116 " (cutoff:3.500A) removed outlier: 5.360A 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: 6.595A pdb=" N LEU r 175 " --> pdb=" O LEU r 343 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE r 176 " --> pdb=" O ILE r 315 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA r 317 " --> pdb=" O ILE r 176 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA r 178 " --> pdb=" O ALA r 317 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA r 319 " --> pdb=" O ALA r 178 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL r 260 " --> pdb=" O THR r 314 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE r 316 " --> pdb=" O VAL r 260 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE r 262 " --> pdb=" O ILE r 316 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N THR r 318 " --> pdb=" O ILE r 262 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU r 264 " --> pdb=" O THR r 318 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N LEU r 320 " --> pdb=" O LEU r 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL r 203 " --> pdb=" O ILE r 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU r 263 " --> pdb=" O VAL r 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET r 205 " --> pdb=" O LEU r 263 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU r 226 " --> pdb=" O VAL r 206 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N LEU r 208 " --> pdb=" O GLU r 226 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL r 228 " --> pdb=" O LEU r 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'q' and resid 79 through 81 removed outlier: 3.836A pdb=" N ILE q 79 " --> pdb=" O LEU q 65 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE q 49 " --> pdb=" O ILE q 101 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS q 100 " --> pdb=" O VAL q 116 " (cutoff:3.500A) removed outlier: 5.360A 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: 6.595A pdb=" N LEU q 175 " --> pdb=" O LEU q 343 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE q 176 " --> pdb=" O ILE q 315 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA q 317 " --> pdb=" O ILE q 176 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA q 178 " --> pdb=" O ALA q 317 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA q 319 " --> pdb=" O ALA q 178 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL q 260 " --> pdb=" O THR q 314 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE q 316 " --> pdb=" O VAL q 260 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE q 262 " --> pdb=" O ILE q 316 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N THR q 318 " --> pdb=" O ILE q 262 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU q 264 " --> pdb=" O THR q 318 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N LEU q 320 " --> pdb=" O LEU q 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL q 203 " --> pdb=" O ILE q 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU q 263 " --> pdb=" O VAL q 203 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET q 205 " --> pdb=" O LEU q 263 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU q 226 " --> pdb=" O VAL q 206 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N LEU q 208 " --> pdb=" O GLU q 226 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL q 228 " --> pdb=" O LEU q 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'p' and resid 79 through 81 removed outlier: 3.836A pdb=" N ILE p 79 " --> pdb=" O LEU p 65 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE p 49 " --> pdb=" O ILE p 101 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS p 100 " --> pdb=" O VAL p 116 " (cutoff:3.500A) removed outlier: 5.359A 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: 6.595A pdb=" N LEU p 175 " --> pdb=" O LEU p 343 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE p 176 " --> pdb=" O ILE p 315 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA p 317 " --> pdb=" O ILE p 176 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA p 178 " --> pdb=" O ALA p 317 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ALA p 319 " --> pdb=" O ALA p 178 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL p 260 " --> pdb=" O THR p 314 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE p 316 " --> pdb=" O VAL p 260 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE p 262 " --> pdb=" O ILE p 316 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N THR p 318 " --> pdb=" O ILE p 262 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU p 264 " --> pdb=" O THR p 318 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N LEU p 320 " --> pdb=" O LEU p 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL p 203 " --> pdb=" O ILE p 261 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU p 263 " --> pdb=" O VAL p 203 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET p 205 " --> pdb=" O LEU p 263 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLU p 226 " --> pdb=" O VAL p 206 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N LEU p 208 " --> pdb=" O GLU p 226 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL p 228 " --> pdb=" O LEU p 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'o' and resid 79 through 81 removed outlier: 3.836A pdb=" N ILE o 79 " --> pdb=" O LEU o 65 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE o 49 " --> pdb=" O ILE o 101 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS o 100 " --> pdb=" O VAL o 116 " (cutoff:3.500A) removed outlier: 5.361A 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: 6.595A pdb=" N LEU o 175 " --> pdb=" O LEU o 343 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE o 176 " --> pdb=" O ILE o 315 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA o 317 " --> pdb=" O ILE o 176 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA o 178 " --> pdb=" O ALA o 317 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA o 319 " --> pdb=" O ALA o 178 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL o 260 " --> pdb=" O THR o 314 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE o 316 " --> pdb=" O VAL o 260 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE o 262 " --> pdb=" O ILE o 316 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N THR o 318 " --> pdb=" O ILE o 262 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU o 264 " --> pdb=" O THR o 318 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N LEU o 320 " --> pdb=" O LEU o 264 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL o 203 " --> pdb=" O ILE o 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU o 263 " --> pdb=" O VAL o 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET o 205 " --> pdb=" O LEU o 263 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLU o 226 " --> pdb=" O VAL o 206 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N LEU o 208 " --> pdb=" O GLU o 226 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL o 228 " --> pdb=" O LEU o 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'n' and resid 79 through 81 removed outlier: 3.836A pdb=" N ILE n 79 " --> pdb=" O LEU n 65 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE n 49 " --> pdb=" O ILE n 101 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS n 100 " --> pdb=" O VAL n 116 " (cutoff:3.500A) removed outlier: 5.361A 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: 6.595A pdb=" N LEU n 175 " --> pdb=" O LEU n 343 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE n 176 " --> pdb=" O ILE n 315 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA n 317 " --> pdb=" O ILE n 176 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA n 178 " --> pdb=" O ALA n 317 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA n 319 " --> pdb=" O ALA n 178 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL n 260 " --> pdb=" O THR n 314 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE n 316 " --> pdb=" O VAL n 260 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE n 262 " --> pdb=" O ILE n 316 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N THR n 318 " --> pdb=" O ILE n 262 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU n 264 " --> pdb=" O THR n 318 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N LEU n 320 " --> pdb=" O LEU n 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL n 203 " --> pdb=" O ILE n 261 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU n 263 " --> pdb=" O VAL n 203 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET n 205 " --> pdb=" O LEU n 263 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU n 226 " --> pdb=" O VAL n 206 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N LEU n 208 " --> pdb=" O GLU n 226 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL n 228 " --> pdb=" O LEU n 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'm' and resid 79 through 81 removed outlier: 3.836A pdb=" N ILE m 79 " --> pdb=" O LEU m 65 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE m 49 " --> pdb=" O ILE m 101 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS m 100 " --> pdb=" O VAL m 116 " (cutoff:3.500A) removed outlier: 5.360A 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: 6.594A pdb=" N LEU m 175 " --> pdb=" O LEU m 343 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE m 176 " --> pdb=" O ILE m 315 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA m 317 " --> pdb=" O ILE m 176 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA m 178 " --> pdb=" O ALA m 317 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA m 319 " --> pdb=" O ALA m 178 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL m 260 " --> pdb=" O THR m 314 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE m 316 " --> pdb=" O VAL m 260 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE m 262 " --> pdb=" O ILE m 316 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR m 318 " --> pdb=" O ILE m 262 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU m 264 " --> pdb=" O THR m 318 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N LEU m 320 " --> pdb=" O LEU m 264 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL m 203 " --> pdb=" O ILE m 261 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU m 263 " --> pdb=" O VAL m 203 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET m 205 " --> pdb=" O LEU m 263 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU m 226 " --> pdb=" O VAL m 206 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N LEU m 208 " --> pdb=" O GLU m 226 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL m 228 " --> pdb=" O LEU m 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'l' and resid 79 through 81 removed outlier: 3.835A pdb=" N ILE l 79 " --> pdb=" O LEU l 65 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE l 49 " --> pdb=" O ILE l 101 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS l 100 " --> pdb=" O VAL l 116 " (cutoff:3.500A) removed outlier: 5.361A 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: 6.595A pdb=" N LEU l 175 " --> pdb=" O LEU l 343 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE l 176 " --> pdb=" O ILE l 315 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA l 317 " --> pdb=" O ILE l 176 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA l 178 " --> pdb=" O ALA l 317 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA l 319 " --> pdb=" O ALA l 178 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL l 260 " --> pdb=" O THR l 314 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE l 316 " --> pdb=" O VAL l 260 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE l 262 " --> pdb=" O ILE l 316 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N THR l 318 " --> pdb=" O ILE l 262 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU l 264 " --> pdb=" O THR l 318 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N LEU l 320 " --> pdb=" O LEU l 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL l 203 " --> pdb=" O ILE l 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU l 263 " --> pdb=" O VAL l 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET l 205 " --> pdb=" O LEU l 263 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLU l 226 " --> pdb=" O VAL l 206 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N LEU l 208 " --> pdb=" O GLU l 226 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL l 228 " --> pdb=" O LEU l 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'k' and resid 79 through 81 removed outlier: 3.836A pdb=" N ILE k 79 " --> pdb=" O LEU k 65 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE k 49 " --> pdb=" O ILE k 101 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS k 100 " --> pdb=" O VAL k 116 " (cutoff:3.500A) removed outlier: 5.361A 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: 6.595A pdb=" N LEU k 175 " --> pdb=" O LEU k 343 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE k 176 " --> pdb=" O ILE k 315 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA k 317 " --> pdb=" O ILE k 176 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA k 178 " --> pdb=" O ALA k 317 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA k 319 " --> pdb=" O ALA k 178 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL k 260 " --> pdb=" O THR k 314 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE k 316 " --> pdb=" O VAL k 260 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE k 262 " --> pdb=" O ILE k 316 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR k 318 " --> pdb=" O ILE k 262 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU k 264 " --> pdb=" O THR k 318 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N LEU k 320 " --> pdb=" O LEU k 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL k 203 " --> pdb=" O ILE k 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU k 263 " --> pdb=" O VAL k 203 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET k 205 " --> pdb=" O LEU k 263 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU k 226 " --> pdb=" O VAL k 206 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N LEU k 208 " --> pdb=" O GLU k 226 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL k 228 " --> pdb=" O LEU k 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'j' and resid 79 through 81 removed outlier: 3.835A pdb=" N ILE j 79 " --> pdb=" O LEU j 65 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE j 49 " --> pdb=" O ILE j 101 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS j 100 " --> pdb=" O VAL j 116 " (cutoff:3.500A) removed outlier: 5.361A 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: 6.595A pdb=" N LEU j 175 " --> pdb=" O LEU j 343 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE j 176 " --> pdb=" O ILE j 315 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA j 317 " --> pdb=" O ILE j 176 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA j 178 " --> pdb=" O ALA j 317 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA j 319 " --> pdb=" O ALA j 178 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL j 260 " --> pdb=" O THR j 314 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE j 316 " --> pdb=" O VAL j 260 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE j 262 " --> pdb=" O ILE j 316 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR j 318 " --> pdb=" O ILE j 262 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU j 264 " --> pdb=" O THR j 318 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N LEU j 320 " --> pdb=" O LEU j 264 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL j 203 " --> pdb=" O ILE j 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU j 263 " --> pdb=" O VAL j 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET j 205 " --> pdb=" O LEU j 263 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU j 226 " --> pdb=" O VAL j 206 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N LEU j 208 " --> pdb=" O GLU j 226 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL j 228 " --> pdb=" O LEU j 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'b' and resid 79 through 81 removed outlier: 3.836A pdb=" N ILE b 79 " --> pdb=" O LEU b 65 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE b 49 " --> pdb=" O ILE b 101 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS b 100 " --> pdb=" O VAL b 116 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL b 116 " --> pdb=" O LYS b 100 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'b' and resid 342 through 344 removed outlier: 6.595A pdb=" N LEU b 175 " --> pdb=" O LEU b 343 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE b 176 " --> pdb=" O ILE b 315 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA b 317 " --> pdb=" O ILE b 176 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA b 178 " --> pdb=" O ALA b 317 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA b 319 " --> pdb=" O ALA b 178 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL b 260 " --> pdb=" O THR b 314 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE b 316 " --> pdb=" O VAL b 260 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE b 262 " --> pdb=" O ILE b 316 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR b 318 " --> pdb=" O ILE b 262 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU b 264 " --> pdb=" O THR b 318 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N LEU b 320 " --> pdb=" O LEU b 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL b 203 " --> pdb=" O ILE b 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU b 263 " --> pdb=" O VAL b 203 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET b 205 " --> pdb=" O LEU b 263 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLU b 226 " --> pdb=" O VAL b 206 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N LEU b 208 " --> pdb=" O GLU b 226 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL b 228 " --> pdb=" O LEU b 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'c' and resid 79 through 81 removed outlier: 3.835A pdb=" N ILE c 79 " --> pdb=" O LEU c 65 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE c 49 " --> pdb=" O ILE c 101 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS c 100 " --> pdb=" O VAL c 116 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL c 116 " --> pdb=" O LYS c 100 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'c' and resid 342 through 344 removed outlier: 6.594A pdb=" N LEU c 175 " --> pdb=" O LEU c 343 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE c 176 " --> pdb=" O ILE c 315 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA c 317 " --> pdb=" O ILE c 176 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA c 178 " --> pdb=" O ALA c 317 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ALA c 319 " --> pdb=" O ALA c 178 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL c 260 " --> pdb=" O THR c 314 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE c 316 " --> pdb=" O VAL c 260 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE c 262 " --> pdb=" O ILE c 316 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N THR c 318 " --> pdb=" O ILE c 262 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU c 264 " --> pdb=" O THR c 318 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N LEU c 320 " --> pdb=" O LEU c 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL c 203 " --> pdb=" O ILE c 261 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU c 263 " --> pdb=" O VAL c 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET c 205 " --> pdb=" O LEU c 263 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU c 226 " --> pdb=" O VAL c 206 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N LEU c 208 " --> pdb=" O GLU c 226 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL c 228 " --> pdb=" O LEU c 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'd' and resid 79 through 81 removed outlier: 3.835A pdb=" N ILE d 79 " --> pdb=" O LEU d 65 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE d 49 " --> pdb=" O ILE d 101 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS d 100 " --> pdb=" O VAL d 116 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL d 116 " --> pdb=" O LYS d 100 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'd' and resid 342 through 344 removed outlier: 6.595A pdb=" N LEU d 175 " --> pdb=" O LEU d 343 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE d 176 " --> pdb=" O ILE d 315 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA d 317 " --> pdb=" O ILE d 176 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA d 178 " --> pdb=" O ALA d 317 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA d 319 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL d 260 " --> pdb=" O THR d 314 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE d 316 " --> pdb=" O VAL d 260 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE d 262 " --> pdb=" O ILE d 316 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR d 318 " --> pdb=" O ILE d 262 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU d 264 " --> pdb=" O THR d 318 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N LEU d 320 " --> pdb=" O LEU d 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL d 203 " --> pdb=" O ILE d 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU d 263 " --> pdb=" O VAL d 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET d 205 " --> pdb=" O LEU d 263 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU d 226 " --> pdb=" O VAL d 206 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N LEU d 208 " --> pdb=" O GLU d 226 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL d 228 " --> pdb=" O LEU d 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'e' and resid 79 through 81 removed outlier: 3.836A pdb=" N ILE e 79 " --> pdb=" O LEU e 65 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE e 49 " --> pdb=" O ILE e 101 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS e 100 " --> pdb=" O VAL e 116 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL e 116 " --> pdb=" O LYS e 100 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'e' and resid 342 through 344 removed outlier: 6.595A pdb=" N LEU e 175 " --> pdb=" O LEU e 343 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE e 176 " --> pdb=" O ILE e 315 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA e 317 " --> pdb=" O ILE e 176 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ALA e 178 " --> pdb=" O ALA e 317 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA e 319 " --> pdb=" O ALA e 178 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL e 260 " --> pdb=" O THR e 314 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE e 316 " --> pdb=" O VAL e 260 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE e 262 " --> pdb=" O ILE e 316 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR e 318 " --> pdb=" O ILE e 262 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU e 264 " --> pdb=" O THR e 318 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N LEU e 320 " --> pdb=" O LEU e 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL e 203 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU e 263 " --> pdb=" O VAL e 203 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET e 205 " --> pdb=" O LEU e 263 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLU e 226 " --> pdb=" O VAL e 206 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N LEU e 208 " --> pdb=" O GLU e 226 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL e 228 " --> pdb=" O LEU e 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'f' and resid 79 through 81 removed outlier: 3.836A pdb=" N ILE f 79 " --> pdb=" O LEU f 65 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE f 49 " --> pdb=" O ILE f 101 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS f 100 " --> pdb=" O VAL f 116 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL f 116 " --> pdb=" O LYS f 100 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'f' and resid 342 through 344 removed outlier: 6.594A pdb=" N LEU f 175 " --> pdb=" O LEU f 343 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE f 176 " --> pdb=" O ILE f 315 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA f 317 " --> pdb=" O ILE f 176 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA f 178 " --> pdb=" O ALA f 317 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ALA f 319 " --> pdb=" O ALA f 178 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL f 260 " --> pdb=" O THR f 314 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE f 316 " --> pdb=" O VAL f 260 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE f 262 " --> pdb=" O ILE f 316 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR f 318 " --> pdb=" O ILE f 262 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU f 264 " --> pdb=" O THR f 318 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N LEU f 320 " --> pdb=" O LEU f 264 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL f 203 " --> pdb=" O ILE f 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU f 263 " --> pdb=" O VAL f 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET f 205 " --> pdb=" O LEU f 263 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLU f 226 " --> pdb=" O VAL f 206 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N LEU f 208 " --> pdb=" O GLU f 226 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL f 228 " --> pdb=" O LEU f 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'g' and resid 79 through 81 removed outlier: 3.836A pdb=" N ILE g 79 " --> pdb=" O LEU g 65 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE g 49 " --> pdb=" O ILE g 101 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS g 100 " --> pdb=" O VAL g 116 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL g 116 " --> pdb=" O LYS g 100 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'g' and resid 342 through 344 removed outlier: 6.595A pdb=" N LEU g 175 " --> pdb=" O LEU g 343 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE g 176 " --> pdb=" O ILE g 315 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA g 317 " --> pdb=" O ILE g 176 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ALA g 178 " --> pdb=" O ALA g 317 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA g 319 " --> pdb=" O ALA g 178 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL g 260 " --> pdb=" O THR g 314 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE g 316 " --> pdb=" O VAL g 260 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE g 262 " --> pdb=" O ILE g 316 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR g 318 " --> pdb=" O ILE g 262 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU g 264 " --> pdb=" O THR g 318 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N LEU g 320 " --> pdb=" O LEU g 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL g 203 " --> pdb=" O ILE g 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU g 263 " --> pdb=" O VAL g 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET g 205 " --> pdb=" O LEU g 263 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU g 226 " --> pdb=" O VAL g 206 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N LEU g 208 " --> pdb=" O GLU g 226 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL g 228 " --> pdb=" O LEU g 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'h' and resid 79 through 81 removed outlier: 3.836A pdb=" N ILE h 79 " --> pdb=" O LEU h 65 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE h 49 " --> pdb=" O ILE h 101 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS h 100 " --> pdb=" O VAL h 116 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL h 116 " --> pdb=" O LYS h 100 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'h' and resid 342 through 344 removed outlier: 6.594A pdb=" N LEU h 175 " --> pdb=" O LEU h 343 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE h 176 " --> pdb=" O ILE h 315 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA h 317 " --> pdb=" O ILE h 176 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA h 178 " --> pdb=" O ALA h 317 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA h 319 " --> pdb=" O ALA h 178 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL h 260 " --> pdb=" O THR h 314 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE h 316 " --> pdb=" O VAL h 260 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE h 262 " --> pdb=" O ILE h 316 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR h 318 " --> pdb=" O ILE h 262 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU h 264 " --> pdb=" O THR h 318 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N LEU h 320 " --> pdb=" O LEU h 264 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL h 203 " --> pdb=" O ILE h 261 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU h 263 " --> pdb=" O VAL h 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET h 205 " --> pdb=" O LEU h 263 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU h 226 " --> pdb=" O VAL h 206 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N LEU h 208 " --> pdb=" O GLU h 226 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL h 228 " --> pdb=" O LEU h 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'i' and resid 79 through 81 removed outlier: 3.835A pdb=" N ILE i 79 " --> pdb=" O LEU i 65 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE i 49 " --> pdb=" O ILE i 101 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS i 100 " --> pdb=" O VAL i 116 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL i 116 " --> pdb=" O LYS i 100 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'i' and resid 342 through 344 removed outlier: 6.595A pdb=" N LEU i 175 " --> pdb=" O LEU i 343 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE i 176 " --> pdb=" O ILE i 315 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA i 317 " --> pdb=" O ILE i 176 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA i 178 " --> pdb=" O ALA i 317 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA i 319 " --> pdb=" O ALA i 178 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL i 260 " --> pdb=" O THR i 314 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE i 316 " --> pdb=" O VAL i 260 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE i 262 " --> pdb=" O ILE i 316 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N THR i 318 " --> pdb=" O ILE i 262 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU i 264 " --> pdb=" O THR i 318 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N LEU i 320 " --> pdb=" O LEU i 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL i 203 " --> pdb=" O ILE i 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU i 263 " --> pdb=" O VAL i 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET i 205 " --> pdb=" O LEU i 263 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU i 226 " --> pdb=" O VAL i 206 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N LEU i 208 " --> pdb=" O GLU i 226 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL i 228 " --> pdb=" O LEU i 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ 2016 hydrogen bonds defined for protein. 5994 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: 20.04 Time building geometry restraints manager: 20.70 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: 20373 1.35 - 1.47: 11971 1.47 - 1.58: 27830 1.58 - 1.70: 54 1.70 - 1.82: 594 Bond restraints: 60822 Sorted by residual: bond pdb=" CB PRO p 103 " pdb=" CG PRO p 103 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.66e+00 bond pdb=" CB PRO b 103 " pdb=" CG PRO b 103 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.66e+00 bond pdb=" CB PRO n 103 " pdb=" CG PRO n 103 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.66e+00 bond pdb=" CB PRO l 103 " pdb=" CG PRO l 103 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.65e+00 bond pdb=" CB PRO k 103 " pdb=" CG PRO k 103 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.64e+00 ... (remaining 60817 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.52: 1746 106.52 - 113.91: 34492 113.91 - 121.29: 30558 121.29 - 128.68: 14942 128.68 - 136.07: 270 Bond angle restraints: 82008 Sorted by residual: angle pdb=" CA TRP n 381 " pdb=" CB TRP n 381 " pdb=" CG TRP n 381 " ideal model delta sigma weight residual 113.60 121.62 -8.02 1.90e+00 2.77e-01 1.78e+01 angle pdb=" CA TRP p 381 " pdb=" CB TRP p 381 " pdb=" CG TRP p 381 " ideal model delta sigma weight residual 113.60 121.60 -8.00 1.90e+00 2.77e-01 1.77e+01 angle pdb=" CA TRP k 381 " pdb=" CB TRP k 381 " pdb=" CG TRP k 381 " ideal model delta sigma weight residual 113.60 121.60 -8.00 1.90e+00 2.77e-01 1.77e+01 angle pdb=" CA TRP g 381 " pdb=" CB TRP g 381 " pdb=" CG TRP g 381 " ideal model delta sigma weight residual 113.60 121.60 -8.00 1.90e+00 2.77e-01 1.77e+01 angle pdb=" CA TRP j 381 " pdb=" CB TRP j 381 " pdb=" CG TRP j 381 " ideal model delta sigma weight residual 113.60 121.60 -8.00 1.90e+00 2.77e-01 1.77e+01 ... (remaining 82003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.87: 32817 21.87 - 43.74: 4245 43.74 - 65.61: 540 65.61 - 87.47: 72 87.47 - 109.34: 18 Dihedral angle restraints: 37692 sinusoidal: 15966 harmonic: 21726 Sorted by residual: dihedral pdb=" O1B ADP k1000 " pdb=" O3A ADP k1000 " pdb=" PB ADP k1000 " pdb=" PA ADP k1000 " ideal model delta sinusoidal sigma weight residual -60.00 -169.35 109.34 1 2.00e+01 2.50e-03 3.19e+01 dihedral pdb=" O1B ADP r1000 " pdb=" O3A ADP r1000 " pdb=" PB ADP r1000 " pdb=" PA ADP r1000 " ideal model delta sinusoidal sigma weight residual -60.00 -169.34 109.34 1 2.00e+01 2.50e-03 3.19e+01 dihedral pdb=" O1B ADP d1000 " pdb=" O3A ADP d1000 " pdb=" PB ADP d1000 " pdb=" PA ADP d1000 " ideal model delta sinusoidal sigma weight residual -60.00 -169.32 109.32 1 2.00e+01 2.50e-03 3.19e+01 ... (remaining 37689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 6107 0.033 - 0.066: 2039 0.066 - 0.098: 738 0.098 - 0.131: 389 0.131 - 0.164: 51 Chirality restraints: 9324 Sorted by residual: chirality pdb=" CA ASP b 150 " pdb=" N ASP b 150 " pdb=" C ASP b 150 " pdb=" CB ASP b 150 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA ASP a 150 " pdb=" N ASP a 150 " pdb=" C ASP a 150 " pdb=" CB ASP a 150 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA ASP f 150 " pdb=" N ASP f 150 " pdb=" C ASP f 150 " pdb=" CB ASP f 150 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 9321 not shown) Planarity restraints: 10620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP f 381 " 0.036 2.00e-02 2.50e+03 2.29e-02 1.31e+01 pdb=" CG TRP f 381 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP f 381 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP f 381 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP f 381 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP f 381 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP f 381 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP f 381 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP f 381 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP f 381 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP i 381 " 0.036 2.00e-02 2.50e+03 2.29e-02 1.31e+01 pdb=" CG TRP i 381 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP i 381 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP i 381 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP i 381 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP i 381 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP i 381 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP i 381 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP i 381 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP i 381 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP m 381 " 0.036 2.00e-02 2.50e+03 2.29e-02 1.31e+01 pdb=" CG TRP m 381 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP m 381 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP m 381 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP m 381 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP m 381 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP m 381 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP m 381 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP m 381 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP m 381 " -0.002 2.00e-02 2.50e+03 ... (remaining 10617 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 1215 2.61 - 3.18: 54474 3.18 - 3.76: 99652 3.76 - 4.33: 129698 4.33 - 4.90: 211286 Nonbonded interactions: 496325 Sorted by model distance: nonbonded pdb=" O2B ADP k1000 " pdb="MG MG k1001 " model vdw 2.041 2.170 nonbonded pdb=" O2B ADP n1000 " pdb="MG MG n1001 " model vdw 2.041 2.170 nonbonded pdb=" O2B ADP r1000 " pdb="MG MG r1001 " model vdw 2.041 2.170 nonbonded pdb=" O2B ADP d1000 " pdb="MG MG d1001 " model vdw 2.041 2.170 nonbonded pdb=" O2B ADP c1000 " pdb="MG MG c1001 " model vdw 2.041 2.170 ... (remaining 496320 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 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: 0.040 Extract box with map and model: 13.280 Check model and map are aligned: 0.660 Set scattering table: 0.410 Process input model: 120.330 Find NCS groups from input model: 3.220 Set up NCS constraints: 0.560 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:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 0.082 60822 Z= 0.250 Angle : 0.829 12.373 82008 Z= 0.400 Chirality : 0.042 0.164 9324 Planarity : 0.006 0.066 10620 Dihedral : 17.667 109.343 23616 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.67 % Allowed : 40.49 % Favored : 57.84 % 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: 0.46 (0.09), residues: 7506 helix: 0.97 (0.09), residues: 3294 sheet: 0.23 (0.14), residues: 1170 loop : -0.29 (0.11), residues: 3042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.013 TRP i 381 HIS 0.004 0.001 HIS b 239 PHE 0.016 0.001 PHE c 398 TYR 0.006 0.001 TYR m 332 ARG 0.011 0.001 ARG f 418 *********************** 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 1508 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1400 time to evaluate : 5.298 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: a 29 MET cc_start: 0.7373 (ptm) cc_final: 0.7093 (ptp) REVERT: a 205 MET cc_start: 0.8528 (tpp) cc_final: 0.8273 (mmt) REVERT: a 218 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8204 (pt0) REVERT: a 329 GLU cc_start: 0.8220 (mp0) cc_final: 0.7956 (mp0) REVERT: r 85 GLN cc_start: 0.9214 (mp10) cc_final: 0.8705 (mp10) REVERT: r 90 ASN cc_start: 0.7955 (t0) cc_final: 0.7696 (t0) REVERT: r 248 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8686 (mm-30) REVERT: r 299 ARG cc_start: 0.8993 (ttp80) cc_final: 0.8742 (mmt180) REVERT: r 381 TRP cc_start: 0.8590 (t60) cc_final: 0.8286 (t60) REVERT: r 390 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.6976 (ptt) REVERT: r 416 MET cc_start: 0.7301 (mmp) cc_final: 0.6786 (ttt) REVERT: q 1 MET cc_start: 0.7301 (mmm) cc_final: 0.6700 (tpt) REVERT: q 72 TYR cc_start: 0.9270 (m-10) cc_final: 0.8821 (m-10) REVERT: q 147 MET cc_start: 0.8590 (mmm) cc_final: 0.8181 (mmm) REVERT: q 162 LEU cc_start: 0.9443 (mm) cc_final: 0.9207 (tt) REVERT: q 204 LEU cc_start: 0.9029 (tp) cc_final: 0.8756 (tp) REVERT: q 241 GLN cc_start: 0.9195 (pt0) cc_final: 0.8779 (pp30) REVERT: q 244 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8445 (mm-30) REVERT: q 249 LYS cc_start: 0.9547 (ttpp) cc_final: 0.9217 (ttpt) REVERT: q 296 ARG cc_start: 0.8924 (tpp80) cc_final: 0.8581 (mmm160) REVERT: q 299 ARG cc_start: 0.9148 (ttp80) cc_final: 0.8562 (ttp80) REVERT: q 411 ASP cc_start: 0.8840 (m-30) cc_final: 0.8568 (m-30) REVERT: p 87 ARG cc_start: 0.9112 (mtp85) cc_final: 0.8674 (ptm160) REVERT: p 189 GLN cc_start: 0.9222 (mt0) cc_final: 0.8961 (mt0) REVERT: p 193 GLN cc_start: 0.9020 (tt0) cc_final: 0.8780 (tt0) REVERT: p 241 GLN cc_start: 0.8807 (pt0) cc_final: 0.8508 (tm-30) REVERT: p 394 ASP cc_start: 0.9017 (p0) cc_final: 0.8631 (p0) REVERT: o 41 GLN cc_start: 0.9065 (tp40) cc_final: 0.8780 (tp40) REVERT: o 193 GLN cc_start: 0.8804 (tt0) cc_final: 0.8544 (tt0) REVERT: o 205 MET cc_start: 0.8535 (tpp) cc_final: 0.8332 (mmt) REVERT: o 326 LYS cc_start: 0.9079 (tmtt) cc_final: 0.8761 (tptp) REVERT: o 329 GLU cc_start: 0.8533 (mp0) cc_final: 0.7886 (mp0) REVERT: o 396 MET cc_start: 0.9596 (tpp) cc_final: 0.8948 (tpp) REVERT: n 100 LYS cc_start: 0.9544 (ttmt) cc_final: 0.9246 (ttmm) REVERT: n 193 GLN cc_start: 0.8748 (tt0) cc_final: 0.8528 (mt0) REVERT: n 326 LYS cc_start: 0.9119 (tmtt) cc_final: 0.8785 (tmtt) REVERT: n 342 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8182 (mm-30) REVERT: n 410 ASP cc_start: 0.9151 (m-30) cc_final: 0.8876 (p0) REVERT: m 12 SER cc_start: 0.9257 (m) cc_final: 0.9006 (m) REVERT: m 100 LYS cc_start: 0.9176 (ttmt) cc_final: 0.8846 (ptmm) REVERT: m 296 ARG cc_start: 0.9007 (tpp80) cc_final: 0.8650 (mmm-85) REVERT: m 326 LYS cc_start: 0.9146 (tmtt) cc_final: 0.8772 (tptt) REVERT: m 342 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8323 (mp0) REVERT: m 396 MET cc_start: 0.9059 (tpp) cc_final: 0.8749 (tpp) REVERT: m 403 LEU cc_start: 0.9268 (mm) cc_final: 0.8896 (mt) REVERT: l 193 GLN cc_start: 0.8456 (tt0) cc_final: 0.7888 (tm-30) REVERT: l 222 LEU cc_start: 0.9240 (tt) cc_final: 0.8967 (mt) REVERT: l 244 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7827 (mm-30) REVERT: l 326 LYS cc_start: 0.9291 (tmtt) cc_final: 0.9041 (tmtt) REVERT: l 342 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7963 (mm-30) REVERT: l 414 GLU cc_start: 0.8927 (pp20) cc_final: 0.8416 (pp20) REVERT: k 41 GLN cc_start: 0.8660 (tp40) cc_final: 0.8357 (tm-30) REVERT: k 325 SER cc_start: 0.7443 (t) cc_final: 0.6919 (p) REVERT: k 342 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8215 (mp0) REVERT: k 397 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8760 (mt-10) REVERT: j 1 MET cc_start: 0.6247 (mmm) cc_final: 0.6022 (mmm) REVERT: j 30 ARG cc_start: 0.7179 (mmm-85) cc_final: 0.6749 (mtp-110) REVERT: j 222 LEU cc_start: 0.9263 (tt) cc_final: 0.8989 (mt) REVERT: j 342 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7867 (pt0) REVERT: j 397 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8749 (mt-10) REVERT: j 415 MET cc_start: 0.9011 (ttp) cc_final: 0.8436 (ttp) REVERT: b 1 MET cc_start: 0.7065 (mmm) cc_final: 0.6821 (tpt) REVERT: b 21 MET cc_start: 0.8316 (ppp) cc_final: 0.7833 (tmm) REVERT: b 29 MET cc_start: 0.7790 (ptm) cc_final: 0.6585 (ptm) REVERT: b 85 GLN cc_start: 0.9464 (mp10) cc_final: 0.9052 (mp10) REVERT: b 215 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7866 (mp0) REVERT: b 244 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8399 (mm-30) REVERT: b 245 MET cc_start: 0.9099 (tpp) cc_final: 0.8819 (tpt) REVERT: b 253 LEU cc_start: 0.9455 (mt) cc_final: 0.9220 (mt) REVERT: b 342 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8291 (mp0) REVERT: c 6 LEU cc_start: 0.9273 (tt) cc_final: 0.8922 (pp) REVERT: c 12 SER cc_start: 0.9560 (m) cc_final: 0.9324 (p) REVERT: c 21 MET cc_start: 0.8421 (ppp) cc_final: 0.8001 (tmm) REVERT: c 30 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7366 (mtp-110) REVERT: c 52 ASP cc_start: 0.8693 (p0) cc_final: 0.8386 (p0) REVERT: c 59 GLN cc_start: 0.8494 (pm20) cc_final: 0.8292 (pm20) REVERT: c 90 ASN cc_start: 0.8390 (t0) cc_final: 0.8154 (t0) REVERT: c 241 GLN cc_start: 0.9084 (pt0) cc_final: 0.8522 (pp30) REVERT: c 292 ASN cc_start: 0.8481 (m-40) cc_final: 0.8193 (p0) REVERT: c 342 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8179 (pm20) REVERT: c 376 GLU cc_start: 0.8396 (tt0) cc_final: 0.8086 (tt0) REVERT: d 52 ASP cc_start: 0.8692 (p0) cc_final: 0.8438 (p0) REVERT: d 322 ASP cc_start: 0.9107 (p0) cc_final: 0.8846 (p0) REVERT: d 342 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7958 (mm-30) REVERT: d 374 GLN cc_start: 0.8904 (tp40) cc_final: 0.8634 (tp-100) REVERT: d 375 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8166 (mp0) REVERT: e 8 ASN cc_start: 0.9160 (m-40) cc_final: 0.8957 (m-40) REVERT: e 52 ASP cc_start: 0.8851 (p0) cc_final: 0.8418 (p0) REVERT: e 95 ASP cc_start: 0.9147 (m-30) cc_final: 0.8892 (m-30) REVERT: e 118 GLU cc_start: 0.8483 (tp30) cc_final: 0.8212 (tp30) REVERT: e 222 LEU cc_start: 0.9410 (tt) cc_final: 0.8909 (tt) REVERT: e 244 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8113 (mm-30) REVERT: e 274 TYR cc_start: 0.8989 (m-80) cc_final: 0.8771 (m-80) REVERT: e 326 LYS cc_start: 0.9190 (tmtt) cc_final: 0.8562 (tptt) REVERT: e 342 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8007 (pt0) REVERT: g 327 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8388 (ttp) REVERT: g 342 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7952 (mt-10) REVERT: g 414 GLU cc_start: 0.8990 (pp20) cc_final: 0.8686 (pp20) REVERT: h 32 GLN cc_start: 0.8993 (mp10) cc_final: 0.8748 (mm-40) REVERT: h 110 TYR cc_start: 0.8606 (m-80) cc_final: 0.8298 (m-80) REVERT: h 378 GLN cc_start: 0.7906 (pm20) cc_final: 0.7420 (pm20) REVERT: h 410 ASP cc_start: 0.9393 (m-30) cc_final: 0.9185 (m-30) REVERT: h 414 GLU cc_start: 0.8787 (pp20) cc_final: 0.8523 (pp20) REVERT: i 8 ASN cc_start: 0.9281 (m-40) cc_final: 0.8963 (m-40) REVERT: i 12 SER cc_start: 0.9246 (m) cc_final: 0.9007 (p) REVERT: i 48 ASP cc_start: 0.8348 (p0) cc_final: 0.7954 (p0) REVERT: i 52 ASP cc_start: 0.8349 (p0) cc_final: 0.8067 (p0) REVERT: i 100 LYS cc_start: 0.9398 (ttmt) cc_final: 0.9132 (ttmm) REVERT: i 342 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8117 (mp0) outliers start: 108 outliers final: 37 residues processed: 1452 average time/residue: 0.6217 time to fit residues: 1470.5167 Evaluate side-chains 999 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 960 time to evaluate : 5.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 70 SER Chi-restraints excluded: chain a residue 260 VAL Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 70 SER Chi-restraints excluded: chain r residue 390 MET Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 70 SER Chi-restraints excluded: chain q residue 260 VAL Chi-restraints excluded: chain p residue 70 SER Chi-restraints excluded: chain p residue 260 VAL Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 260 VAL Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 70 SER Chi-restraints excluded: chain n residue 260 VAL Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain j residue 70 SER Chi-restraints excluded: chain j residue 260 VAL Chi-restraints excluded: chain b residue 260 VAL Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 260 VAL Chi-restraints excluded: chain e residue 260 VAL Chi-restraints excluded: chain e residue 380 MET Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain f residue 260 VAL Chi-restraints excluded: chain f residue 380 MET Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 260 VAL Chi-restraints excluded: chain g residue 327 MET Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 260 VAL Chi-restraints excluded: chain h residue 327 MET Chi-restraints excluded: chain i residue 260 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 623 optimal weight: 0.6980 chunk 559 optimal weight: 5.9990 chunk 310 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 377 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 chunk 578 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 351 optimal weight: 9.9990 chunk 430 optimal weight: 10.0000 chunk 670 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 189 GLN ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 42 HIS r 140 HIS r 172 GLN r 344 HIS r 388 HIS q 42 HIS q 388 HIS p 59 GLN l 220 GLN l 388 HIS k 193 GLN b 8 ASN b 193 GLN c 172 GLN c 189 GLN c 388 HIS d 8 ASN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 374 GLN i 126 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 60822 Z= 0.236 Angle : 0.642 9.964 82008 Z= 0.308 Chirality : 0.043 0.165 9324 Planarity : 0.004 0.038 10620 Dihedral : 5.751 77.333 8438 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 6.42 % Allowed : 27.79 % Favored : 65.79 % 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: 0.55 (0.10), residues: 7506 helix: 1.02 (0.09), residues: 3348 sheet: 0.29 (0.15), residues: 1170 loop : -0.22 (0.11), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.009 TRP b 381 HIS 0.009 0.001 HIS r 388 PHE 0.014 0.001 PHE q 412 TYR 0.015 0.001 TYR c 110 ARG 0.010 0.001 ARG r 160 *********************** 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 1395 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 416 poor density : 979 time to evaluate : 5.377 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: a 29 MET cc_start: 0.7622 (ptm) cc_final: 0.7211 (ptp) REVERT: a 215 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: a 244 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8243 (mm-30) REVERT: a 375 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8261 (mp0) REVERT: a 396 MET cc_start: 0.9401 (tpp) cc_final: 0.9149 (tpp) REVERT: r 244 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8510 (mm-30) REVERT: r 248 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8607 (mm-30) REVERT: r 295 HIS cc_start: 0.8697 (t70) cc_final: 0.8219 (t-170) REVERT: r 403 LEU cc_start: 0.9043 (tp) cc_final: 0.8569 (tp) REVERT: r 410 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8432 (p0) REVERT: r 416 MET cc_start: 0.7675 (mmp) cc_final: 0.6867 (ttt) REVERT: q 1 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6767 (tpt) REVERT: q 244 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8519 (mm-30) REVERT: q 394 ASP cc_start: 0.8991 (OUTLIER) cc_final: 0.8583 (p0) REVERT: p 1 MET cc_start: 0.7176 (tpt) cc_final: 0.6871 (tpt) REVERT: p 33 ASP cc_start: 0.9168 (m-30) cc_final: 0.8863 (m-30) REVERT: p 91 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8790 (pp) REVERT: p 193 GLN cc_start: 0.8938 (tt0) cc_final: 0.8712 (tt0) REVERT: p 219 MET cc_start: 0.9434 (tpp) cc_final: 0.9213 (mmm) REVERT: p 222 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8789 (mp) REVERT: p 241 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8582 (tm-30) REVERT: p 325 SER cc_start: 0.7833 (t) cc_final: 0.7330 (p) REVERT: p 394 ASP cc_start: 0.9028 (OUTLIER) cc_final: 0.8602 (p0) REVERT: o 205 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8302 (mtt) REVERT: o 244 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8500 (mm-30) REVERT: o 259 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8229 (p0) REVERT: o 326 LYS cc_start: 0.9080 (tmtt) cc_final: 0.8578 (tptp) REVERT: o 397 GLU cc_start: 0.8712 (mp0) cc_final: 0.8431 (mp0) REVERT: n 41 GLN cc_start: 0.9261 (tp40) cc_final: 0.8904 (tp40) REVERT: n 100 LYS cc_start: 0.9559 (ttmt) cc_final: 0.9219 (ttmm) REVERT: n 140 HIS cc_start: 0.8892 (OUTLIER) cc_final: 0.8606 (m90) REVERT: n 193 GLN cc_start: 0.8738 (tt0) cc_final: 0.8492 (mt0) REVERT: n 205 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8431 (mtp) REVERT: n 259 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.7935 (p0) REVERT: n 326 LYS cc_start: 0.9131 (tmtt) cc_final: 0.8838 (tmtt) REVERT: n 342 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8345 (mt-10) REVERT: n 410 ASP cc_start: 0.9212 (m-30) cc_final: 0.8990 (p0) REVERT: m 44 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8592 (ptpp) REVERT: m 100 LYS cc_start: 0.9214 (ttmt) cc_final: 0.8993 (ptmm) REVERT: m 125 GLU cc_start: 0.8672 (mp0) cc_final: 0.8421 (pm20) REVERT: m 244 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8292 (mm-30) REVERT: m 296 ARG cc_start: 0.9059 (tpp80) cc_final: 0.8679 (mmm-85) REVERT: m 326 LYS cc_start: 0.9240 (tmtt) cc_final: 0.8846 (tptt) REVERT: m 342 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8338 (mp0) REVERT: m 354 VAL cc_start: 0.7549 (OUTLIER) cc_final: 0.7097 (t) REVERT: m 396 MET cc_start: 0.9180 (tpp) cc_final: 0.8903 (tpp) REVERT: m 397 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8890 (mm-30) REVERT: m 403 LEU cc_start: 0.9420 (mm) cc_final: 0.9191 (mp) REVERT: l 140 HIS cc_start: 0.8756 (OUTLIER) cc_final: 0.8260 (m90) REVERT: l 193 GLN cc_start: 0.8565 (tt0) cc_final: 0.7987 (tm-30) REVERT: l 222 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9029 (mt) REVERT: l 244 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7791 (mm-30) REVERT: l 334 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8979 (mm-30) REVERT: l 342 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7935 (mm-30) REVERT: k 41 GLN cc_start: 0.8732 (tp40) cc_final: 0.8395 (tm-30) REVERT: k 60 ASP cc_start: 0.8911 (t0) cc_final: 0.8678 (t70) REVERT: k 140 HIS cc_start: 0.8776 (OUTLIER) cc_final: 0.8114 (m170) REVERT: k 259 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8392 (p0) REVERT: k 325 SER cc_start: 0.7404 (t) cc_final: 0.7012 (p) REVERT: k 342 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8234 (mp0) REVERT: k 397 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8903 (mt-10) REVERT: j 1 MET cc_start: 0.6380 (OUTLIER) cc_final: 0.5456 (tmm) REVERT: j 23 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8205 (mm) REVERT: j 193 GLN cc_start: 0.8874 (tt0) cc_final: 0.8642 (tt0) REVERT: j 222 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8992 (mt) REVERT: j 334 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8666 (tp30) REVERT: j 342 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7894 (pt0) REVERT: j 375 GLU cc_start: 0.8958 (tp30) cc_final: 0.8731 (tp30) REVERT: j 397 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8902 (mt-10) REVERT: j 407 LYS cc_start: 0.9064 (ptmm) cc_final: 0.8798 (ttmm) REVERT: b 1 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6677 (tpt) REVERT: b 21 MET cc_start: 0.8357 (ppp) cc_final: 0.7818 (tmm) REVERT: b 85 GLN cc_start: 0.9431 (mp10) cc_final: 0.9076 (mp10) REVERT: b 193 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8824 (tm-30) REVERT: b 244 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8525 (mm-30) REVERT: b 253 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9204 (mt) REVERT: b 342 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8311 (mp0) REVERT: b 397 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8629 (mt-10) REVERT: c 12 SER cc_start: 0.9553 (OUTLIER) cc_final: 0.9315 (p) REVERT: c 30 ARG cc_start: 0.8089 (mmm-85) cc_final: 0.7571 (mtp-110) REVERT: c 56 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8066 (tm-30) REVERT: c 140 HIS cc_start: 0.9097 (OUTLIER) cc_final: 0.8537 (m90) REVERT: c 186 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8609 (mtm) REVERT: c 241 GLN cc_start: 0.9131 (pt0) cc_final: 0.8544 (pp30) REVERT: c 292 ASN cc_start: 0.8584 (m-40) cc_final: 0.8286 (p0) REVERT: c 375 GLU cc_start: 0.8386 (tp30) cc_final: 0.8064 (tp30) REVERT: c 376 GLU cc_start: 0.8556 (tt0) cc_final: 0.8355 (tt0) REVERT: d 21 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7527 (ppp) REVERT: d 39 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9147 (mm) REVERT: d 140 HIS cc_start: 0.8868 (OUTLIER) cc_final: 0.8520 (m170) REVERT: d 342 GLU cc_start: 0.8712 (mt-10) cc_final: 0.7977 (mm-30) REVERT: e 140 HIS cc_start: 0.8904 (OUTLIER) cc_final: 0.8497 (m-70) REVERT: e 205 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8447 (mmm) REVERT: e 222 LEU cc_start: 0.9460 (tt) cc_final: 0.8928 (tt) REVERT: e 241 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8749 (tm-30) REVERT: e 342 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7996 (pt0) REVERT: e 374 GLN cc_start: 0.9493 (tp40) cc_final: 0.9182 (tp-100) REVERT: f 1 MET cc_start: 0.6297 (OUTLIER) cc_final: 0.5166 (tmm) REVERT: f 140 HIS cc_start: 0.8705 (OUTLIER) cc_final: 0.8106 (m90) REVERT: f 326 LYS cc_start: 0.9055 (tmtt) cc_final: 0.8527 (tmtt) REVERT: f 329 GLU cc_start: 0.7954 (mp0) cc_final: 0.7461 (mp0) REVERT: g 23 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7518 (mm) REVERT: g 30 ARG cc_start: 0.7426 (mmm-85) cc_final: 0.6861 (mtp-110) REVERT: g 126 ASN cc_start: 0.9115 (m-40) cc_final: 0.8818 (m-40) REVERT: g 375 GLU cc_start: 0.8498 (tp30) cc_final: 0.7934 (tp30) REVERT: g 397 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8812 (mt-10) REVERT: h 110 TYR cc_start: 0.8827 (m-80) cc_final: 0.8576 (m-80) REVERT: h 205 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8053 (mtp) REVERT: h 259 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.7771 (p0) REVERT: i 1 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.5817 (tpt) REVERT: i 91 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8421 (pp) REVERT: i 329 GLU cc_start: 0.8759 (tp30) cc_final: 0.8558 (mm-30) REVERT: i 333 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8670 (mm-30) REVERT: i 342 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8102 (mp0) REVERT: i 375 GLU cc_start: 0.8290 (tp30) cc_final: 0.7911 (tp30) outliers start: 416 outliers final: 195 residues processed: 1267 average time/residue: 0.5615 time to fit residues: 1192.1264 Evaluate side-chains 1109 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 873 time to evaluate : 5.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 110 TYR Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 202 CYS Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 259 ASP Chi-restraints excluded: chain a residue 260 VAL Chi-restraints excluded: chain a residue 264 LEU Chi-restraints excluded: chain a residue 295 HIS Chi-restraints excluded: chain a residue 323 THR Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain a residue 371 LEU Chi-restraints excluded: chain a residue 376 GLU Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain r residue 29 MET Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 215 GLU Chi-restraints excluded: chain r residue 323 THR Chi-restraints excluded: chain r residue 354 VAL Chi-restraints excluded: chain r residue 394 ASP Chi-restraints excluded: chain r residue 410 ASP Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 12 SER Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 166 SER Chi-restraints excluded: chain q residue 253 LEU Chi-restraints excluded: chain q residue 259 ASP Chi-restraints excluded: chain q residue 260 VAL Chi-restraints excluded: chain q residue 323 THR Chi-restraints excluded: chain q residue 330 VAL Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain q residue 372 THR Chi-restraints excluded: chain q residue 394 ASP Chi-restraints excluded: chain q residue 401 ASN Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 29 MET Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain p residue 91 LEU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 222 LEU Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 260 VAL Chi-restraints excluded: chain p residue 286 THR Chi-restraints excluded: chain p residue 376 GLU Chi-restraints excluded: chain p residue 394 ASP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 70 SER Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 205 MET Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 259 ASP Chi-restraints excluded: chain o residue 260 VAL Chi-restraints excluded: chain o residue 286 THR Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 372 THR Chi-restraints excluded: chain o residue 394 ASP Chi-restraints excluded: chain o residue 410 ASP Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 23 LEU Chi-restraints excluded: chain n residue 91 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 140 HIS Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 205 MET Chi-restraints excluded: chain n residue 241 GLN Chi-restraints excluded: chain n residue 253 LEU Chi-restraints excluded: chain n residue 259 ASP Chi-restraints excluded: chain n residue 260 VAL Chi-restraints excluded: chain n residue 264 LEU Chi-restraints excluded: chain n residue 323 THR Chi-restraints excluded: chain n residue 338 THR Chi-restraints excluded: chain n residue 376 GLU Chi-restraints excluded: chain n residue 405 MET Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 44 LYS Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 205 MET Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain m residue 327 MET Chi-restraints excluded: chain m residue 354 VAL Chi-restraints excluded: chain m residue 387 ILE Chi-restraints excluded: chain m residue 394 ASP Chi-restraints excluded: chain m residue 415 MET Chi-restraints excluded: chain m residue 418 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 140 HIS Chi-restraints excluded: chain l residue 205 MET Chi-restraints excluded: chain l residue 222 LEU Chi-restraints excluded: chain l residue 241 GLN Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain l residue 264 LEU Chi-restraints excluded: chain l residue 338 THR Chi-restraints excluded: chain l residue 341 MET Chi-restraints excluded: chain l residue 376 GLU Chi-restraints excluded: chain l residue 394 ASP Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 91 LEU Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 140 HIS Chi-restraints excluded: chain k residue 162 LEU Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 205 MET Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 259 ASP Chi-restraints excluded: chain k residue 260 VAL Chi-restraints excluded: chain k residue 327 MET Chi-restraints excluded: chain k residue 338 THR Chi-restraints excluded: chain k residue 370 LEU Chi-restraints excluded: chain k residue 371 LEU Chi-restraints excluded: chain k residue 373 THR Chi-restraints excluded: chain k residue 394 ASP Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 29 MET Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 202 CYS Chi-restraints excluded: chain j residue 205 MET Chi-restraints excluded: chain j residue 222 LEU Chi-restraints excluded: chain j residue 241 GLN Chi-restraints excluded: chain j residue 260 VAL Chi-restraints excluded: chain j residue 264 LEU Chi-restraints excluded: chain j residue 373 THR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 193 GLN Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 253 LEU Chi-restraints excluded: chain b residue 260 VAL Chi-restraints excluded: chain b residue 264 LEU Chi-restraints excluded: chain b residue 338 THR Chi-restraints excluded: chain b residue 341 MET Chi-restraints excluded: chain b residue 410 ASP Chi-restraints excluded: chain c residue 12 SER Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 70 SER Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 140 HIS Chi-restraints excluded: chain c residue 186 MET Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 140 HIS Chi-restraints excluded: chain d residue 205 MET Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 259 ASP Chi-restraints excluded: chain d residue 260 VAL Chi-restraints excluded: chain d residue 292 ASN Chi-restraints excluded: chain d residue 338 THR Chi-restraints excluded: chain d residue 394 ASP Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 140 HIS Chi-restraints excluded: chain e residue 205 MET Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 327 MET Chi-restraints excluded: chain e residue 338 THR Chi-restraints excluded: chain e residue 341 MET Chi-restraints excluded: chain e residue 394 ASP Chi-restraints excluded: chain e residue 410 ASP Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 12 SER Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 29 MET Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 140 HIS Chi-restraints excluded: chain f residue 205 MET Chi-restraints excluded: chain f residue 241 GLN Chi-restraints excluded: chain f residue 253 LEU Chi-restraints excluded: chain f residue 259 ASP Chi-restraints excluded: chain f residue 260 VAL Chi-restraints excluded: chain f residue 308 GLU Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 338 THR Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 394 ASP Chi-restraints excluded: chain g residue 12 SER Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 29 MET Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 162 LEU Chi-restraints excluded: chain g residue 205 MET Chi-restraints excluded: chain g residue 259 ASP Chi-restraints excluded: chain g residue 260 VAL Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 338 THR Chi-restraints excluded: chain g residue 341 MET Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 21 MET Chi-restraints excluded: chain h residue 23 LEU Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 123 LYS Chi-restraints excluded: chain h residue 126 ASN Chi-restraints excluded: chain h residue 205 MET Chi-restraints excluded: chain h residue 259 ASP Chi-restraints excluded: chain h residue 260 VAL Chi-restraints excluded: chain h residue 327 MET Chi-restraints excluded: chain h residue 338 THR Chi-restraints excluded: chain h residue 394 ASP Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 91 LEU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 126 ASN Chi-restraints excluded: chain i residue 241 GLN Chi-restraints excluded: chain i residue 260 VAL Chi-restraints excluded: chain i residue 264 LEU Chi-restraints excluded: chain i residue 290 ASP Chi-restraints excluded: chain i residue 338 THR Chi-restraints excluded: chain i residue 341 MET Chi-restraints excluded: chain i residue 354 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 372 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 557 optimal weight: 2.9990 chunk 456 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 chunk 671 optimal weight: 0.0170 chunk 725 optimal weight: 2.9990 chunk 597 optimal weight: 5.9990 chunk 665 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 538 optimal weight: 9.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 172 GLN r 241 GLN r 295 HIS p 59 GLN ** p 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 374 GLN o 199 HIS o 388 HIS l 374 GLN k 193 GLN ** j 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 8 ASN b 189 GLN b 193 GLN c 172 GLN c 189 GLN d 8 ASN d 193 GLN d 374 GLN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 374 GLN ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 374 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 60822 Z= 0.300 Angle : 0.634 11.875 82008 Z= 0.307 Chirality : 0.044 0.167 9324 Planarity : 0.004 0.038 10620 Dihedral : 5.275 55.607 8412 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 6.74 % Allowed : 26.19 % Favored : 67.07 % 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: 0.51 (0.10), residues: 7506 helix: 1.00 (0.09), residues: 3348 sheet: 0.14 (0.15), residues: 1134 loop : -0.20 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.009 TRP f 381 HIS 0.012 0.001 HIS o 388 PHE 0.013 0.001 PHE c 398 TYR 0.019 0.001 TYR n 80 ARG 0.007 0.001 ARG k 269 *********************** 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 1371 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 437 poor density : 934 time to evaluate : 5.410 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: a 215 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: a 244 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8212 (mm-30) REVERT: a 375 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8261 (mp0) REVERT: r 244 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8544 (mm-30) REVERT: r 248 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8668 (mm-30) REVERT: r 366 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7805 (tpt170) REVERT: r 410 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8461 (p0) REVERT: r 416 MET cc_start: 0.7524 (mmp) cc_final: 0.6644 (ttt) REVERT: q 1 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.6737 (tpt) REVERT: q 244 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8544 (mm-30) REVERT: q 380 MET cc_start: 0.8920 (ptp) cc_final: 0.8490 (ptm) REVERT: q 390 MET cc_start: 0.8849 (pmm) cc_final: 0.8426 (pmm) REVERT: q 394 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8631 (p0) REVERT: q 416 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8357 (ptt) REVERT: p 1 MET cc_start: 0.7361 (tpt) cc_final: 0.7069 (tpt) REVERT: p 33 ASP cc_start: 0.9122 (m-30) cc_final: 0.8732 (m-30) REVERT: p 91 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8818 (pp) REVERT: p 193 GLN cc_start: 0.9050 (tt0) cc_final: 0.8698 (tt0) REVERT: p 325 SER cc_start: 0.8007 (t) cc_final: 0.7600 (p) REVERT: p 329 GLU cc_start: 0.8375 (mp0) cc_final: 0.8173 (mp0) REVERT: p 394 ASP cc_start: 0.9040 (OUTLIER) cc_final: 0.8451 (p0) REVERT: o 205 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8320 (mtt) REVERT: o 259 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8224 (p0) REVERT: o 326 LYS cc_start: 0.9127 (tmtt) cc_final: 0.8207 (tptt) REVERT: o 397 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8462 (mp0) REVERT: n 41 GLN cc_start: 0.9283 (tp40) cc_final: 0.8875 (tp40) REVERT: n 100 LYS cc_start: 0.9524 (ttmt) cc_final: 0.9161 (ttmm) REVERT: n 259 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.7883 (p0) REVERT: n 342 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8385 (mt-10) REVERT: n 374 GLN cc_start: 0.9085 (tp-100) cc_final: 0.8809 (tp40) REVERT: n 411 ASP cc_start: 0.9226 (m-30) cc_final: 0.8977 (m-30) REVERT: m 100 LYS cc_start: 0.9208 (ttmt) cc_final: 0.8980 (ptmm) REVERT: m 125 GLU cc_start: 0.8738 (mp0) cc_final: 0.8483 (pm20) REVERT: m 296 ARG cc_start: 0.9096 (tpp80) cc_final: 0.8685 (mmm-85) REVERT: m 326 LYS cc_start: 0.9181 (tmtt) cc_final: 0.8972 (tptt) REVERT: m 329 GLU cc_start: 0.8531 (pm20) cc_final: 0.8238 (pm20) REVERT: m 341 MET cc_start: 0.9292 (tmm) cc_final: 0.8970 (tmm) REVERT: m 342 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8403 (mp0) REVERT: m 403 LEU cc_start: 0.9484 (mm) cc_final: 0.9271 (mp) REVERT: l 109 ARG cc_start: 0.8064 (ptp-170) cc_final: 0.7783 (mtm-85) REVERT: l 140 HIS cc_start: 0.8801 (OUTLIER) cc_final: 0.8372 (m90) REVERT: l 193 GLN cc_start: 0.8553 (tt0) cc_final: 0.7998 (tm-30) REVERT: l 215 GLU cc_start: 0.9008 (tp30) cc_final: 0.8733 (tp30) REVERT: l 244 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7829 (mm-30) REVERT: l 290 ASP cc_start: 0.7913 (t0) cc_final: 0.7563 (t0) REVERT: l 342 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8347 (mt-10) REVERT: l 397 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8833 (mm-30) REVERT: k 12 SER cc_start: 0.9199 (OUTLIER) cc_final: 0.8863 (p) REVERT: k 41 GLN cc_start: 0.8770 (tp40) cc_final: 0.8468 (tm-30) REVERT: k 60 ASP cc_start: 0.8942 (t0) cc_final: 0.8686 (t70) REVERT: k 205 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7963 (mtp) REVERT: k 259 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8207 (p0) REVERT: k 342 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8328 (mt-10) REVERT: k 397 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8977 (mt-10) REVERT: j 1 MET cc_start: 0.6337 (OUTLIER) cc_final: 0.5382 (tmm) REVERT: j 23 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8285 (mm) REVERT: j 205 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8131 (mtp) REVERT: j 222 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8989 (mt) REVERT: j 342 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7937 (pt0) REVERT: j 352 LYS cc_start: 0.7890 (tptp) cc_final: 0.7499 (tptp) REVERT: j 397 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8860 (mt-10) REVERT: j 407 LYS cc_start: 0.9227 (ptmm) cc_final: 0.8993 (ttmm) REVERT: b 1 MET cc_start: 0.7004 (mmm) cc_final: 0.6600 (tpt) REVERT: b 244 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8550 (mm-30) REVERT: b 253 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9185 (mt) REVERT: b 342 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8335 (mp0) REVERT: b 397 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8757 (mt-10) REVERT: c 12 SER cc_start: 0.9562 (OUTLIER) cc_final: 0.9334 (p) REVERT: c 30 ARG cc_start: 0.8452 (mmm-85) cc_final: 0.8054 (mtp-110) REVERT: c 140 HIS cc_start: 0.9141 (OUTLIER) cc_final: 0.8606 (m90) REVERT: c 186 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8706 (mtm) REVERT: c 241 GLN cc_start: 0.9187 (pp30) cc_final: 0.8532 (pp30) REVERT: c 292 ASN cc_start: 0.8756 (m-40) cc_final: 0.8453 (p0) REVERT: c 375 GLU cc_start: 0.8559 (tp30) cc_final: 0.8235 (tp30) REVERT: d 8 ASN cc_start: 0.9135 (m-40) cc_final: 0.8672 (m110) REVERT: d 21 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7211 (ppp) REVERT: d 29 MET cc_start: 0.8599 (ptp) cc_final: 0.8118 (ptp) REVERT: d 140 HIS cc_start: 0.8993 (OUTLIER) cc_final: 0.8645 (m90) REVERT: d 342 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8081 (mm-30) REVERT: e 222 LEU cc_start: 0.9453 (tt) cc_final: 0.9180 (tt) REVERT: e 241 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8811 (tm-30) REVERT: e 259 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8569 (p0) REVERT: e 396 MET cc_start: 0.9298 (tpp) cc_final: 0.8981 (tpp) REVERT: f 1 MET cc_start: 0.6424 (OUTLIER) cc_final: 0.5407 (tmm) REVERT: f 123 LYS cc_start: 0.8383 (ptmm) cc_final: 0.8145 (ptmm) REVERT: f 140 HIS cc_start: 0.8791 (OUTLIER) cc_final: 0.8254 (m90) REVERT: f 326 LYS cc_start: 0.9065 (tmtt) cc_final: 0.8652 (tmtt) REVERT: f 329 GLU cc_start: 0.8075 (mp0) cc_final: 0.7509 (mp0) REVERT: g 23 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7696 (mm) REVERT: g 30 ARG cc_start: 0.7940 (mmm-85) cc_final: 0.7509 (mtp-110) REVERT: g 193 GLN cc_start: 0.9177 (tt0) cc_final: 0.8968 (mt0) REVERT: g 205 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8177 (mtt) REVERT: g 375 GLU cc_start: 0.8583 (tp30) cc_final: 0.8052 (tp30) REVERT: g 397 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8880 (mt-10) REVERT: h 21 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8288 (ppp) REVERT: h 259 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.7733 (p0) REVERT: h 374 GLN cc_start: 0.9530 (tp40) cc_final: 0.9231 (tp-100) REVERT: i 1 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.5867 (tpt) REVERT: i 91 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8607 (pp) REVERT: i 329 GLU cc_start: 0.8775 (tp30) cc_final: 0.8457 (mm-30) REVERT: i 333 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8621 (mm-30) REVERT: i 342 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8121 (mp0) REVERT: i 375 GLU cc_start: 0.8488 (tp30) cc_final: 0.8109 (tp30) outliers start: 437 outliers final: 241 residues processed: 1231 average time/residue: 0.5659 time to fit residues: 1165.3686 Evaluate side-chains 1125 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 849 time to evaluate : 5.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 110 TYR Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 202 CYS Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 259 ASP Chi-restraints excluded: chain a residue 264 LEU Chi-restraints excluded: chain a residue 292 ASN Chi-restraints excluded: chain a residue 323 THR Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain a residue 371 LEU Chi-restraints excluded: chain a residue 376 GLU Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain r residue 12 SER Chi-restraints excluded: chain r residue 21 MET Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 29 MET Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 323 THR Chi-restraints excluded: chain r residue 366 ARG Chi-restraints excluded: chain r residue 394 ASP Chi-restraints excluded: chain r residue 398 PHE Chi-restraints excluded: chain r residue 410 ASP Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 12 SER Chi-restraints excluded: chain q residue 44 LYS Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 195 ILE Chi-restraints excluded: chain q residue 202 CYS Chi-restraints excluded: chain q residue 260 VAL Chi-restraints excluded: chain q residue 286 THR Chi-restraints excluded: chain q residue 323 THR Chi-restraints excluded: chain q residue 330 VAL Chi-restraints excluded: chain q residue 338 THR Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain q residue 372 THR Chi-restraints excluded: chain q residue 394 ASP Chi-restraints excluded: chain q residue 401 ASN 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 29 MET Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain p residue 91 LEU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 202 CYS Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 260 VAL Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 286 THR Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain p residue 323 THR Chi-restraints excluded: chain p residue 338 THR Chi-restraints excluded: chain p residue 394 ASP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain o residue 29 MET Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 70 SER Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 126 ASN Chi-restraints excluded: chain o residue 205 MET Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 259 ASP Chi-restraints excluded: chain o residue 286 THR Chi-restraints excluded: chain o residue 292 ASN Chi-restraints excluded: chain o residue 338 THR Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 370 LEU Chi-restraints excluded: chain o residue 394 ASP Chi-restraints excluded: chain o residue 408 THR Chi-restraints excluded: chain o residue 410 ASP Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 23 LEU Chi-restraints excluded: chain n residue 56 GLU Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 241 GLN Chi-restraints excluded: chain n residue 253 LEU Chi-restraints excluded: chain n residue 259 ASP Chi-restraints excluded: chain n residue 264 LEU Chi-restraints excluded: chain n residue 323 THR Chi-restraints excluded: chain n residue 338 THR Chi-restraints excluded: chain n residue 387 ILE Chi-restraints excluded: chain n residue 394 ASP Chi-restraints excluded: chain n residue 405 MET Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 60 ASP Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain m residue 205 MET Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain m residue 292 ASN Chi-restraints excluded: chain m residue 338 THR Chi-restraints excluded: chain m residue 381 TRP Chi-restraints excluded: chain m residue 394 ASP Chi-restraints excluded: chain m residue 415 MET Chi-restraints excluded: chain m residue 418 ARG Chi-restraints excluded: chain l residue 29 MET Chi-restraints excluded: chain l residue 49 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 140 HIS Chi-restraints excluded: chain l residue 205 MET Chi-restraints excluded: chain l residue 241 GLN Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain l residue 264 LEU Chi-restraints excluded: chain l residue 338 THR Chi-restraints excluded: chain l residue 341 MET Chi-restraints excluded: chain l residue 372 THR Chi-restraints excluded: chain l residue 381 TRP Chi-restraints excluded: chain l residue 394 ASP Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain k residue 29 MET Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 162 LEU Chi-restraints excluded: chain k residue 193 GLN Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 205 MET Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 259 ASP Chi-restraints excluded: chain k residue 260 VAL Chi-restraints excluded: chain k residue 327 MET Chi-restraints excluded: chain k residue 338 THR Chi-restraints excluded: chain k residue 370 LEU Chi-restraints excluded: chain k residue 373 THR Chi-restraints excluded: chain k residue 394 ASP Chi-restraints excluded: chain k residue 400 ILE Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 29 MET Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 154 THR Chi-restraints excluded: chain j residue 162 LEU Chi-restraints excluded: chain j residue 205 MET Chi-restraints excluded: chain j residue 222 LEU Chi-restraints excluded: chain j residue 260 VAL Chi-restraints excluded: chain j residue 264 LEU Chi-restraints excluded: chain j residue 338 THR Chi-restraints excluded: chain j residue 373 THR Chi-restraints excluded: chain j residue 394 ASP Chi-restraints excluded: chain b residue 12 SER Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 253 LEU Chi-restraints excluded: chain b residue 260 VAL Chi-restraints excluded: chain b residue 264 LEU Chi-restraints excluded: chain b residue 338 THR Chi-restraints excluded: chain b residue 341 MET Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 410 ASP Chi-restraints excluded: chain c residue 12 SER Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 55 LEU Chi-restraints excluded: chain c residue 70 SER Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 140 HIS Chi-restraints excluded: chain c residue 186 MET Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 379 LYS Chi-restraints excluded: chain c residue 387 ILE Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 140 HIS Chi-restraints excluded: chain d residue 205 MET Chi-restraints excluded: chain d residue 241 GLN Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 259 ASP Chi-restraints excluded: chain d residue 292 ASN Chi-restraints excluded: chain d residue 338 THR Chi-restraints excluded: chain d residue 371 LEU Chi-restraints excluded: chain d residue 381 TRP Chi-restraints excluded: chain d residue 394 ASP Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 60 ASP Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 140 HIS Chi-restraints excluded: chain e residue 205 MET Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 259 ASP Chi-restraints excluded: chain e residue 292 ASN Chi-restraints excluded: chain e residue 327 MET Chi-restraints excluded: chain e residue 338 THR Chi-restraints excluded: chain e residue 394 ASP Chi-restraints excluded: chain e residue 410 ASP Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 12 SER Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 29 MET Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 140 HIS Chi-restraints excluded: chain f residue 205 MET Chi-restraints excluded: chain f residue 241 GLN Chi-restraints excluded: chain f residue 253 LEU Chi-restraints excluded: chain f residue 260 VAL Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 338 THR Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 354 VAL Chi-restraints excluded: chain f residue 381 TRP Chi-restraints excluded: chain f residue 394 ASP Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 56 GLU Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 205 MET Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 260 VAL Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 338 THR Chi-restraints excluded: chain g residue 341 MET Chi-restraints excluded: chain g residue 354 VAL Chi-restraints excluded: chain g residue 381 TRP Chi-restraints excluded: chain g residue 394 ASP Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 21 MET Chi-restraints excluded: chain h residue 23 LEU Chi-restraints excluded: chain h residue 29 MET Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 123 LYS Chi-restraints excluded: chain h residue 126 ASN Chi-restraints excluded: chain h residue 259 ASP Chi-restraints excluded: chain h residue 260 VAL Chi-restraints excluded: chain h residue 338 THR Chi-restraints excluded: chain h residue 372 THR Chi-restraints excluded: chain h residue 381 TRP Chi-restraints excluded: chain h residue 394 ASP Chi-restraints excluded: chain h residue 408 THR Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 29 MET Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 91 LEU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 126 ASN Chi-restraints excluded: chain i residue 241 GLN Chi-restraints excluded: chain i residue 260 VAL Chi-restraints excluded: chain i residue 264 LEU Chi-restraints excluded: chain i residue 277 VAL Chi-restraints excluded: chain i residue 290 ASP Chi-restraints excluded: chain i residue 338 THR Chi-restraints excluded: chain i residue 341 MET Chi-restraints excluded: chain i residue 354 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 663 optimal weight: 6.9990 chunk 504 optimal weight: 7.9990 chunk 348 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 320 optimal weight: 3.9990 chunk 450 optimal weight: 9.9990 chunk 673 optimal weight: 0.9980 chunk 713 optimal weight: 3.9990 chunk 352 optimal weight: 0.8980 chunk 638 optimal weight: 8.9990 chunk 192 optimal weight: 3.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 189 GLN ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 193 GLN ** r 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 295 HIS ** q 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 189 GLN ** o 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 292 ASN ** j 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 8 ASN b 193 GLN c 172 GLN c 189 GLN c 374 GLN d 41 GLN d 220 GLN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 41 GLN ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 199 HIS i 126 ASN i 193 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 60822 Z= 0.226 Angle : 0.606 10.027 82008 Z= 0.288 Chirality : 0.043 0.166 9324 Planarity : 0.004 0.038 10620 Dihedral : 4.968 42.486 8405 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 5.56 % Allowed : 27.01 % Favored : 67.44 % 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: 0.55 (0.10), residues: 7506 helix: 1.10 (0.09), residues: 3348 sheet: 0.10 (0.15), residues: 1134 loop : -0.24 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.008 TRP l 381 HIS 0.008 0.001 HIS r 295 PHE 0.012 0.001 PHE q 413 TYR 0.022 0.001 TYR k 197 ARG 0.009 0.000 ARG n 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 1262 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 360 poor density : 902 time to evaluate : 5.486 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: a 29 MET cc_start: 0.8000 (ptm) cc_final: 0.7631 (ptp) REVERT: a 215 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: a 244 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8192 (mm-30) REVERT: a 375 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8238 (mp0) REVERT: r 244 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8516 (mm-30) REVERT: r 248 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8711 (mm-30) REVERT: r 366 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7868 (tpt170) REVERT: r 416 MET cc_start: 0.7771 (mmp) cc_final: 0.6543 (ttt) REVERT: q 1 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6748 (tpt) REVERT: q 211 GLU cc_start: 0.8583 (tp30) cc_final: 0.8221 (tp30) REVERT: q 244 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8462 (mm-30) REVERT: q 390 MET cc_start: 0.8878 (pmm) cc_final: 0.8500 (pmm) REVERT: q 394 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8606 (p0) REVERT: q 396 MET cc_start: 0.9094 (tpp) cc_final: 0.8783 (tpp) REVERT: p 1 MET cc_start: 0.7419 (tpt) cc_final: 0.7219 (tpt) REVERT: p 33 ASP cc_start: 0.9095 (m-30) cc_final: 0.8683 (m-30) REVERT: p 91 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8875 (pp) REVERT: p 193 GLN cc_start: 0.8976 (tt0) cc_final: 0.8682 (tt0) REVERT: p 325 SER cc_start: 0.7991 (t) cc_final: 0.7567 (p) REVERT: p 394 ASP cc_start: 0.8981 (OUTLIER) cc_final: 0.8614 (p0) REVERT: o 259 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8171 (p0) REVERT: o 292 ASN cc_start: 0.8708 (m-40) cc_final: 0.8436 (p0) REVERT: o 333 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8619 (tm-30) REVERT: o 397 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8506 (mp0) REVERT: o 413 PHE cc_start: 0.8912 (m-80) cc_final: 0.8656 (m-80) REVERT: n 41 GLN cc_start: 0.9261 (tp40) cc_final: 0.8763 (tp-100) REVERT: n 100 LYS cc_start: 0.9529 (ttmt) cc_final: 0.9180 (ttmm) REVERT: n 259 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.7836 (p0) REVERT: n 342 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8432 (mt-10) REVERT: n 374 GLN cc_start: 0.9030 (tp-100) cc_final: 0.8497 (tp-100) REVERT: n 394 ASP cc_start: 0.9194 (OUTLIER) cc_final: 0.8952 (m-30) REVERT: m 40 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.9062 (ttpp) REVERT: m 44 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8801 (ptpp) REVERT: m 100 LYS cc_start: 0.9212 (ttmt) cc_final: 0.8997 (ptmm) REVERT: m 125 GLU cc_start: 0.8747 (mp0) cc_final: 0.8467 (pm20) REVERT: m 244 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8229 (mm-30) REVERT: m 296 ARG cc_start: 0.9087 (tpp80) cc_final: 0.8692 (mmm-85) REVERT: m 326 LYS cc_start: 0.9209 (tmtt) cc_final: 0.8957 (tptt) REVERT: m 329 GLU cc_start: 0.8537 (pm20) cc_final: 0.8240 (pm20) REVERT: m 334 GLU cc_start: 0.8840 (tp30) cc_final: 0.8604 (tm-30) REVERT: m 342 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8340 (mp0) REVERT: m 403 LEU cc_start: 0.9491 (mm) cc_final: 0.9287 (mp) REVERT: l 140 HIS cc_start: 0.8800 (OUTLIER) cc_final: 0.8339 (m90) REVERT: l 215 GLU cc_start: 0.9061 (tp30) cc_final: 0.8746 (tp30) REVERT: l 222 LEU cc_start: 0.9373 (tt) cc_final: 0.8797 (tt) REVERT: l 244 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7817 (mm-30) REVERT: l 290 ASP cc_start: 0.8010 (t0) cc_final: 0.6819 (t0) REVERT: l 292 ASN cc_start: 0.9073 (m110) cc_final: 0.8720 (p0) REVERT: l 298 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8901 (mmtm) REVERT: l 329 GLU cc_start: 0.8033 (mp0) cc_final: 0.7772 (mp0) REVERT: l 342 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8340 (mt-10) REVERT: l 397 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8947 (mm-30) REVERT: k 12 SER cc_start: 0.9213 (OUTLIER) cc_final: 0.8854 (p) REVERT: k 13 GLU cc_start: 0.8614 (pm20) cc_final: 0.8307 (pm20) REVERT: k 41 GLN cc_start: 0.8820 (tp40) cc_final: 0.8502 (tm-30) REVERT: k 205 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7952 (mtp) REVERT: k 259 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8166 (p0) REVERT: k 342 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8332 (mt-10) REVERT: k 397 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8951 (mt-10) REVERT: j 1 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.5398 (tmm) REVERT: j 23 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8322 (mm) REVERT: j 205 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7989 (mtp) REVERT: j 222 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9016 (mt) REVERT: j 298 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8856 (mmtm) REVERT: j 342 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7913 (pt0) REVERT: j 352 LYS cc_start: 0.7934 (tptp) cc_final: 0.7439 (tptp) REVERT: j 381 TRP cc_start: 0.8424 (OUTLIER) cc_final: 0.8170 (t60) REVERT: j 397 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8807 (mt-10) REVERT: j 407 LYS cc_start: 0.9252 (ptmm) cc_final: 0.9003 (ttmm) REVERT: b 1 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6407 (tpt) REVERT: b 224 LYS cc_start: 0.8744 (pttt) cc_final: 0.8541 (pttp) REVERT: b 244 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8573 (mm-30) REVERT: b 253 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9146 (mt) REVERT: b 342 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8327 (mp0) REVERT: b 397 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8724 (mt-10) REVERT: c 12 SER cc_start: 0.9561 (OUTLIER) cc_final: 0.9334 (p) REVERT: c 30 ARG cc_start: 0.8546 (mmm-85) cc_final: 0.8131 (mtp-110) REVERT: c 41 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8518 (tm-30) REVERT: c 56 GLU cc_start: 0.8805 (tt0) cc_final: 0.8385 (tm-30) REVERT: c 90 ASN cc_start: 0.8394 (t0) cc_final: 0.8020 (t0) REVERT: c 140 HIS cc_start: 0.9156 (OUTLIER) cc_final: 0.8655 (m90) REVERT: c 186 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8590 (mtm) REVERT: c 241 GLN cc_start: 0.9115 (pp30) cc_final: 0.8598 (pp30) REVERT: c 292 ASN cc_start: 0.8764 (m-40) cc_final: 0.8454 (p0) REVERT: c 375 GLU cc_start: 0.8539 (tp30) cc_final: 0.8294 (tp30) REVERT: c 381 TRP cc_start: 0.8656 (OUTLIER) cc_final: 0.8290 (t60) REVERT: d 8 ASN cc_start: 0.8912 (m-40) cc_final: 0.8668 (m110) REVERT: d 21 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7867 (ppp) REVERT: d 29 MET cc_start: 0.8646 (ptp) cc_final: 0.8174 (ptp) REVERT: d 140 HIS cc_start: 0.9018 (OUTLIER) cc_final: 0.8645 (m90) REVERT: d 342 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8182 (mm-30) REVERT: d 374 GLN cc_start: 0.9064 (tp40) cc_final: 0.8863 (tp-100) REVERT: d 381 TRP cc_start: 0.8615 (OUTLIER) cc_final: 0.8199 (t60) REVERT: e 197 TYR cc_start: 0.9392 (t80) cc_final: 0.9161 (t80) REVERT: e 222 LEU cc_start: 0.9470 (tt) cc_final: 0.9219 (tt) REVERT: e 241 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8762 (tm-30) REVERT: e 259 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8547 (p0) REVERT: f 134 GLU cc_start: 0.8886 (mp0) cc_final: 0.8656 (mp0) REVERT: f 140 HIS cc_start: 0.8785 (OUTLIER) cc_final: 0.8264 (m90) REVERT: f 326 LYS cc_start: 0.9049 (tmtt) cc_final: 0.8651 (tmtt) REVERT: f 329 GLU cc_start: 0.8084 (mp0) cc_final: 0.7488 (mp0) REVERT: g 23 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7765 (mm) REVERT: g 30 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7630 (mtp-110) REVERT: g 205 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8202 (mtp) REVERT: g 397 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8907 (mt-10) REVERT: h 259 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.7616 (p0) REVERT: i 1 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.5869 (tpt) REVERT: i 91 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8583 (pp) REVERT: i 329 GLU cc_start: 0.8770 (tp30) cc_final: 0.8475 (mm-30) REVERT: i 333 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8644 (mm-30) REVERT: i 342 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8127 (mp0) REVERT: i 375 GLU cc_start: 0.8496 (tp30) cc_final: 0.8184 (tp30) outliers start: 360 outliers final: 229 residues processed: 1152 average time/residue: 0.5612 time to fit residues: 1085.8995 Evaluate side-chains 1113 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 845 time to evaluate : 5.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 110 TYR Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 162 LEU Chi-restraints excluded: chain a residue 202 CYS Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 259 ASP Chi-restraints excluded: chain a residue 264 LEU Chi-restraints excluded: chain a residue 292 ASN Chi-restraints excluded: chain a residue 295 HIS Chi-restraints excluded: chain a residue 323 THR Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain a residue 371 LEU Chi-restraints excluded: chain a residue 376 GLU Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain r residue 12 SER Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 29 MET Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 193 GLN Chi-restraints excluded: chain r residue 202 CYS Chi-restraints excluded: chain r residue 323 THR Chi-restraints excluded: chain r residue 366 ARG Chi-restraints excluded: chain r residue 394 ASP Chi-restraints excluded: chain r residue 398 PHE Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 12 SER Chi-restraints excluded: chain q residue 44 LYS Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 195 ILE Chi-restraints excluded: chain q residue 241 GLN Chi-restraints excluded: chain q residue 260 VAL Chi-restraints excluded: chain q residue 264 LEU Chi-restraints excluded: chain q residue 286 THR Chi-restraints excluded: chain q residue 323 THR Chi-restraints excluded: chain q residue 338 THR Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain q residue 379 LYS Chi-restraints excluded: chain q residue 394 ASP Chi-restraints excluded: chain q residue 401 ASN Chi-restraints excluded: chain q residue 405 MET Chi-restraints excluded: chain q residue 410 ASP Chi-restraints excluded: chain q residue 411 ASP Chi-restraints excluded: chain p residue 29 MET Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain p residue 91 LEU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 260 VAL Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 286 THR Chi-restraints excluded: chain p residue 323 THR Chi-restraints excluded: chain p residue 338 THR Chi-restraints excluded: chain p residue 376 GLU Chi-restraints excluded: chain p residue 379 LYS Chi-restraints excluded: chain p residue 394 ASP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain o residue 29 MET Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 70 SER Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 126 ASN Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 259 ASP Chi-restraints excluded: chain o residue 286 THR Chi-restraints excluded: chain o residue 338 THR Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 372 THR Chi-restraints excluded: chain o residue 394 ASP Chi-restraints excluded: chain o residue 410 ASP Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 23 LEU Chi-restraints excluded: chain n residue 56 GLU Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 241 GLN Chi-restraints excluded: chain n residue 253 LEU Chi-restraints excluded: chain n residue 259 ASP Chi-restraints excluded: chain n residue 264 LEU Chi-restraints excluded: chain n residue 323 THR Chi-restraints excluded: chain n residue 338 THR Chi-restraints excluded: chain n residue 354 VAL Chi-restraints excluded: chain n residue 376 GLU Chi-restraints excluded: chain n residue 394 ASP Chi-restraints excluded: chain n residue 408 THR Chi-restraints excluded: chain m residue 40 LYS Chi-restraints excluded: chain m residue 44 LYS Chi-restraints excluded: chain m residue 60 ASP Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain m residue 162 LEU Chi-restraints excluded: chain m residue 205 MET Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain m residue 327 MET Chi-restraints excluded: chain m residue 338 THR Chi-restraints excluded: chain m residue 380 MET Chi-restraints excluded: chain m residue 381 TRP Chi-restraints excluded: chain m residue 387 ILE Chi-restraints excluded: chain m residue 394 ASP Chi-restraints excluded: chain m residue 415 MET Chi-restraints excluded: chain m residue 418 ARG Chi-restraints excluded: chain l residue 49 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 140 HIS Chi-restraints excluded: chain l residue 205 MET Chi-restraints excluded: chain l residue 241 GLN Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain l residue 264 LEU Chi-restraints excluded: chain l residue 277 VAL Chi-restraints excluded: chain l residue 298 LYS Chi-restraints excluded: chain l residue 338 THR Chi-restraints excluded: chain l residue 341 MET Chi-restraints excluded: chain l residue 394 ASP Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 162 LEU Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 205 MET Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 259 ASP Chi-restraints excluded: chain k residue 277 VAL Chi-restraints excluded: chain k residue 327 MET Chi-restraints excluded: chain k residue 338 THR Chi-restraints excluded: chain k residue 371 LEU Chi-restraints excluded: chain k residue 373 THR Chi-restraints excluded: chain k residue 394 ASP Chi-restraints excluded: chain k residue 400 ILE Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 29 MET Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 162 LEU Chi-restraints excluded: chain j residue 205 MET Chi-restraints excluded: chain j residue 222 LEU Chi-restraints excluded: chain j residue 241 GLN Chi-restraints excluded: chain j residue 260 VAL Chi-restraints excluded: chain j residue 264 LEU Chi-restraints excluded: chain j residue 298 LYS Chi-restraints excluded: chain j residue 338 THR Chi-restraints excluded: chain j residue 373 THR Chi-restraints excluded: chain j residue 381 TRP Chi-restraints excluded: chain j residue 394 ASP Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 16 THR Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 91 LEU Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 193 GLN Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 253 LEU Chi-restraints excluded: chain b residue 264 LEU Chi-restraints excluded: chain b residue 338 THR Chi-restraints excluded: chain b residue 341 MET Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 410 ASP Chi-restraints excluded: chain c residue 12 SER Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 55 LEU Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 140 HIS Chi-restraints excluded: chain c residue 186 MET Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 381 TRP Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 140 HIS Chi-restraints excluded: chain d residue 205 MET Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 259 ASP Chi-restraints excluded: chain d residue 292 ASN Chi-restraints excluded: chain d residue 338 THR Chi-restraints excluded: chain d residue 371 LEU Chi-restraints excluded: chain d residue 381 TRP Chi-restraints excluded: chain d residue 394 ASP Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 60 ASP Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 140 HIS Chi-restraints excluded: chain e residue 205 MET Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 259 ASP Chi-restraints excluded: chain e residue 338 THR Chi-restraints excluded: chain e residue 394 ASP Chi-restraints excluded: chain e residue 410 ASP Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 29 MET Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 140 HIS Chi-restraints excluded: chain f residue 205 MET Chi-restraints excluded: chain f residue 241 GLN Chi-restraints excluded: chain f residue 253 LEU Chi-restraints excluded: chain f residue 264 LEU Chi-restraints excluded: chain f residue 277 VAL Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 338 THR Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 354 VAL Chi-restraints excluded: chain f residue 381 TRP Chi-restraints excluded: chain f residue 394 ASP Chi-restraints excluded: chain f residue 411 ASP Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 205 MET Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 338 THR Chi-restraints excluded: chain g residue 341 MET Chi-restraints excluded: chain g residue 354 VAL Chi-restraints excluded: chain g residue 379 LYS Chi-restraints excluded: chain g residue 381 TRP Chi-restraints excluded: chain g residue 394 ASP Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 8 ASN Chi-restraints excluded: chain h residue 21 MET Chi-restraints excluded: chain h residue 23 LEU Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 123 LYS Chi-restraints excluded: chain h residue 126 ASN Chi-restraints excluded: chain h residue 241 GLN Chi-restraints excluded: chain h residue 259 ASP Chi-restraints excluded: chain h residue 260 VAL Chi-restraints excluded: chain h residue 338 THR Chi-restraints excluded: chain h residue 381 TRP Chi-restraints excluded: chain h residue 394 ASP Chi-restraints excluded: chain h residue 408 THR Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 29 MET Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 91 LEU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 264 LEU Chi-restraints excluded: chain i residue 277 VAL Chi-restraints excluded: chain i residue 290 ASP Chi-restraints excluded: chain i residue 338 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 594 optimal weight: 2.9990 chunk 404 optimal weight: 0.0070 chunk 10 optimal weight: 20.0000 chunk 531 optimal weight: 1.9990 chunk 294 optimal weight: 6.9990 chunk 608 optimal weight: 1.9990 chunk 493 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 364 optimal weight: 5.9990 chunk 640 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 220 GLN ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 295 HIS ** q 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 189 GLN ** o 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 275 ASN k 189 GLN k 193 GLN ** j 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 8 ASN b 193 GLN c 172 GLN e 275 ASN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 220 GLN ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 41 GLN g 374 GLN ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 374 GLN i 374 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 60822 Z= 0.189 Angle : 0.595 12.190 82008 Z= 0.281 Chirality : 0.042 0.166 9324 Planarity : 0.003 0.044 10620 Dihedral : 4.779 38.983 8400 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.22 % Allowed : 27.50 % Favored : 67.28 % 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: 0.60 (0.10), residues: 7506 helix: 1.19 (0.09), residues: 3330 sheet: 0.10 (0.15), residues: 1134 loop : -0.26 (0.11), residues: 3042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.008 TRP f 381 HIS 0.007 0.001 HIS r 388 PHE 0.017 0.001 PHE q 412 TYR 0.022 0.001 TYR k 197 ARG 0.010 0.000 ARG n 418 *********************** 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 1236 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 898 time to evaluate : 5.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 29 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7659 (ptp) REVERT: a 215 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: a 244 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8197 (mm-30) REVERT: a 375 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8190 (mp0) REVERT: r 244 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8543 (mm-30) REVERT: r 248 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8633 (mm-30) REVERT: r 366 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7867 (tpt170) REVERT: r 412 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7909 (m-80) REVERT: r 416 MET cc_start: 0.7759 (mmp) cc_final: 0.6444 (ttt) REVERT: q 1 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.6783 (tpt) REVERT: q 211 GLU cc_start: 0.8566 (tp30) cc_final: 0.8240 (tp30) REVERT: q 244 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8425 (mm-30) REVERT: q 269 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8717 (mmm160) REVERT: q 390 MET cc_start: 0.8845 (pmm) cc_final: 0.8513 (pmm) REVERT: q 394 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8609 (p0) REVERT: q 396 MET cc_start: 0.9123 (tpp) cc_final: 0.8744 (tpp) REVERT: p 33 ASP cc_start: 0.9100 (m-30) cc_final: 0.8794 (m-30) REVERT: p 91 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8812 (pp) REVERT: p 193 GLN cc_start: 0.8988 (tt0) cc_final: 0.8695 (tt0) REVERT: p 241 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8572 (tm-30) REVERT: p 325 SER cc_start: 0.8000 (t) cc_final: 0.7550 (p) REVERT: p 390 MET cc_start: 0.8510 (pmm) cc_final: 0.8272 (pmm) REVERT: p 394 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8454 (p0) REVERT: o 259 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8127 (p0) REVERT: o 292 ASN cc_start: 0.8708 (m-40) cc_final: 0.8438 (p0) REVERT: o 333 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8595 (tm-30) REVERT: o 387 ILE cc_start: 0.9586 (OUTLIER) cc_final: 0.9354 (mt) REVERT: o 397 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8531 (mp0) REVERT: n 41 GLN cc_start: 0.9253 (tp40) cc_final: 0.8835 (tp40) REVERT: n 100 LYS cc_start: 0.9515 (ttmt) cc_final: 0.9164 (ttmm) REVERT: n 244 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8481 (mm-30) REVERT: n 259 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.7784 (p0) REVERT: n 342 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8417 (mt-10) REVERT: n 374 GLN cc_start: 0.9020 (tp-100) cc_final: 0.8544 (tp-100) REVERT: m 40 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.9062 (ttpp) REVERT: m 44 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8773 (ptpp) REVERT: m 100 LYS cc_start: 0.9201 (ttmt) cc_final: 0.8997 (ptmm) REVERT: m 125 GLU cc_start: 0.8793 (mp0) cc_final: 0.8508 (pm20) REVERT: m 244 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8241 (mm-30) REVERT: m 296 ARG cc_start: 0.9087 (tpp80) cc_final: 0.8701 (mmm-85) REVERT: m 329 GLU cc_start: 0.8525 (pm20) cc_final: 0.8307 (pm20) REVERT: m 334 GLU cc_start: 0.8840 (tp30) cc_final: 0.8633 (tm-30) REVERT: m 341 MET cc_start: 0.9288 (tmm) cc_final: 0.8954 (tmm) REVERT: m 342 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8392 (mp0) REVERT: m 403 LEU cc_start: 0.9481 (mm) cc_final: 0.9270 (mp) REVERT: l 140 HIS cc_start: 0.8806 (OUTLIER) cc_final: 0.8351 (m90) REVERT: l 215 GLU cc_start: 0.9054 (tp30) cc_final: 0.8768 (tp30) REVERT: l 244 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7796 (mm-30) REVERT: l 290 ASP cc_start: 0.8025 (t0) cc_final: 0.6771 (t0) REVERT: l 292 ASN cc_start: 0.9052 (m110) cc_final: 0.8699 (p0) REVERT: l 342 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8326 (mt-10) REVERT: l 397 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8930 (mm-30) REVERT: k 12 SER cc_start: 0.9287 (OUTLIER) cc_final: 0.8885 (p) REVERT: k 13 GLU cc_start: 0.8622 (pm20) cc_final: 0.8342 (pm20) REVERT: k 41 GLN cc_start: 0.8809 (tp40) cc_final: 0.8490 (tm-30) REVERT: k 205 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7943 (mtt) REVERT: k 259 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8144 (p0) REVERT: k 333 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8593 (mm-30) REVERT: k 342 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8346 (mt-10) REVERT: k 397 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8929 (mt-10) REVERT: j 1 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.5353 (tmm) REVERT: j 23 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8303 (mm) REVERT: j 109 ARG cc_start: 0.8154 (ptp-170) cc_final: 0.7732 (mtm110) REVERT: j 205 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8058 (mtt) REVERT: j 222 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9005 (mt) REVERT: j 298 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8851 (mmtm) REVERT: j 342 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7912 (pt0) REVERT: j 381 TRP cc_start: 0.8344 (OUTLIER) cc_final: 0.8132 (t60) REVERT: j 407 LYS cc_start: 0.9253 (ptmm) cc_final: 0.8948 (ttmm) REVERT: b 1 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6350 (tpt) REVERT: b 30 ARG cc_start: 0.8560 (ttm110) cc_final: 0.8214 (mtm-85) REVERT: b 193 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8871 (tm-30) REVERT: b 244 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8636 (mm-30) REVERT: b 253 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9129 (mt) REVERT: b 342 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8330 (mp0) REVERT: b 397 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8727 (mt-10) REVERT: c 12 SER cc_start: 0.9550 (OUTLIER) cc_final: 0.9319 (p) REVERT: c 29 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8126 (ptm) REVERT: c 30 ARG cc_start: 0.8504 (mmm-85) cc_final: 0.8127 (mtp-110) REVERT: c 56 GLU cc_start: 0.8751 (tt0) cc_final: 0.8405 (tm-30) REVERT: c 90 ASN cc_start: 0.8392 (t0) cc_final: 0.8018 (t0) REVERT: c 140 HIS cc_start: 0.9158 (OUTLIER) cc_final: 0.8665 (m90) REVERT: c 195 ILE cc_start: 0.9522 (mt) cc_final: 0.9271 (mt) REVERT: c 241 GLN cc_start: 0.9153 (pp30) cc_final: 0.8582 (pp30) REVERT: c 292 ASN cc_start: 0.8758 (m-40) cc_final: 0.8457 (p0) REVERT: c 381 TRP cc_start: 0.8598 (OUTLIER) cc_final: 0.8253 (t60) REVERT: d 8 ASN cc_start: 0.8876 (m-40) cc_final: 0.8644 (m110) REVERT: d 21 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7749 (ppp) REVERT: d 29 MET cc_start: 0.8657 (ptp) cc_final: 0.8206 (ptp) REVERT: d 60 ASP cc_start: 0.9025 (t0) cc_final: 0.8595 (t0) REVERT: d 140 HIS cc_start: 0.9023 (OUTLIER) cc_final: 0.8657 (m90) REVERT: d 342 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8196 (mm-30) REVERT: d 374 GLN cc_start: 0.9071 (tp40) cc_final: 0.8860 (tp-100) REVERT: d 381 TRP cc_start: 0.8580 (OUTLIER) cc_final: 0.8188 (t60) REVERT: d 397 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8751 (mt-10) REVERT: e 140 HIS cc_start: 0.8950 (OUTLIER) cc_final: 0.8447 (m-70) REVERT: e 197 TYR cc_start: 0.9409 (t80) cc_final: 0.9146 (t80) REVERT: e 222 LEU cc_start: 0.9457 (tt) cc_final: 0.9203 (tt) REVERT: e 259 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8535 (p0) REVERT: f 134 GLU cc_start: 0.8895 (mp0) cc_final: 0.8671 (mp0) REVERT: f 140 HIS cc_start: 0.8757 (OUTLIER) cc_final: 0.8187 (m90) REVERT: f 226 GLU cc_start: 0.8205 (pp20) cc_final: 0.7955 (pp20) REVERT: f 326 LYS cc_start: 0.9031 (tmtt) cc_final: 0.8749 (tttm) REVERT: f 329 GLU cc_start: 0.8134 (mp0) cc_final: 0.7525 (mp0) REVERT: g 23 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7783 (mm) REVERT: g 30 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7634 (mtp-110) REVERT: g 205 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8199 (mtp) REVERT: g 374 GLN cc_start: 0.9324 (OUTLIER) cc_final: 0.8971 (tp-100) REVERT: g 397 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8911 (mt-10) REVERT: h 259 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.7548 (p0) REVERT: h 374 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.8973 (tp-100) REVERT: i 1 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.5825 (tpt) REVERT: i 329 GLU cc_start: 0.8794 (tp30) cc_final: 0.8588 (mm-30) REVERT: i 333 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8757 (mm-30) REVERT: i 342 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8120 (mp0) REVERT: i 375 GLU cc_start: 0.8485 (tp30) cc_final: 0.8176 (tp30) outliers start: 338 outliers final: 214 residues processed: 1123 average time/residue: 0.5844 time to fit residues: 1112.1044 Evaluate side-chains 1127 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 869 time to evaluate : 5.414 ------------------------------------------------------------------------------- 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 29 MET Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 110 TYR Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 202 CYS Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 259 ASP Chi-restraints excluded: chain a residue 264 LEU Chi-restraints excluded: chain a residue 292 ASN Chi-restraints excluded: chain a residue 323 THR Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain a residue 371 LEU Chi-restraints excluded: chain a residue 376 GLU Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 29 MET Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 323 THR Chi-restraints excluded: chain r residue 366 ARG Chi-restraints excluded: chain r residue 394 ASP Chi-restraints excluded: chain r residue 412 PHE Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 12 SER Chi-restraints excluded: chain q residue 44 LYS Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 260 VAL Chi-restraints excluded: chain q residue 264 LEU Chi-restraints excluded: chain q residue 269 ARG Chi-restraints excluded: chain q residue 286 THR Chi-restraints excluded: chain q residue 323 THR Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain q residue 372 THR Chi-restraints excluded: chain q residue 379 LYS Chi-restraints excluded: chain q residue 394 ASP Chi-restraints excluded: chain q residue 405 MET Chi-restraints excluded: chain q residue 411 ASP Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain p residue 91 LEU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 202 CYS Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 263 LEU Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 286 THR Chi-restraints excluded: chain p residue 323 THR Chi-restraints excluded: chain p residue 338 THR Chi-restraints excluded: chain p residue 379 LYS Chi-restraints excluded: chain p residue 394 ASP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain o residue 70 SER Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 259 ASP Chi-restraints excluded: chain o residue 286 THR Chi-restraints excluded: chain o residue 338 THR Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 372 THR Chi-restraints excluded: chain o residue 381 TRP Chi-restraints excluded: chain o residue 387 ILE Chi-restraints excluded: chain o residue 394 ASP Chi-restraints excluded: chain o residue 410 ASP Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 56 GLU Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 233 ASP Chi-restraints excluded: chain n residue 253 LEU Chi-restraints excluded: chain n residue 259 ASP Chi-restraints excluded: chain n residue 264 LEU Chi-restraints excluded: chain n residue 323 THR Chi-restraints excluded: chain n residue 354 VAL Chi-restraints excluded: chain n residue 376 GLU Chi-restraints excluded: chain n residue 381 TRP Chi-restraints excluded: chain n residue 387 ILE Chi-restraints excluded: chain n residue 394 ASP Chi-restraints excluded: chain n residue 408 THR Chi-restraints excluded: chain n residue 410 ASP Chi-restraints excluded: chain n residue 411 ASP Chi-restraints excluded: chain m residue 29 MET Chi-restraints excluded: chain m residue 40 LYS Chi-restraints excluded: chain m residue 44 LYS Chi-restraints excluded: chain m residue 60 ASP Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain m residue 205 MET Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain m residue 327 MET Chi-restraints excluded: chain m residue 338 THR Chi-restraints excluded: chain m residue 354 VAL Chi-restraints excluded: chain m residue 380 MET Chi-restraints excluded: chain m residue 381 TRP Chi-restraints excluded: chain m residue 394 ASP Chi-restraints excluded: chain m residue 418 ARG Chi-restraints excluded: chain l residue 49 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 140 HIS Chi-restraints excluded: chain l residue 205 MET Chi-restraints excluded: chain l residue 241 GLN Chi-restraints excluded: chain l residue 264 LEU Chi-restraints excluded: chain l residue 277 VAL Chi-restraints excluded: chain l residue 338 THR Chi-restraints excluded: chain l residue 341 MET Chi-restraints excluded: chain l residue 381 TRP Chi-restraints excluded: chain l residue 394 ASP Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 162 LEU Chi-restraints excluded: chain k residue 193 GLN Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 205 MET Chi-restraints excluded: chain k residue 259 ASP Chi-restraints excluded: chain k residue 277 VAL Chi-restraints excluded: chain k residue 327 MET Chi-restraints excluded: chain k residue 338 THR Chi-restraints excluded: chain k residue 373 THR Chi-restraints excluded: chain k residue 394 ASP Chi-restraints excluded: chain k residue 400 ILE Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 162 LEU Chi-restraints excluded: chain j residue 205 MET Chi-restraints excluded: chain j residue 222 LEU Chi-restraints excluded: chain j residue 241 GLN Chi-restraints excluded: chain j residue 260 VAL Chi-restraints excluded: chain j residue 264 LEU Chi-restraints excluded: chain j residue 298 LYS Chi-restraints excluded: chain j residue 338 THR Chi-restraints excluded: chain j residue 373 THR Chi-restraints excluded: chain j residue 381 TRP Chi-restraints excluded: chain j residue 394 ASP Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 91 LEU Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 193 GLN Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 253 LEU Chi-restraints excluded: chain b residue 264 LEU Chi-restraints excluded: chain b residue 338 THR Chi-restraints excluded: chain b residue 341 MET Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 408 THR Chi-restraints excluded: chain b residue 410 ASP Chi-restraints excluded: chain c residue 12 SER Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 55 LEU Chi-restraints excluded: chain c residue 70 SER Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 140 HIS Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 381 TRP Chi-restraints excluded: chain c residue 411 ASP Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 140 HIS Chi-restraints excluded: chain d residue 205 MET Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 259 ASP Chi-restraints excluded: chain d residue 292 ASN Chi-restraints excluded: chain d residue 338 THR Chi-restraints excluded: chain d residue 371 LEU Chi-restraints excluded: chain d residue 381 TRP Chi-restraints excluded: chain d residue 394 ASP Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 60 ASP Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 140 HIS Chi-restraints excluded: chain e residue 205 MET Chi-restraints excluded: chain e residue 259 ASP Chi-restraints excluded: chain e residue 327 MET Chi-restraints excluded: chain e residue 381 TRP Chi-restraints excluded: chain e residue 394 ASP Chi-restraints excluded: chain e residue 410 ASP Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 23 LEU Chi-restraints excluded: chain f residue 29 MET Chi-restraints excluded: chain f residue 44 LYS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 140 HIS Chi-restraints excluded: chain f residue 205 MET Chi-restraints excluded: chain f residue 241 GLN Chi-restraints excluded: chain f residue 259 ASP Chi-restraints excluded: chain f residue 264 LEU Chi-restraints excluded: chain f residue 277 VAL Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 338 THR Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 354 VAL Chi-restraints excluded: chain f residue 381 TRP Chi-restraints excluded: chain f residue 394 ASP Chi-restraints excluded: chain f residue 411 ASP Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 205 MET Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 341 MET Chi-restraints excluded: chain g residue 354 VAL Chi-restraints excluded: chain g residue 374 GLN Chi-restraints excluded: chain g residue 379 LYS Chi-restraints excluded: chain g residue 381 TRP Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 8 ASN Chi-restraints excluded: chain h residue 21 MET Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 123 LYS Chi-restraints excluded: chain h residue 126 ASN Chi-restraints excluded: chain h residue 162 LEU Chi-restraints excluded: chain h residue 241 GLN Chi-restraints excluded: chain h residue 259 ASP Chi-restraints excluded: chain h residue 338 THR Chi-restraints excluded: chain h residue 374 GLN Chi-restraints excluded: chain h residue 381 TRP Chi-restraints excluded: chain h residue 394 ASP Chi-restraints excluded: chain h residue 408 THR Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 23 LEU Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 241 GLN Chi-restraints excluded: chain i residue 264 LEU Chi-restraints excluded: chain i residue 277 VAL Chi-restraints excluded: chain i residue 290 ASP Chi-restraints excluded: chain i residue 373 THR 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: 10.0000 chunk 418 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 chunk 714 optimal weight: 3.9990 chunk 592 optimal weight: 0.9980 chunk 330 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 chunk 374 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 220 GLN a 241 GLN ** r 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 135 ASN ** p 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 189 GLN n 292 ASN l 193 GLN k 193 GLN ** j 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 126 ASN b 193 GLN c 172 GLN c 189 GLN ** d 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 60822 Z= 0.356 Angle : 0.660 10.301 82008 Z= 0.317 Chirality : 0.044 0.170 9324 Planarity : 0.004 0.049 10620 Dihedral : 5.063 42.478 8397 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.88 % Allowed : 27.28 % 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: 0.48 (0.10), residues: 7506 helix: 1.06 (0.09), residues: 3312 sheet: -0.03 (0.15), residues: 1134 loop : -0.24 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.009 TRP f 381 HIS 0.006 0.001 HIS q 140 PHE 0.024 0.001 PHE o 412 TYR 0.020 0.002 TYR l 197 ARG 0.011 0.001 ARG n 418 *********************** 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 1251 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 381 poor density : 870 time to evaluate : 5.404 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: 0.8120 (OUTLIER) cc_final: 0.7709 (ptp) REVERT: a 215 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: a 244 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8216 (mm-30) REVERT: a 259 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8102 (p0) REVERT: a 375 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8317 (mp0) REVERT: r 12 SER cc_start: 0.9445 (OUTLIER) cc_final: 0.9121 (p) REVERT: r 147 MET cc_start: 0.7765 (tpp) cc_final: 0.7553 (tpp) REVERT: r 244 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8580 (mm-30) REVERT: r 366 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7812 (tpt170) REVERT: q 1 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.6900 (tpt) REVERT: q 244 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8479 (mm-30) REVERT: q 390 MET cc_start: 0.8863 (pmm) cc_final: 0.8570 (pmm) REVERT: q 394 ASP cc_start: 0.8991 (OUTLIER) cc_final: 0.8636 (p0) REVERT: p 33 ASP cc_start: 0.9082 (m-30) cc_final: 0.8811 (m-30) REVERT: p 91 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8925 (pp) REVERT: p 193 GLN cc_start: 0.8945 (tt0) cc_final: 0.8645 (tt0) REVERT: p 394 ASP cc_start: 0.9002 (OUTLIER) cc_final: 0.8684 (p0) REVERT: o 29 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8507 (ptm) REVERT: o 259 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8135 (p0) REVERT: o 333 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8563 (tm-30) REVERT: o 397 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8510 (mp0) REVERT: o 405 MET cc_start: 0.9342 (ptp) cc_final: 0.8847 (pmm) REVERT: n 41 GLN cc_start: 0.9288 (tp40) cc_final: 0.8786 (tp-100) REVERT: n 100 LYS cc_start: 0.9510 (ttmt) cc_final: 0.9123 (ttmm) REVERT: n 326 LYS cc_start: 0.9075 (tptp) cc_final: 0.8832 (tptp) REVERT: n 374 GLN cc_start: 0.9059 (tp-100) cc_final: 0.8624 (tp-100) REVERT: m 40 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9065 (ttpp) REVERT: m 44 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8766 (ptpp) REVERT: m 125 GLU cc_start: 0.8820 (mp0) cc_final: 0.8569 (pm20) REVERT: m 296 ARG cc_start: 0.9092 (tpp80) cc_final: 0.8730 (mmm-85) REVERT: m 334 GLU cc_start: 0.8848 (tp30) cc_final: 0.8598 (tm-30) REVERT: m 342 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8412 (mp0) REVERT: m 374 GLN cc_start: 0.9486 (tp40) cc_final: 0.9064 (tp40) REVERT: m 392 GLU cc_start: 0.8582 (pm20) cc_final: 0.7783 (pt0) REVERT: l 140 HIS cc_start: 0.8793 (OUTLIER) cc_final: 0.8485 (m-70) REVERT: l 215 GLU cc_start: 0.9111 (tp30) cc_final: 0.8796 (tp30) REVERT: l 244 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7834 (mm-30) REVERT: l 290 ASP cc_start: 0.7926 (t0) cc_final: 0.6717 (t0) REVERT: l 292 ASN cc_start: 0.9041 (m110) cc_final: 0.8594 (p0) REVERT: l 375 GLU cc_start: 0.9221 (tp30) cc_final: 0.8855 (tp30) REVERT: l 397 GLU cc_start: 0.9301 (mm-30) cc_final: 0.8906 (mm-30) REVERT: k 12 SER cc_start: 0.9318 (OUTLIER) cc_final: 0.8966 (p) REVERT: k 13 GLU cc_start: 0.8595 (pm20) cc_final: 0.8250 (pm20) REVERT: k 41 GLN cc_start: 0.8906 (tp40) cc_final: 0.8560 (tm-30) REVERT: k 259 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8174 (p0) REVERT: k 292 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8647 (p0) REVERT: k 333 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8575 (mm-30) REVERT: k 342 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8441 (mt-10) REVERT: k 351 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8498 (mm-30) REVERT: k 352 LYS cc_start: 0.8902 (tptp) cc_final: 0.8525 (tptp) REVERT: k 397 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8877 (mt-10) REVERT: j 1 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5618 (tmm) REVERT: j 23 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8329 (mm) REVERT: j 109 ARG cc_start: 0.8370 (ptp-170) cc_final: 0.7970 (mtm110) REVERT: j 222 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8983 (mt) REVERT: j 298 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8836 (mmtm) REVERT: j 342 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7916 (pt0) REVERT: j 381 TRP cc_start: 0.8608 (OUTLIER) cc_final: 0.8283 (t60) REVERT: j 407 LYS cc_start: 0.9356 (ptmm) cc_final: 0.9058 (ttmm) REVERT: b 30 ARG cc_start: 0.8636 (ttm110) cc_final: 0.8426 (mtm-85) REVERT: b 193 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8774 (tm-30) REVERT: b 215 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8468 (mp0) REVERT: b 244 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8652 (mm-30) REVERT: b 342 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8352 (mp0) REVERT: b 397 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8748 (mt-10) REVERT: c 12 SER cc_start: 0.9566 (OUTLIER) cc_final: 0.9350 (p) REVERT: c 29 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8214 (ptm) REVERT: c 30 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.8398 (mtp-110) REVERT: c 41 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8520 (tm-30) REVERT: c 56 GLU cc_start: 0.8744 (tt0) cc_final: 0.8358 (tm-30) REVERT: c 90 ASN cc_start: 0.8408 (t0) cc_final: 0.8083 (t0) REVERT: c 140 HIS cc_start: 0.9159 (OUTLIER) cc_final: 0.8631 (m90) REVERT: c 241 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8605 (pp30) REVERT: c 352 LYS cc_start: 0.8421 (tptp) cc_final: 0.8122 (tptt) REVERT: c 381 TRP cc_start: 0.8755 (OUTLIER) cc_final: 0.8358 (t60) REVERT: d 8 ASN cc_start: 0.8938 (m-40) cc_final: 0.8723 (m110) REVERT: d 21 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7708 (ppp) REVERT: d 84 SER cc_start: 0.9480 (m) cc_final: 0.9238 (t) REVERT: d 140 HIS cc_start: 0.8989 (OUTLIER) cc_final: 0.8708 (m90) REVERT: d 202 CYS cc_start: 0.8903 (m) cc_final: 0.8659 (m) REVERT: d 352 LYS cc_start: 0.8638 (tptp) cc_final: 0.8388 (tptp) REVERT: d 374 GLN cc_start: 0.9093 (tp40) cc_final: 0.8741 (tp-100) REVERT: d 381 TRP cc_start: 0.8797 (OUTLIER) cc_final: 0.8442 (t60) REVERT: d 397 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8728 (mt-10) REVERT: e 205 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8506 (mtp) REVERT: e 259 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8545 (p0) REVERT: e 396 MET cc_start: 0.9272 (tpp) cc_final: 0.9066 (tpp) REVERT: e 397 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8949 (mt-10) REVERT: f 123 LYS cc_start: 0.8319 (ptmm) cc_final: 0.8036 (ptmm) REVERT: f 134 GLU cc_start: 0.8920 (mp0) cc_final: 0.8682 (mp0) REVERT: f 140 HIS cc_start: 0.8825 (OUTLIER) cc_final: 0.8286 (m90) REVERT: f 329 GLU cc_start: 0.8164 (mp0) cc_final: 0.7657 (mp0) REVERT: g 23 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7702 (mm) REVERT: g 30 ARG cc_start: 0.8364 (mmm-85) cc_final: 0.8024 (mtp-110) REVERT: g 375 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8345 (tp30) REVERT: g 397 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8946 (mt-10) REVERT: h 258 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8666 (mttp) REVERT: h 259 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.7758 (p0) REVERT: i 91 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8687 (pp) REVERT: i 342 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8129 (mp0) REVERT: i 375 GLU cc_start: 0.8368 (tp30) cc_final: 0.8091 (tp30) outliers start: 381 outliers final: 248 residues processed: 1138 average time/residue: 0.5470 time to fit residues: 1047.8955 Evaluate side-chains 1104 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 817 time to evaluate : 6.654 ------------------------------------------------------------------------------- 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 29 MET Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 202 CYS Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 259 ASP Chi-restraints excluded: chain a residue 264 LEU Chi-restraints excluded: chain a residue 292 ASN Chi-restraints excluded: chain a residue 323 THR Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain a residue 371 LEU Chi-restraints excluded: chain a residue 376 GLU Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain r residue 12 SER Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 29 MET Chi-restraints excluded: chain r residue 114 LEU Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 202 CYS Chi-restraints excluded: chain r residue 323 THR Chi-restraints excluded: chain r residue 366 ARG Chi-restraints excluded: chain r residue 394 ASP Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 12 SER Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 44 LYS Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 166 SER Chi-restraints excluded: chain q residue 195 ILE Chi-restraints excluded: chain q residue 241 GLN Chi-restraints excluded: chain q residue 260 VAL Chi-restraints excluded: chain q residue 264 LEU Chi-restraints excluded: chain q residue 286 THR Chi-restraints excluded: chain q residue 323 THR Chi-restraints excluded: chain q residue 330 VAL Chi-restraints excluded: chain q residue 338 THR Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain q residue 372 THR Chi-restraints excluded: chain q residue 379 LYS Chi-restraints excluded: chain q residue 394 ASP Chi-restraints excluded: chain q residue 401 ASN Chi-restraints excluded: chain q residue 411 ASP Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain p residue 91 LEU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 168 ILE Chi-restraints excluded: chain p residue 202 CYS Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 286 THR Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain p residue 323 THR Chi-restraints excluded: chain p residue 338 THR Chi-restraints excluded: chain p residue 379 LYS Chi-restraints excluded: chain p residue 394 ASP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain o residue 29 MET Chi-restraints excluded: chain o residue 70 SER Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 126 ASN Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 259 ASP Chi-restraints excluded: chain o residue 290 ASP Chi-restraints excluded: chain o residue 338 THR Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 370 LEU Chi-restraints excluded: chain o residue 372 THR Chi-restraints excluded: chain o residue 381 TRP Chi-restraints excluded: chain o residue 394 ASP Chi-restraints excluded: chain o residue 410 ASP Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 23 LEU Chi-restraints excluded: chain n residue 56 GLU Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 233 ASP Chi-restraints excluded: chain n residue 241 GLN Chi-restraints excluded: chain n residue 253 LEU Chi-restraints excluded: chain n residue 264 LEU Chi-restraints excluded: chain n residue 292 ASN Chi-restraints excluded: chain n residue 323 THR Chi-restraints excluded: chain n residue 338 THR Chi-restraints excluded: chain n residue 354 VAL Chi-restraints excluded: chain n residue 381 TRP Chi-restraints excluded: chain n residue 387 ILE Chi-restraints excluded: chain n residue 393 ILE Chi-restraints excluded: chain n residue 394 ASP Chi-restraints excluded: chain n residue 408 THR Chi-restraints excluded: chain n residue 410 ASP Chi-restraints excluded: chain n residue 411 ASP Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 11 VAL Chi-restraints excluded: chain m residue 29 MET Chi-restraints excluded: chain m residue 40 LYS Chi-restraints excluded: chain m residue 44 LYS Chi-restraints excluded: chain m residue 60 ASP Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain m residue 162 LEU Chi-restraints excluded: chain m residue 205 MET Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain m residue 338 THR Chi-restraints excluded: chain m residue 380 MET Chi-restraints excluded: chain m residue 381 TRP Chi-restraints excluded: chain m residue 387 ILE Chi-restraints excluded: chain m residue 394 ASP Chi-restraints excluded: chain m residue 418 ARG Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 29 MET Chi-restraints excluded: chain l residue 56 GLU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 140 HIS Chi-restraints excluded: chain l residue 205 MET Chi-restraints excluded: chain l residue 241 GLN Chi-restraints excluded: chain l residue 264 LEU Chi-restraints excluded: chain l residue 277 VAL Chi-restraints excluded: chain l residue 338 THR Chi-restraints excluded: chain l residue 341 MET Chi-restraints excluded: chain l residue 372 THR Chi-restraints excluded: chain l residue 381 TRP Chi-restraints excluded: chain l residue 394 ASP Chi-restraints excluded: chain l residue 410 ASP Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain k residue 29 MET Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 162 LEU 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 292 ASN Chi-restraints excluded: chain k residue 327 MET Chi-restraints excluded: chain k residue 338 THR Chi-restraints excluded: chain k residue 373 THR Chi-restraints excluded: chain k residue 381 TRP Chi-restraints excluded: chain k residue 394 ASP Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 29 MET Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 162 LEU Chi-restraints excluded: chain j residue 222 LEU Chi-restraints excluded: chain j residue 260 VAL Chi-restraints excluded: chain j residue 264 LEU Chi-restraints excluded: chain j residue 298 LYS Chi-restraints excluded: chain j residue 338 THR Chi-restraints excluded: chain j residue 373 THR Chi-restraints excluded: chain j residue 381 TRP Chi-restraints excluded: chain j residue 394 ASP Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 193 GLN Chi-restraints excluded: chain b residue 218 GLU Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 264 LEU Chi-restraints excluded: chain b residue 338 THR Chi-restraints excluded: chain b residue 341 MET Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 408 THR Chi-restraints excluded: chain b residue 410 ASP Chi-restraints excluded: chain c residue 12 SER Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 55 LEU Chi-restraints excluded: chain c residue 70 SER Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 140 HIS Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain c residue 241 GLN Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 381 TRP Chi-restraints excluded: chain c residue 387 ILE Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 140 HIS Chi-restraints excluded: chain d residue 205 MET Chi-restraints excluded: chain d residue 241 GLN Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 259 ASP Chi-restraints excluded: chain d residue 292 ASN Chi-restraints excluded: chain d residue 338 THR Chi-restraints excluded: chain d residue 381 TRP Chi-restraints excluded: chain d residue 394 ASP Chi-restraints excluded: chain e residue 12 SER Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 60 ASP Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 140 HIS Chi-restraints excluded: chain e residue 205 MET Chi-restraints excluded: chain e residue 259 ASP Chi-restraints excluded: chain e residue 292 ASN Chi-restraints excluded: chain e residue 327 MET Chi-restraints excluded: chain e residue 338 THR Chi-restraints excluded: chain e residue 381 TRP Chi-restraints excluded: chain e residue 394 ASP Chi-restraints excluded: chain e residue 410 ASP Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 12 SER Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 29 MET Chi-restraints excluded: chain f residue 44 LYS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 140 HIS Chi-restraints excluded: chain f residue 153 SER Chi-restraints excluded: chain f residue 205 MET Chi-restraints excluded: chain f residue 241 GLN Chi-restraints excluded: chain f residue 253 LEU Chi-restraints excluded: chain f residue 259 ASP Chi-restraints excluded: chain f residue 264 LEU Chi-restraints excluded: chain f residue 277 VAL Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 338 THR Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 381 TRP Chi-restraints excluded: chain f residue 394 ASP Chi-restraints excluded: chain f residue 411 ASP Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 237 SER Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 338 THR Chi-restraints excluded: chain g residue 354 VAL Chi-restraints excluded: chain g residue 375 GLU Chi-restraints excluded: chain g residue 379 LYS Chi-restraints excluded: chain g residue 381 TRP Chi-restraints excluded: chain g residue 394 ASP Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 8 ASN Chi-restraints excluded: chain h residue 21 MET Chi-restraints excluded: chain h residue 23 LEU Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 126 ASN Chi-restraints excluded: chain h residue 241 GLN Chi-restraints excluded: chain h residue 258 LYS Chi-restraints excluded: chain h residue 259 ASP Chi-restraints excluded: chain h residue 260 VAL Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain h residue 338 THR Chi-restraints excluded: chain h residue 372 THR Chi-restraints excluded: chain h residue 381 TRP Chi-restraints excluded: chain h residue 394 ASP Chi-restraints excluded: chain h residue 408 THR Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 60 ASP Chi-restraints excluded: chain i residue 91 LEU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 241 GLN Chi-restraints excluded: chain i residue 260 VAL Chi-restraints excluded: chain i residue 264 LEU Chi-restraints excluded: chain i residue 277 VAL Chi-restraints excluded: chain i residue 290 ASP Chi-restraints excluded: chain i residue 338 THR Chi-restraints excluded: chain i residue 379 LYS Chi-restraints excluded: chain i 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: 8.9990 chunk 80 optimal weight: 7.9990 chunk 406 optimal weight: 5.9990 chunk 521 optimal weight: 0.8980 chunk 404 optimal weight: 0.8980 chunk 601 optimal weight: 0.9980 chunk 398 optimal weight: 0.8980 chunk 711 optimal weight: 4.9990 chunk 445 optimal weight: 0.9980 chunk 433 optimal weight: 6.9990 chunk 328 optimal weight: 7.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 220 GLN ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 388 HIS ** q 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 59 GLN ** p 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 189 GLN ** o 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 388 HIS k 193 GLN ** j 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 8 ASN b 193 GLN b 295 HIS c 172 GLN c 189 GLN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 60822 Z= 0.163 Angle : 0.612 11.747 82008 Z= 0.288 Chirality : 0.042 0.167 9324 Planarity : 0.003 0.050 10620 Dihedral : 4.684 43.224 8397 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.86 % Allowed : 29.54 % Favored : 66.60 % 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: 0.67 (0.10), residues: 7506 helix: 1.29 (0.09), residues: 3240 sheet: 0.03 (0.15), residues: 1134 loop : -0.18 (0.11), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.008 TRP f 381 HIS 0.019 0.001 HIS r 388 PHE 0.022 0.001 PHE r 412 TYR 0.024 0.001 TYR k 197 ARG 0.012 0.000 ARG n 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 1160 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 910 time to evaluate : 5.435 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: 0.8079 (OUTLIER) cc_final: 0.7674 (ptp) REVERT: a 210 ASP cc_start: 0.8274 (m-30) cc_final: 0.7400 (m-30) REVERT: a 215 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7751 (mt-10) REVERT: a 244 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8199 (mm-30) REVERT: a 375 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8220 (mp0) REVERT: a 396 MET cc_start: 0.9436 (tpp) cc_final: 0.9225 (tpp) REVERT: r 244 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8540 (mm-30) REVERT: r 366 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7825 (tpt170) REVERT: q 1 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6854 (tpt) REVERT: q 211 GLU cc_start: 0.8570 (tp30) cc_final: 0.8264 (tp30) REVERT: q 244 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8363 (mm-30) REVERT: q 299 ARG cc_start: 0.9325 (ptm160) cc_final: 0.9043 (mtp-110) REVERT: q 390 MET cc_start: 0.8758 (pmm) cc_final: 0.8516 (pmm) REVERT: q 394 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8577 (p0) REVERT: q 396 MET cc_start: 0.9084 (tpp) cc_final: 0.8744 (tpp) REVERT: p 33 ASP cc_start: 0.9068 (m-30) cc_final: 0.8780 (m-30) REVERT: p 72 TYR cc_start: 0.9297 (m-10) cc_final: 0.9095 (m-80) REVERT: p 91 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8784 (pp) REVERT: p 193 GLN cc_start: 0.8976 (tt0) cc_final: 0.8682 (tt0) REVERT: p 241 GLN cc_start: 0.8920 (pp30) cc_final: 0.8612 (tm-30) REVERT: p 379 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.9071 (mtmm) REVERT: p 394 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8663 (p0) REVERT: o 259 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7987 (p0) REVERT: o 292 ASN cc_start: 0.8773 (m-40) cc_final: 0.8467 (p0) REVERT: o 333 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8556 (tm-30) REVERT: o 397 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8449 (mp0) REVERT: n 41 GLN cc_start: 0.9278 (tp40) cc_final: 0.8857 (tp40) REVERT: n 100 LYS cc_start: 0.9507 (ttmt) cc_final: 0.9142 (ttmm) REVERT: n 244 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8475 (mm-30) REVERT: n 326 LYS cc_start: 0.9164 (tptp) cc_final: 0.8815 (tptp) REVERT: n 334 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8604 (mp0) REVERT: n 374 GLN cc_start: 0.8953 (tp-100) cc_final: 0.8535 (tp-100) REVERT: m 40 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.9061 (ttpp) REVERT: m 44 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8780 (ptpp) REVERT: m 125 GLU cc_start: 0.8848 (mp0) cc_final: 0.8611 (pm20) REVERT: m 186 MET cc_start: 0.8723 (mtm) cc_final: 0.8502 (mtm) REVERT: m 244 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8281 (mm-30) REVERT: m 296 ARG cc_start: 0.9064 (tpp80) cc_final: 0.8706 (mmm-85) REVERT: m 334 GLU cc_start: 0.8859 (tp30) cc_final: 0.8579 (tp30) REVERT: m 342 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8369 (mp0) REVERT: m 374 GLN cc_start: 0.9439 (tp40) cc_final: 0.9044 (tp40) REVERT: m 392 GLU cc_start: 0.8554 (pm20) cc_final: 0.7803 (pt0) REVERT: l 140 HIS cc_start: 0.8815 (OUTLIER) cc_final: 0.8461 (m-70) REVERT: l 215 GLU cc_start: 0.9098 (tp30) cc_final: 0.8801 (mm-30) REVERT: l 244 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7780 (mm-30) REVERT: l 290 ASP cc_start: 0.7978 (t0) cc_final: 0.6803 (t0) REVERT: l 292 ASN cc_start: 0.9075 (m110) cc_final: 0.8712 (p0) REVERT: l 375 GLU cc_start: 0.9188 (tp30) cc_final: 0.8498 (tp30) REVERT: l 397 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8925 (mm-30) REVERT: k 12 SER cc_start: 0.9316 (m) cc_final: 0.8968 (p) REVERT: k 13 GLU cc_start: 0.8670 (pm20) cc_final: 0.8382 (pm20) REVERT: k 19 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8728 (mm-30) REVERT: k 41 GLN cc_start: 0.8870 (tp40) cc_final: 0.8567 (tm-30) REVERT: k 259 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8195 (p0) REVERT: k 351 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8367 (mm-30) REVERT: k 397 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8920 (mt-10) REVERT: j 1 MET cc_start: 0.6069 (OUTLIER) cc_final: 0.5249 (tmm) REVERT: j 23 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8347 (mm) REVERT: j 342 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7886 (pt0) REVERT: j 381 TRP cc_start: 0.8469 (OUTLIER) cc_final: 0.8246 (t60) REVERT: j 407 LYS cc_start: 0.9307 (ptmm) cc_final: 0.8985 (ttmm) REVERT: b 1 MET cc_start: 0.7156 (tpt) cc_final: 0.6421 (tpt) REVERT: b 30 ARG cc_start: 0.8676 (ttm110) cc_final: 0.8451 (mtm-85) REVERT: b 41 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8626 (tm-30) REVERT: b 193 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8867 (tm-30) REVERT: b 215 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8467 (mp0) REVERT: b 244 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8655 (mm-30) REVERT: b 342 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8292 (mp0) REVERT: c 12 SER cc_start: 0.9559 (m) cc_final: 0.9337 (p) REVERT: c 29 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8132 (ptm) REVERT: c 30 ARG cc_start: 0.8548 (mmm-85) cc_final: 0.8340 (mtp-110) REVERT: c 41 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8493 (tm-30) REVERT: c 56 GLU cc_start: 0.8616 (tt0) cc_final: 0.8362 (tm-30) REVERT: c 90 ASN cc_start: 0.8379 (t0) cc_final: 0.7819 (t0) REVERT: c 140 HIS cc_start: 0.9152 (OUTLIER) cc_final: 0.8700 (m90) REVERT: c 195 ILE cc_start: 0.9519 (mt) cc_final: 0.9267 (mt) REVERT: c 309 GLU cc_start: 0.8716 (mp0) cc_final: 0.8499 (mp0) REVERT: c 381 TRP cc_start: 0.8647 (OUTLIER) cc_final: 0.8353 (t60) REVERT: c 397 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8617 (mt-10) REVERT: d 8 ASN cc_start: 0.8976 (m-40) cc_final: 0.8689 (m110) REVERT: d 21 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8158 (ppp) REVERT: d 84 SER cc_start: 0.9485 (m) cc_final: 0.9231 (t) REVERT: d 140 HIS cc_start: 0.9018 (OUTLIER) cc_final: 0.8677 (m90) REVERT: d 202 CYS cc_start: 0.8693 (m) cc_final: 0.8435 (m) REVERT: d 342 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8244 (mm-30) REVERT: d 343 LEU cc_start: 0.8679 (tp) cc_final: 0.8337 (tp) REVERT: d 374 GLN cc_start: 0.8938 (tp40) cc_final: 0.8671 (tm-30) REVERT: d 375 GLU cc_start: 0.9016 (mp0) cc_final: 0.8629 (mp0) REVERT: d 381 TRP cc_start: 0.8731 (OUTLIER) cc_final: 0.8374 (t60) REVERT: d 397 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8810 (mt-10) REVERT: e 140 HIS cc_start: 0.8939 (OUTLIER) cc_final: 0.8515 (m-70) REVERT: e 222 LEU cc_start: 0.9465 (tt) cc_final: 0.9214 (tt) REVERT: e 259 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8549 (p0) REVERT: e 375 GLU cc_start: 0.9016 (tp30) cc_final: 0.8222 (tp30) REVERT: e 397 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8949 (mt-10) REVERT: f 29 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8314 (ptm) REVERT: f 134 GLU cc_start: 0.8941 (mp0) cc_final: 0.8677 (mp0) REVERT: f 140 HIS cc_start: 0.8770 (OUTLIER) cc_final: 0.8268 (m90) REVERT: f 226 GLU cc_start: 0.8255 (pp20) cc_final: 0.8038 (pp20) REVERT: f 329 GLU cc_start: 0.8169 (mp0) cc_final: 0.7549 (mp0) REVERT: g 23 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7891 (mm) REVERT: g 30 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7828 (mtp-110) REVERT: g 397 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8907 (mt-10) REVERT: h 140 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.8519 (m90) REVERT: h 259 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.7545 (p0) REVERT: h 374 GLN cc_start: 0.9208 (tp-100) cc_final: 0.8779 (tp-100) REVERT: i 91 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8497 (pp) REVERT: i 326 LYS cc_start: 0.9337 (tppt) cc_final: 0.9129 (mmmt) REVERT: i 342 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8092 (mp0) REVERT: i 375 GLU cc_start: 0.8271 (tp30) cc_final: 0.7936 (tp30) outliers start: 250 outliers final: 161 residues processed: 1077 average time/residue: 0.5514 time to fit residues: 1002.9904 Evaluate side-chains 1048 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 855 time to evaluate : 5.327 ------------------------------------------------------------------------------- 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 29 MET Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 220 GLN Chi-restraints excluded: chain a residue 259 ASP Chi-restraints excluded: chain a residue 264 LEU Chi-restraints excluded: chain a residue 323 THR Chi-restraints excluded: chain a residue 371 LEU Chi-restraints excluded: chain a residue 376 GLU Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 323 THR Chi-restraints excluded: chain r residue 366 ARG Chi-restraints excluded: chain r residue 394 ASP Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 44 LYS Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 260 VAL Chi-restraints excluded: chain q residue 264 LEU Chi-restraints excluded: chain q residue 286 THR Chi-restraints excluded: chain q residue 323 THR Chi-restraints excluded: chain q residue 330 VAL Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain q residue 379 LYS Chi-restraints excluded: chain q residue 394 ASP Chi-restraints excluded: chain q residue 399 LEU Chi-restraints excluded: chain q residue 411 ASP Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain p residue 91 LEU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 168 ILE Chi-restraints excluded: chain p residue 202 CYS Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 286 THR Chi-restraints excluded: chain p residue 338 THR Chi-restraints excluded: chain p residue 379 LYS Chi-restraints excluded: chain p residue 394 ASP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 126 ASN Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 259 ASP Chi-restraints excluded: chain o residue 372 THR Chi-restraints excluded: chain o residue 394 ASP Chi-restraints excluded: chain o residue 410 ASP Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 23 LEU Chi-restraints excluded: chain n residue 56 GLU Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 233 ASP Chi-restraints excluded: chain n residue 253 LEU Chi-restraints excluded: chain n residue 264 LEU Chi-restraints excluded: chain n residue 323 THR Chi-restraints excluded: chain n residue 334 GLU Chi-restraints excluded: chain n residue 338 THR Chi-restraints excluded: chain n residue 354 VAL Chi-restraints excluded: chain n residue 381 TRP Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 11 VAL Chi-restraints excluded: chain m residue 23 LEU Chi-restraints excluded: chain m residue 40 LYS Chi-restraints excluded: chain m residue 44 LYS Chi-restraints excluded: chain m residue 59 GLN Chi-restraints excluded: chain m residue 60 ASP Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain m residue 205 MET Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain m residue 381 TRP Chi-restraints excluded: chain m residue 394 ASP Chi-restraints excluded: chain m residue 418 ARG Chi-restraints excluded: chain l residue 29 MET Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 140 HIS Chi-restraints excluded: chain l residue 205 MET Chi-restraints excluded: chain l residue 264 LEU Chi-restraints excluded: chain l residue 277 VAL Chi-restraints excluded: chain l residue 394 ASP Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 162 LEU Chi-restraints excluded: chain k residue 259 ASP Chi-restraints excluded: chain k residue 327 MET Chi-restraints excluded: chain k residue 373 THR Chi-restraints excluded: chain k residue 394 ASP Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 29 MET Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 162 LEU Chi-restraints excluded: chain j residue 260 VAL Chi-restraints excluded: chain j residue 264 LEU Chi-restraints excluded: chain j residue 381 TRP Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 193 GLN Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 264 LEU Chi-restraints excluded: chain b residue 341 MET Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 408 THR Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 55 LEU Chi-restraints excluded: chain c residue 70 SER Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 140 HIS Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 381 TRP Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 140 HIS Chi-restraints excluded: chain d residue 205 MET Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 259 ASP Chi-restraints excluded: chain d residue 292 ASN Chi-restraints excluded: chain d residue 381 TRP Chi-restraints excluded: chain d residue 394 ASP Chi-restraints excluded: chain d residue 411 ASP Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 60 ASP Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 140 HIS Chi-restraints excluded: chain e residue 205 MET Chi-restraints excluded: chain e residue 259 ASP Chi-restraints excluded: chain e residue 327 MET Chi-restraints excluded: chain e residue 381 TRP Chi-restraints excluded: chain e residue 394 ASP Chi-restraints excluded: chain e residue 410 ASP Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 23 LEU Chi-restraints excluded: chain f residue 29 MET Chi-restraints excluded: chain f residue 44 LYS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 140 HIS Chi-restraints excluded: chain f residue 205 MET Chi-restraints excluded: chain f residue 259 ASP Chi-restraints excluded: chain f residue 264 LEU Chi-restraints excluded: chain f residue 277 VAL Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 381 TRP Chi-restraints excluded: chain f residue 394 ASP Chi-restraints excluded: chain f residue 411 ASP Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 341 MET Chi-restraints excluded: chain g residue 381 TRP Chi-restraints excluded: chain g residue 415 MET Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 8 ASN Chi-restraints excluded: chain h residue 21 MET Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 140 HIS Chi-restraints excluded: chain h residue 162 LEU Chi-restraints excluded: chain h residue 259 ASP Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain h residue 333 GLU Chi-restraints excluded: chain h residue 340 ASN Chi-restraints excluded: chain h residue 381 TRP Chi-restraints excluded: chain h residue 394 ASP Chi-restraints excluded: chain h residue 408 THR Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 91 LEU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 264 LEU Chi-restraints excluded: chain i residue 373 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 440 optimal weight: 3.9990 chunk 284 optimal weight: 0.9990 chunk 424 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 452 optimal weight: 4.9990 chunk 484 optimal weight: 2.9990 chunk 351 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 559 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 32 GLN ** a 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 306 ASN ** q 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 378 GLN ** j 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 189 GLN b 193 GLN ** b 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 172 GLN d 193 GLN ** e 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 401 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 60822 Z= 0.299 Angle : 0.653 11.574 82008 Z= 0.310 Chirality : 0.043 0.187 9324 Planarity : 0.004 0.054 10620 Dihedral : 4.859 44.450 8397 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.54 % Allowed : 29.07 % Favored : 66.39 % 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: 0.60 (0.10), residues: 7506 helix: 1.23 (0.09), residues: 3276 sheet: -0.02 (0.15), residues: 1134 loop : -0.23 (0.11), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.008 TRP l 381 HIS 0.006 0.001 HIS r 388 PHE 0.015 0.001 PHE c 398 TYR 0.025 0.002 TYR k 197 ARG 0.013 0.001 ARG n 418 *********************** 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 1160 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 866 time to evaluate : 5.466 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: a 29 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7825 (ptp) REVERT: a 186 MET cc_start: 0.8692 (ptt) cc_final: 0.8398 (ptt) REVERT: a 215 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: a 244 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8225 (mm-30) REVERT: a 327 MET cc_start: 0.8968 (ttp) cc_final: 0.8754 (ttp) REVERT: a 375 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8293 (mp0) REVERT: a 396 MET cc_start: 0.9470 (tpp) cc_final: 0.9261 (tpp) REVERT: r 85 GLN cc_start: 0.9160 (mp10) cc_final: 0.8693 (mp10) REVERT: r 244 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8585 (mm-30) REVERT: r 366 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7741 (tpt170) REVERT: r 416 MET cc_start: 0.7394 (mmm) cc_final: 0.5762 (ttt) REVERT: q 1 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.6976 (tpt) REVERT: q 244 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8407 (mm-30) REVERT: q 299 ARG cc_start: 0.9366 (ptm160) cc_final: 0.9031 (mtp-110) REVERT: q 390 MET cc_start: 0.8796 (pmm) cc_final: 0.8535 (pmm) REVERT: q 394 ASP cc_start: 0.8988 (OUTLIER) cc_final: 0.8638 (p0) REVERT: q 396 MET cc_start: 0.9067 (tpp) cc_final: 0.8734 (tpp) REVERT: p 33 ASP cc_start: 0.9097 (m-30) cc_final: 0.8817 (m-30) REVERT: p 41 GLN cc_start: 0.9349 (tp40) cc_final: 0.9149 (tp40) REVERT: p 91 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8895 (pp) REVERT: p 193 GLN cc_start: 0.8964 (tt0) cc_final: 0.8659 (tt0) REVERT: p 197 TYR cc_start: 0.8998 (t80) cc_final: 0.8760 (t80) REVERT: p 394 ASP cc_start: 0.9066 (OUTLIER) cc_final: 0.8788 (p0) REVERT: o 259 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8089 (p0) REVERT: o 333 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8573 (tm-30) REVERT: o 412 PHE cc_start: 0.9255 (t80) cc_final: 0.8917 (t80) REVERT: n 41 GLN cc_start: 0.9277 (tp40) cc_final: 0.8839 (tp40) REVERT: n 100 LYS cc_start: 0.9510 (ttmt) cc_final: 0.9122 (ttmm) REVERT: n 326 LYS cc_start: 0.9175 (tptp) cc_final: 0.8921 (tptp) REVERT: n 342 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8071 (tt0) REVERT: n 374 GLN cc_start: 0.8987 (tp-100) cc_final: 0.8567 (tp-100) REVERT: m 40 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.9062 (ttpp) REVERT: m 44 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8747 (ptpp) REVERT: m 125 GLU cc_start: 0.8834 (mp0) cc_final: 0.8608 (pm20) REVERT: m 244 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8323 (mm-30) REVERT: m 296 ARG cc_start: 0.9086 (tpp80) cc_final: 0.8720 (mmm-85) REVERT: m 334 GLU cc_start: 0.8863 (tp30) cc_final: 0.8574 (tp30) REVERT: m 342 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8412 (mp0) REVERT: m 374 GLN cc_start: 0.9475 (tp40) cc_final: 0.9077 (tp40) REVERT: m 392 GLU cc_start: 0.8569 (pm20) cc_final: 0.7826 (pt0) REVERT: l 140 HIS cc_start: 0.8801 (OUTLIER) cc_final: 0.8503 (m-70) REVERT: l 244 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7865 (mm-30) REVERT: l 290 ASP cc_start: 0.7918 (t0) cc_final: 0.6844 (t0) REVERT: l 292 ASN cc_start: 0.9056 (m110) cc_final: 0.8654 (p0) REVERT: l 375 GLU cc_start: 0.9098 (tp30) cc_final: 0.8742 (tp30) REVERT: l 397 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8933 (mm-30) REVERT: k 12 SER cc_start: 0.9314 (m) cc_final: 0.8990 (p) REVERT: k 13 GLU cc_start: 0.8629 (pm20) cc_final: 0.8329 (pm20) REVERT: k 19 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8708 (mm-30) REVERT: k 41 GLN cc_start: 0.8892 (tp40) cc_final: 0.8570 (tm-30) REVERT: k 259 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8200 (p0) REVERT: k 290 ASP cc_start: 0.9139 (m-30) cc_final: 0.8289 (t0) REVERT: k 351 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8464 (mm-30) REVERT: k 397 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8945 (mt-10) REVERT: j 1 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.5483 (tmm) REVERT: j 23 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8389 (mm) REVERT: j 222 LEU cc_start: 0.9328 (tt) cc_final: 0.8932 (mt) REVERT: j 342 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7905 (pt0) REVERT: j 381 TRP cc_start: 0.8612 (OUTLIER) cc_final: 0.8310 (t60) REVERT: j 407 LYS cc_start: 0.9345 (ptmm) cc_final: 0.9053 (ttmm) REVERT: b 1 MET cc_start: 0.7136 (tpt) cc_final: 0.6452 (tpt) REVERT: b 41 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8667 (tm-30) REVERT: b 193 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8789 (tm-30) REVERT: b 215 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8465 (mp0) REVERT: b 244 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8663 (mm-30) REVERT: b 342 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8347 (mp0) REVERT: b 374 GLN cc_start: 0.9064 (tp-100) cc_final: 0.8863 (tp-100) REVERT: c 12 SER cc_start: 0.9563 (m) cc_final: 0.9348 (p) REVERT: c 21 MET cc_start: 0.8290 (ppp) cc_final: 0.7856 (ppp) REVERT: c 29 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8223 (ptm) REVERT: c 30 ARG cc_start: 0.8634 (mmm-85) cc_final: 0.8413 (mtp-110) REVERT: c 41 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8423 (tm-30) REVERT: c 56 GLU cc_start: 0.8665 (tt0) cc_final: 0.8320 (tm-30) REVERT: c 90 ASN cc_start: 0.8429 (t0) cc_final: 0.7872 (t0) REVERT: c 140 HIS cc_start: 0.9162 (OUTLIER) cc_final: 0.8635 (m90) REVERT: c 195 ILE cc_start: 0.9512 (mt) cc_final: 0.9252 (mt) REVERT: c 241 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8592 (pp30) REVERT: c 352 LYS cc_start: 0.8439 (tptp) cc_final: 0.8111 (tptt) REVERT: c 381 TRP cc_start: 0.8798 (OUTLIER) cc_final: 0.8417 (t60) REVERT: c 397 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8532 (mt-10) REVERT: d 8 ASN cc_start: 0.9016 (m-40) cc_final: 0.8729 (m110) REVERT: d 21 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8219 (ppp) REVERT: d 84 SER cc_start: 0.9492 (m) cc_final: 0.9249 (t) REVERT: d 140 HIS cc_start: 0.8995 (OUTLIER) cc_final: 0.8702 (m90) REVERT: d 202 CYS cc_start: 0.8865 (m) cc_final: 0.8620 (m) REVERT: d 343 LEU cc_start: 0.8980 (tp) cc_final: 0.8635 (tp) REVERT: d 352 LYS cc_start: 0.8687 (tptp) cc_final: 0.8267 (tptp) REVERT: d 374 GLN cc_start: 0.8989 (tp40) cc_final: 0.8716 (tp-100) REVERT: d 375 GLU cc_start: 0.9051 (mp0) cc_final: 0.8684 (mp0) REVERT: d 381 TRP cc_start: 0.8828 (OUTLIER) cc_final: 0.8468 (t60) REVERT: d 397 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8792 (mt-10) REVERT: e 205 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8475 (mtt) REVERT: e 259 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8565 (p0) REVERT: f 134 GLU cc_start: 0.8934 (mp0) cc_final: 0.8678 (mp0) REVERT: f 140 HIS cc_start: 0.8808 (OUTLIER) cc_final: 0.8238 (m90) REVERT: f 205 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8272 (mtp) REVERT: f 329 GLU cc_start: 0.8174 (mp0) cc_final: 0.7640 (mp0) REVERT: g 23 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7852 (mm) REVERT: g 30 ARG cc_start: 0.8309 (mmm-85) cc_final: 0.7966 (mtp-110) REVERT: g 397 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8951 (mt-10) REVERT: h 140 HIS cc_start: 0.8822 (OUTLIER) cc_final: 0.8560 (m90) REVERT: h 259 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.7695 (p0) REVERT: h 374 GLN cc_start: 0.9214 (tp-100) cc_final: 0.8798 (tp-100) REVERT: i 91 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8631 (pp) REVERT: i 342 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8117 (mp0) REVERT: i 375 GLU cc_start: 0.8284 (tp30) cc_final: 0.7624 (tp30) REVERT: i 379 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8647 (mttp) outliers start: 294 outliers final: 216 residues processed: 1070 average time/residue: 0.5549 time to fit residues: 1005.5015 Evaluate side-chains 1075 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 827 time to evaluate : 5.391 ------------------------------------------------------------------------------- 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 29 MET Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 202 CYS Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 264 LEU Chi-restraints excluded: chain a residue 323 THR Chi-restraints excluded: chain a residue 371 LEU Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain a residue 410 ASP Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 263 LEU Chi-restraints excluded: chain r residue 323 THR Chi-restraints excluded: chain r residue 366 ARG Chi-restraints excluded: chain r residue 394 ASP Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 44 LYS Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 195 ILE Chi-restraints excluded: chain q residue 260 VAL Chi-restraints excluded: chain q residue 264 LEU Chi-restraints excluded: chain q residue 286 THR Chi-restraints excluded: chain q residue 323 THR Chi-restraints excluded: chain q residue 330 VAL Chi-restraints excluded: chain q residue 338 THR Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain q residue 379 LYS Chi-restraints excluded: chain q residue 394 ASP Chi-restraints excluded: chain q residue 399 LEU Chi-restraints excluded: chain q residue 401 ASN Chi-restraints excluded: chain q residue 411 ASP Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain p residue 91 LEU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 168 ILE Chi-restraints excluded: chain p residue 202 CYS Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 286 THR Chi-restraints excluded: chain p residue 323 THR Chi-restraints excluded: chain p residue 338 THR Chi-restraints excluded: chain p residue 394 ASP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 70 SER Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 126 ASN Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 259 ASP Chi-restraints excluded: chain o residue 338 THR Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 372 THR Chi-restraints excluded: chain o residue 394 ASP Chi-restraints excluded: chain o residue 410 ASP Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 23 LEU Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 56 GLU Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 233 ASP Chi-restraints excluded: chain n residue 241 GLN Chi-restraints excluded: chain n residue 253 LEU Chi-restraints excluded: chain n residue 264 LEU Chi-restraints excluded: chain n residue 323 THR Chi-restraints excluded: chain n residue 338 THR Chi-restraints excluded: chain n residue 354 VAL Chi-restraints excluded: chain n residue 376 GLU Chi-restraints excluded: chain n residue 381 TRP Chi-restraints excluded: chain n residue 393 ILE Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 23 LEU Chi-restraints excluded: chain m residue 29 MET Chi-restraints excluded: chain m residue 40 LYS Chi-restraints excluded: chain m residue 44 LYS Chi-restraints excluded: chain m residue 59 GLN Chi-restraints excluded: chain m residue 60 ASP Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 205 MET Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain m residue 380 MET Chi-restraints excluded: chain m residue 381 TRP Chi-restraints excluded: chain m residue 387 ILE Chi-restraints excluded: chain m residue 394 ASP Chi-restraints excluded: chain m residue 418 ARG Chi-restraints excluded: chain l residue 29 MET Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 56 GLU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 140 HIS Chi-restraints excluded: chain l residue 205 MET Chi-restraints excluded: chain l residue 241 GLN Chi-restraints excluded: chain l residue 264 LEU Chi-restraints excluded: chain l residue 277 VAL Chi-restraints excluded: chain l residue 372 THR Chi-restraints excluded: chain l residue 381 TRP Chi-restraints excluded: chain l residue 383 LEU Chi-restraints excluded: chain l residue 394 ASP Chi-restraints excluded: chain l residue 410 ASP Chi-restraints excluded: chain k residue 29 MET Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 162 LEU Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 259 ASP Chi-restraints excluded: chain k residue 327 MET Chi-restraints excluded: chain k residue 338 THR Chi-restraints excluded: chain k residue 373 THR Chi-restraints excluded: chain k residue 381 TRP Chi-restraints excluded: chain k residue 394 ASP Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 29 MET Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 162 LEU Chi-restraints excluded: chain j residue 260 VAL Chi-restraints excluded: chain j residue 264 LEU Chi-restraints excluded: chain j residue 266 SER Chi-restraints excluded: chain j residue 338 THR Chi-restraints excluded: chain j residue 373 THR Chi-restraints excluded: chain j residue 381 TRP Chi-restraints excluded: chain j residue 394 ASP Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 193 GLN Chi-restraints excluded: chain b residue 218 GLU Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 264 LEU Chi-restraints excluded: chain b residue 341 MET Chi-restraints excluded: chain b residue 408 THR Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 55 LEU Chi-restraints excluded: chain c residue 70 SER Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 140 HIS Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain c residue 241 GLN Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain c residue 292 ASN Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 354 VAL Chi-restraints excluded: chain c residue 381 TRP Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 15 ILE Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 69 ASP Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 140 HIS Chi-restraints excluded: chain d residue 205 MET Chi-restraints excluded: chain d residue 241 GLN Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 259 ASP Chi-restraints excluded: chain d residue 292 ASN Chi-restraints excluded: chain d residue 338 THR Chi-restraints excluded: chain d residue 381 TRP Chi-restraints excluded: chain d residue 394 ASP Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 60 ASP Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 140 HIS Chi-restraints excluded: chain e residue 153 SER Chi-restraints excluded: chain e residue 205 MET Chi-restraints excluded: chain e residue 259 ASP Chi-restraints excluded: chain e residue 292 ASN Chi-restraints excluded: chain e residue 327 MET Chi-restraints excluded: chain e residue 338 THR Chi-restraints excluded: chain e residue 381 TRP Chi-restraints excluded: chain e residue 394 ASP Chi-restraints excluded: chain e residue 410 ASP Chi-restraints excluded: chain e residue 415 MET Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 23 LEU Chi-restraints excluded: chain f residue 44 LYS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 140 HIS Chi-restraints excluded: chain f residue 205 MET Chi-restraints excluded: chain f residue 241 GLN Chi-restraints excluded: chain f residue 264 LEU Chi-restraints excluded: chain f residue 277 VAL Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 338 THR Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 381 TRP Chi-restraints excluded: chain f residue 394 ASP Chi-restraints excluded: chain f residue 411 ASP Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 327 MET Chi-restraints excluded: chain g residue 338 THR Chi-restraints excluded: chain g residue 381 TRP Chi-restraints excluded: chain g residue 415 MET Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 8 ASN Chi-restraints excluded: chain h residue 21 MET Chi-restraints excluded: chain h residue 23 LEU Chi-restraints excluded: chain h residue 56 GLU Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 126 ASN Chi-restraints excluded: chain h residue 140 HIS Chi-restraints excluded: chain h residue 259 ASP Chi-restraints excluded: chain h residue 260 VAL Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain h residue 333 GLU Chi-restraints excluded: chain h residue 340 ASN Chi-restraints excluded: chain h residue 381 TRP Chi-restraints excluded: chain h residue 394 ASP Chi-restraints excluded: chain h residue 408 THR Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 91 LEU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 241 GLN Chi-restraints excluded: chain i residue 260 VAL Chi-restraints excluded: chain i residue 264 LEU Chi-restraints excluded: chain i residue 277 VAL Chi-restraints excluded: chain i residue 290 ASP Chi-restraints excluded: chain i residue 373 THR Chi-restraints excluded: chain i residue 379 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 647 optimal weight: 0.5980 chunk 681 optimal weight: 0.9980 chunk 621 optimal weight: 5.9990 chunk 662 optimal weight: 7.9990 chunk 398 optimal weight: 2.9990 chunk 288 optimal weight: 0.9980 chunk 520 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 chunk 598 optimal weight: 0.9990 chunk 626 optimal weight: 6.9990 chunk 660 optimal weight: 0.0000 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 220 GLN ** r 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 32 GLN ** r 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 59 GLN ** p 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 378 GLN ** j 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 193 GLN b 220 GLN c 172 GLN d 193 GLN e 374 GLN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 60822 Z= 0.163 Angle : 0.635 12.239 82008 Z= 0.298 Chirality : 0.042 0.192 9324 Planarity : 0.003 0.052 10620 Dihedral : 4.593 44.211 8397 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.21 % Allowed : 30.40 % Favored : 66.39 % 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: 0.66 (0.10), residues: 7506 helix: 1.38 (0.09), residues: 3276 sheet: 0.02 (0.15), residues: 1134 loop : -0.32 (0.11), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.007 TRP b 381 HIS 0.006 0.000 HIS r 388 PHE 0.011 0.001 PHE m 398 TYR 0.023 0.001 TYR k 197 ARG 0.009 0.000 ARG a 269 *********************** 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 1102 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 894 time to evaluate : 5.504 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: a 29 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7815 (ptp) REVERT: a 205 MET cc_start: 0.8097 (tpp) cc_final: 0.7833 (mmt) REVERT: a 215 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: a 244 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8282 (mm-30) REVERT: a 327 MET cc_start: 0.8898 (ttp) cc_final: 0.8689 (ttp) REVERT: a 375 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8260 (mp0) REVERT: a 396 MET cc_start: 0.9484 (tpp) cc_final: 0.9254 (tpp) REVERT: r 244 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8546 (mm-30) REVERT: r 366 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7780 (tpt170) REVERT: q 1 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.6920 (tpt) REVERT: q 211 GLU cc_start: 0.8565 (tp30) cc_final: 0.8182 (tp30) REVERT: q 244 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8372 (mm-30) REVERT: q 299 ARG cc_start: 0.9310 (ptm160) cc_final: 0.9025 (mtp-110) REVERT: q 375 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8529 (tm-30) REVERT: q 394 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8541 (p0) REVERT: p 33 ASP cc_start: 0.9069 (m-30) cc_final: 0.8776 (m-30) REVERT: p 72 TYR cc_start: 0.9283 (m-10) cc_final: 0.9002 (m-10) REVERT: p 91 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8766 (pp) REVERT: p 172 GLN cc_start: 0.8551 (tp40) cc_final: 0.8342 (tp40) REVERT: p 193 GLN cc_start: 0.8973 (tt0) cc_final: 0.8688 (tt0) REVERT: p 241 GLN cc_start: 0.8890 (pp30) cc_final: 0.8587 (tm-30) REVERT: p 394 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8775 (p0) REVERT: o 259 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7960 (p0) REVERT: o 292 ASN cc_start: 0.8802 (m-40) cc_final: 0.8497 (p0) REVERT: o 333 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8570 (tm-30) REVERT: o 352 LYS cc_start: 0.8703 (tptp) cc_final: 0.8450 (tptp) REVERT: n 41 GLN cc_start: 0.9260 (tp40) cc_final: 0.8817 (tp40) REVERT: n 100 LYS cc_start: 0.9499 (ttmt) cc_final: 0.9129 (ttmm) REVERT: n 244 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8510 (mm-30) REVERT: n 259 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.7952 (p0) REVERT: n 326 LYS cc_start: 0.9203 (tptp) cc_final: 0.8923 (tptp) REVERT: n 374 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8510 (tp-100) REVERT: m 44 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8755 (ptpp) REVERT: m 125 GLU cc_start: 0.8850 (mp0) cc_final: 0.8638 (pm20) REVERT: m 244 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8308 (mm-30) REVERT: m 296 ARG cc_start: 0.9065 (tpp80) cc_final: 0.8705 (mmm-85) REVERT: m 334 GLU cc_start: 0.8869 (tp30) cc_final: 0.8563 (tp30) REVERT: m 341 MET cc_start: 0.9238 (tmm) cc_final: 0.8967 (tmm) REVERT: m 342 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8429 (mp0) REVERT: m 374 GLN cc_start: 0.9437 (tp40) cc_final: 0.9079 (tp40) REVERT: l 140 HIS cc_start: 0.8825 (OUTLIER) cc_final: 0.8471 (m-70) REVERT: l 244 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7804 (mm-30) REVERT: l 290 ASP cc_start: 0.8002 (t0) cc_final: 0.6863 (t0) REVERT: l 292 ASN cc_start: 0.9083 (m110) cc_final: 0.8737 (p0) REVERT: l 375 GLU cc_start: 0.9108 (tp30) cc_final: 0.8744 (tp30) REVERT: l 390 MET cc_start: 0.9232 (ptp) cc_final: 0.8982 (ptp) REVERT: l 397 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8909 (mm-30) REVERT: k 12 SER cc_start: 0.9306 (m) cc_final: 0.8963 (p) REVERT: k 13 GLU cc_start: 0.8669 (pm20) cc_final: 0.8386 (pm20) REVERT: k 19 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8729 (mm-30) REVERT: k 41 GLN cc_start: 0.8857 (tp40) cc_final: 0.8563 (tm-30) REVERT: k 244 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7929 (mm-30) REVERT: k 290 ASP cc_start: 0.9092 (m-30) cc_final: 0.8255 (t0) REVERT: k 334 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8719 (mm-30) REVERT: k 342 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8195 (mp0) REVERT: k 351 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8394 (mm-30) REVERT: k 397 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8910 (mt-10) REVERT: j 1 MET cc_start: 0.5930 (OUTLIER) cc_final: 0.5369 (tmm) REVERT: j 23 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8393 (mm) REVERT: j 342 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7862 (pt0) REVERT: j 381 TRP cc_start: 0.8522 (OUTLIER) cc_final: 0.8274 (t60) REVERT: j 407 LYS cc_start: 0.9317 (ptmm) cc_final: 0.9029 (ttmm) REVERT: b 1 MET cc_start: 0.7127 (tpt) cc_final: 0.6428 (tpt) REVERT: b 41 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8646 (tm-30) REVERT: b 110 TYR cc_start: 0.8181 (m-80) cc_final: 0.7648 (m-10) REVERT: b 193 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8768 (tm-30) REVERT: b 215 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8448 (mp0) REVERT: b 244 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8654 (mm-30) REVERT: b 342 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8298 (mp0) REVERT: b 374 GLN cc_start: 0.8950 (tp-100) cc_final: 0.8749 (tp40) REVERT: c 12 SER cc_start: 0.9558 (m) cc_final: 0.9334 (p) REVERT: c 29 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8188 (ptm) REVERT: c 30 ARG cc_start: 0.8560 (mmm-85) cc_final: 0.8359 (mtp-110) REVERT: c 41 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8784 (tm-30) REVERT: c 56 GLU cc_start: 0.8543 (tt0) cc_final: 0.8321 (tm-30) REVERT: c 90 ASN cc_start: 0.8402 (t0) cc_final: 0.7899 (t0) REVERT: c 140 HIS cc_start: 0.9132 (OUTLIER) cc_final: 0.8655 (m90) REVERT: c 352 LYS cc_start: 0.8249 (tptp) cc_final: 0.7920 (tptt) REVERT: c 381 TRP cc_start: 0.8717 (OUTLIER) cc_final: 0.8411 (t60) REVERT: c 397 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8765 (mt-10) REVERT: d 8 ASN cc_start: 0.8978 (m-40) cc_final: 0.8696 (m110) REVERT: d 21 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8249 (ppp) REVERT: d 84 SER cc_start: 0.9474 (m) cc_final: 0.9231 (t) REVERT: d 140 HIS cc_start: 0.9030 (OUTLIER) cc_final: 0.8781 (m-70) REVERT: d 202 CYS cc_start: 0.8667 (m) cc_final: 0.8409 (m) REVERT: d 342 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8243 (mm-30) REVERT: d 343 LEU cc_start: 0.8615 (tp) cc_final: 0.8333 (tp) REVERT: d 352 LYS cc_start: 0.8541 (tptp) cc_final: 0.8190 (tptp) REVERT: d 374 GLN cc_start: 0.8997 (tp40) cc_final: 0.8723 (tp-100) REVERT: d 375 GLU cc_start: 0.9029 (mp0) cc_final: 0.8570 (mp0) REVERT: d 381 TRP cc_start: 0.8782 (OUTLIER) cc_final: 0.8425 (t60) REVERT: d 397 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8758 (mt-10) REVERT: e 140 HIS cc_start: 0.8940 (OUTLIER) cc_final: 0.8508 (m-70) REVERT: e 222 LEU cc_start: 0.9468 (tt) cc_final: 0.9205 (tt) REVERT: e 259 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8527 (p0) REVERT: f 134 GLU cc_start: 0.8949 (mp0) cc_final: 0.8630 (mp0) REVERT: f 329 GLU cc_start: 0.8160 (mp0) cc_final: 0.7521 (mp0) REVERT: f 375 GLU cc_start: 0.8931 (mp0) cc_final: 0.8519 (mp0) REVERT: g 23 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7918 (mm) REVERT: g 30 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.7778 (mtp-110) REVERT: g 32 GLN cc_start: 0.9087 (mp10) cc_final: 0.8784 (mp10) REVERT: g 397 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8903 (mt-10) REVERT: h 140 HIS cc_start: 0.8756 (OUTLIER) cc_final: 0.8496 (m90) REVERT: h 244 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7896 (mm-30) REVERT: h 259 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.7483 (p0) REVERT: h 374 GLN cc_start: 0.9211 (tp-100) cc_final: 0.8789 (tp-100) REVERT: i 91 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8428 (pp) REVERT: i 342 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8063 (mp0) REVERT: i 375 GLU cc_start: 0.8260 (tp30) cc_final: 0.7622 (tp30) REVERT: i 379 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8613 (mttp) outliers start: 208 outliers final: 141 residues processed: 1039 average time/residue: 0.5509 time to fit residues: 968.2374 Evaluate side-chains 1030 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 860 time to evaluate : 5.338 ------------------------------------------------------------------------------- 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 29 MET Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 220 GLN Chi-restraints excluded: chain a residue 264 LEU Chi-restraints excluded: chain a residue 323 THR Chi-restraints excluded: chain a residue 371 LEU Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 263 LEU Chi-restraints excluded: chain r residue 323 THR Chi-restraints excluded: chain r residue 366 ARG Chi-restraints excluded: chain r residue 394 ASP Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 44 LYS Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 260 VAL Chi-restraints excluded: chain q residue 264 LEU Chi-restraints excluded: chain q residue 323 THR Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain q residue 379 LYS Chi-restraints excluded: chain q residue 394 ASP Chi-restraints excluded: chain q residue 399 LEU Chi-restraints excluded: chain q residue 411 ASP Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain p residue 91 LEU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 168 ILE Chi-restraints excluded: chain p residue 202 CYS Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 286 THR Chi-restraints excluded: chain p residue 338 THR Chi-restraints excluded: chain p residue 394 ASP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 126 ASN Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 259 ASP Chi-restraints excluded: chain o residue 394 ASP Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 23 LEU Chi-restraints excluded: chain n residue 56 GLU Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 253 LEU Chi-restraints excluded: chain n residue 259 ASP Chi-restraints excluded: chain n residue 264 LEU Chi-restraints excluded: chain n residue 338 THR Chi-restraints excluded: chain n residue 354 VAL Chi-restraints excluded: chain n residue 374 GLN Chi-restraints excluded: chain n residue 376 GLU Chi-restraints excluded: chain n residue 393 ILE Chi-restraints excluded: chain m residue 44 LYS Chi-restraints excluded: chain m residue 60 ASP Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 205 MET Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain m residue 381 TRP Chi-restraints excluded: chain m residue 394 ASP Chi-restraints excluded: chain m residue 418 ARG Chi-restraints excluded: chain l residue 29 MET Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 140 HIS Chi-restraints excluded: chain l residue 205 MET Chi-restraints excluded: chain l residue 264 LEU Chi-restraints excluded: chain l residue 277 VAL Chi-restraints excluded: chain l residue 394 ASP Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 162 LEU Chi-restraints excluded: chain k residue 327 MET Chi-restraints excluded: chain k residue 373 THR Chi-restraints excluded: chain k residue 381 TRP Chi-restraints excluded: chain k residue 394 ASP Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 29 MET Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 162 LEU Chi-restraints excluded: chain j residue 260 VAL Chi-restraints excluded: chain j residue 264 LEU Chi-restraints excluded: chain j residue 326 LYS Chi-restraints excluded: chain j residue 381 TRP Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 193 GLN Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain b residue 220 GLN Chi-restraints excluded: chain b residue 253 LEU Chi-restraints excluded: chain b residue 264 LEU Chi-restraints excluded: chain b residue 341 MET Chi-restraints excluded: chain b residue 408 THR Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 55 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 140 HIS Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 354 VAL Chi-restraints excluded: chain c residue 381 TRP Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 140 HIS Chi-restraints excluded: chain d residue 193 GLN Chi-restraints excluded: chain d residue 205 MET Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 259 ASP Chi-restraints excluded: chain d residue 381 TRP Chi-restraints excluded: chain d residue 394 ASP Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 140 HIS Chi-restraints excluded: chain e residue 205 MET Chi-restraints excluded: chain e residue 259 ASP Chi-restraints excluded: chain e residue 381 TRP Chi-restraints excluded: chain e residue 394 ASP Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 23 LEU Chi-restraints excluded: chain f residue 44 LYS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 264 LEU Chi-restraints excluded: chain f residue 277 VAL Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 381 TRP Chi-restraints excluded: chain f residue 394 ASP Chi-restraints excluded: chain f residue 411 ASP Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 233 ASP Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 327 MET Chi-restraints excluded: chain g residue 381 TRP Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 8 ASN Chi-restraints excluded: chain h residue 21 MET Chi-restraints excluded: chain h residue 56 GLU Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 140 HIS Chi-restraints excluded: chain h residue 259 ASP Chi-restraints excluded: chain h residue 333 GLU Chi-restraints excluded: chain h residue 340 ASN Chi-restraints excluded: chain h residue 381 TRP Chi-restraints excluded: chain h residue 394 ASP Chi-restraints excluded: chain h residue 408 THR Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 91 LEU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 264 LEU Chi-restraints excluded: chain i residue 373 THR Chi-restraints excluded: chain i residue 379 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 435 optimal weight: 8.9990 chunk 700 optimal weight: 0.8980 chunk 427 optimal weight: 9.9990 chunk 332 optimal weight: 0.8980 chunk 487 optimal weight: 9.9990 chunk 735 optimal weight: 1.9990 chunk 676 optimal weight: 0.7980 chunk 585 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 452 optimal weight: 2.9990 chunk 358 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 32 GLN a 220 GLN ** r 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 172 GLN ** j 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 193 GLN b 220 GLN c 172 GLN c 189 GLN d 193 GLN ** e 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 60822 Z= 0.195 Angle : 0.643 11.878 82008 Z= 0.302 Chirality : 0.043 0.180 9324 Planarity : 0.004 0.064 10620 Dihedral : 4.612 44.978 8396 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.99 % Allowed : 30.71 % Favored : 66.30 % 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: 0.65 (0.10), residues: 7506 helix: 1.36 (0.09), residues: 3294 sheet: 0.04 (0.15), residues: 1134 loop : -0.34 (0.11), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.008 TRP n 381 HIS 0.013 0.001 HIS r 388 PHE 0.011 0.001 PHE c 398 TYR 0.024 0.001 TYR a 80 ARG 0.014 0.000 ARG n 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 1056 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 862 time to evaluate : 5.391 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: a 29 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7869 (ptp) REVERT: a 186 MET cc_start: 0.8467 (ptt) cc_final: 0.7816 (ptt) REVERT: a 215 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: a 244 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8297 (mm-30) REVERT: a 375 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8284 (mp0) REVERT: a 396 MET cc_start: 0.9492 (tpp) cc_final: 0.9246 (tpp) REVERT: r 244 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8554 (mm-30) REVERT: r 274 TYR cc_start: 0.9458 (m-10) cc_final: 0.8368 (m-10) REVERT: r 366 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7829 (tpt170) REVERT: q 1 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.6917 (tpt) REVERT: q 211 GLU cc_start: 0.8549 (tp30) cc_final: 0.8348 (tp30) REVERT: q 244 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8389 (mm-30) REVERT: q 299 ARG cc_start: 0.9329 (ptm160) cc_final: 0.9017 (mtp-110) REVERT: q 375 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8550 (tm-30) REVERT: q 394 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8504 (p0) REVERT: p 33 ASP cc_start: 0.9091 (m-30) cc_final: 0.8809 (m-30) REVERT: p 72 TYR cc_start: 0.9304 (m-10) cc_final: 0.9012 (m-10) REVERT: p 91 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8810 (pp) REVERT: p 193 GLN cc_start: 0.8976 (tt0) cc_final: 0.8712 (tt0) REVERT: p 241 GLN cc_start: 0.8929 (pp30) cc_final: 0.8620 (tm-30) REVERT: p 394 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8770 (p0) REVERT: o 205 MET cc_start: 0.8386 (mtt) cc_final: 0.7937 (mtt) REVERT: o 244 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8271 (mm-30) REVERT: o 259 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7968 (p0) REVERT: o 333 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8573 (tm-30) REVERT: o 397 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8464 (mp0) REVERT: o 405 MET cc_start: 0.9367 (pmm) cc_final: 0.9105 (pmm) REVERT: n 41 GLN cc_start: 0.9262 (tp40) cc_final: 0.8814 (tp40) REVERT: n 100 LYS cc_start: 0.9501 (ttmt) cc_final: 0.9132 (ttmm) REVERT: n 244 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8530 (mm-30) REVERT: n 326 LYS cc_start: 0.9198 (tptp) cc_final: 0.8977 (tptp) REVERT: n 374 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8494 (tp-100) REVERT: m 41 GLN cc_start: 0.9069 (tp40) cc_final: 0.8747 (tp40) REVERT: m 44 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8598 (ptpp) REVERT: m 244 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8300 (mm-30) REVERT: m 296 ARG cc_start: 0.9073 (tpp80) cc_final: 0.8696 (mmm-85) REVERT: m 334 GLU cc_start: 0.8873 (tp30) cc_final: 0.8565 (tp30) REVERT: m 341 MET cc_start: 0.9253 (tmm) cc_final: 0.8980 (tmm) REVERT: m 342 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8438 (mp0) REVERT: m 374 GLN cc_start: 0.9446 (tp40) cc_final: 0.9075 (tp40) REVERT: l 32 GLN cc_start: 0.9001 (mp10) cc_final: 0.8439 (mm-40) REVERT: l 140 HIS cc_start: 0.8825 (OUTLIER) cc_final: 0.8491 (m-70) REVERT: l 244 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7827 (mm-30) REVERT: l 290 ASP cc_start: 0.7961 (t0) cc_final: 0.6917 (t0) REVERT: l 292 ASN cc_start: 0.9065 (m110) cc_final: 0.8661 (p0) REVERT: l 375 GLU cc_start: 0.9127 (tp30) cc_final: 0.8763 (tp30) REVERT: l 397 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8858 (mm-30) REVERT: k 12 SER cc_start: 0.9309 (m) cc_final: 0.8955 (p) REVERT: k 13 GLU cc_start: 0.8639 (pm20) cc_final: 0.8352 (pm20) REVERT: k 19 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8732 (mm-30) REVERT: k 41 GLN cc_start: 0.8862 (tp40) cc_final: 0.8564 (tm-30) REVERT: k 244 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7956 (mm-30) REVERT: k 290 ASP cc_start: 0.9113 (m-30) cc_final: 0.8256 (t0) REVERT: k 333 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8470 (mm-30) REVERT: k 334 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8729 (mm-30) REVERT: k 342 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8225 (mp0) REVERT: k 351 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8439 (mm-30) REVERT: k 397 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8925 (mt-10) REVERT: j 1 MET cc_start: 0.6012 (OUTLIER) cc_final: 0.5219 (tmm) REVERT: j 23 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8418 (mm) REVERT: j 342 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7877 (pt0) REVERT: j 381 TRP cc_start: 0.8577 (OUTLIER) cc_final: 0.8308 (t60) REVERT: j 407 LYS cc_start: 0.9324 (ptmm) cc_final: 0.9043 (ttmm) REVERT: b 1 MET cc_start: 0.7142 (tpt) cc_final: 0.6437 (tpt) REVERT: b 41 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8681 (tm-30) REVERT: b 110 TYR cc_start: 0.8227 (m-80) cc_final: 0.7688 (m-10) REVERT: b 193 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8831 (tm-30) REVERT: b 215 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8463 (mp0) REVERT: b 342 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8325 (mp0) REVERT: b 374 GLN cc_start: 0.8939 (tp-100) cc_final: 0.8710 (tp40) REVERT: c 21 MET cc_start: 0.8248 (ppp) cc_final: 0.7811 (ppp) REVERT: c 29 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8208 (ptm) REVERT: c 41 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8429 (tm-30) REVERT: c 56 GLU cc_start: 0.8574 (tt0) cc_final: 0.8297 (tm-30) REVERT: c 90 ASN cc_start: 0.8424 (t0) cc_final: 0.7929 (t0) REVERT: c 140 HIS cc_start: 0.9139 (OUTLIER) cc_final: 0.8618 (m90) REVERT: c 195 ILE cc_start: 0.9494 (mt) cc_final: 0.9185 (mt) REVERT: c 224 LYS cc_start: 0.8270 (pttt) cc_final: 0.8039 (pttm) REVERT: c 241 GLN cc_start: 0.9172 (pp30) cc_final: 0.8902 (pp30) REVERT: c 352 LYS cc_start: 0.8339 (tptp) cc_final: 0.8009 (tptt) REVERT: c 381 TRP cc_start: 0.8748 (OUTLIER) cc_final: 0.8425 (t60) REVERT: c 397 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8529 (mt-10) REVERT: d 8 ASN cc_start: 0.8991 (m-40) cc_final: 0.8708 (m110) REVERT: d 21 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8247 (ppp) REVERT: d 84 SER cc_start: 0.9489 (m) cc_final: 0.9242 (t) REVERT: d 140 HIS cc_start: 0.9018 (OUTLIER) cc_final: 0.8696 (m90) REVERT: d 202 CYS cc_start: 0.8690 (m) cc_final: 0.8428 (m) REVERT: d 215 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8383 (mt-10) REVERT: d 342 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8259 (mm-30) REVERT: d 343 LEU cc_start: 0.8772 (tp) cc_final: 0.8489 (tp) REVERT: d 352 LYS cc_start: 0.8586 (tptp) cc_final: 0.8220 (tptp) REVERT: d 374 GLN cc_start: 0.9007 (tp40) cc_final: 0.8699 (tm-30) REVERT: d 375 GLU cc_start: 0.9040 (mp0) cc_final: 0.8587 (mp0) REVERT: d 381 TRP cc_start: 0.8806 (OUTLIER) cc_final: 0.8461 (t60) REVERT: d 397 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8782 (mt-10) REVERT: e 205 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8480 (mtp) REVERT: e 259 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8507 (p0) REVERT: e 397 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8944 (mt-10) REVERT: f 134 GLU cc_start: 0.8945 (mp0) cc_final: 0.8625 (mp0) REVERT: f 205 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8082 (mtp) REVERT: f 329 GLU cc_start: 0.8177 (mp0) cc_final: 0.7608 (mp0) REVERT: f 375 GLU cc_start: 0.8968 (mp0) cc_final: 0.8552 (mp0) REVERT: f 397 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8671 (mm-30) REVERT: g 23 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7883 (mm) REVERT: g 30 ARG cc_start: 0.8078 (mmm-85) cc_final: 0.7683 (mtp-110) REVERT: g 32 GLN cc_start: 0.9094 (mp10) cc_final: 0.8789 (mp10) REVERT: g 397 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8914 (mt-10) REVERT: h 140 HIS cc_start: 0.8779 (OUTLIER) cc_final: 0.8502 (m90) REVERT: h 259 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7483 (p0) REVERT: h 374 GLN cc_start: 0.9215 (tp-100) cc_final: 0.8791 (tp-100) REVERT: h 418 ARG cc_start: 0.8013 (mmp80) cc_final: 0.7760 (mmp80) REVERT: i 91 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8579 (pp) REVERT: i 342 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8107 (mp0) REVERT: i 375 GLU cc_start: 0.8250 (tp30) cc_final: 0.7641 (tp30) REVERT: i 379 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8638 (mttp) outliers start: 194 outliers final: 148 residues processed: 1003 average time/residue: 0.5487 time to fit residues: 930.1095 Evaluate side-chains 1020 residues out of total 6480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 843 time to evaluate : 5.365 ------------------------------------------------------------------------------- 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 29 MET Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 202 CYS Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 220 GLN Chi-restraints excluded: chain a residue 264 LEU Chi-restraints excluded: chain a residue 323 THR Chi-restraints excluded: chain a residue 371 LEU Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 394 ASP Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 263 LEU Chi-restraints excluded: chain r residue 323 THR Chi-restraints excluded: chain r residue 366 ARG Chi-restraints excluded: chain r residue 394 ASP Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 44 LYS Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 260 VAL Chi-restraints excluded: chain q residue 264 LEU Chi-restraints excluded: chain q residue 323 THR Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain q residue 379 LYS Chi-restraints excluded: chain q residue 394 ASP Chi-restraints excluded: chain q residue 399 LEU Chi-restraints excluded: chain q residue 411 ASP Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain p residue 91 LEU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 168 ILE Chi-restraints excluded: chain p residue 202 CYS Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 286 THR Chi-restraints excluded: chain p residue 338 THR Chi-restraints excluded: chain p residue 394 ASP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 126 ASN Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 259 ASP Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 394 ASP Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 23 LEU Chi-restraints excluded: chain n residue 56 GLU Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 264 LEU Chi-restraints excluded: chain n residue 338 THR Chi-restraints excluded: chain n residue 374 GLN Chi-restraints excluded: chain n residue 376 GLU Chi-restraints excluded: chain n residue 393 ILE Chi-restraints excluded: chain m residue 44 LYS Chi-restraints excluded: chain m residue 59 GLN Chi-restraints excluded: chain m residue 60 ASP Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 205 MET Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain m residue 381 TRP Chi-restraints excluded: chain m residue 394 ASP Chi-restraints excluded: chain m residue 418 ARG Chi-restraints excluded: chain l residue 29 MET Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 140 HIS Chi-restraints excluded: chain l residue 205 MET Chi-restraints excluded: chain l residue 264 LEU Chi-restraints excluded: chain l residue 277 VAL Chi-restraints excluded: chain l residue 394 ASP Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 162 LEU Chi-restraints excluded: chain k residue 228 VAL Chi-restraints excluded: chain k residue 327 MET Chi-restraints excluded: chain k residue 373 THR Chi-restraints excluded: chain k residue 381 TRP Chi-restraints excluded: chain k residue 394 ASP Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 162 LEU Chi-restraints excluded: chain j residue 264 LEU Chi-restraints excluded: chain j residue 381 TRP Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 193 GLN Chi-restraints excluded: chain b residue 220 GLN Chi-restraints excluded: chain b residue 253 LEU Chi-restraints excluded: chain b residue 264 LEU Chi-restraints excluded: chain b residue 341 MET Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 408 THR Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 55 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 140 HIS Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 354 VAL Chi-restraints excluded: chain c residue 381 TRP Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 140 HIS Chi-restraints excluded: chain d residue 193 GLN Chi-restraints excluded: chain d residue 205 MET Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 259 ASP Chi-restraints excluded: chain d residue 381 TRP Chi-restraints excluded: chain d residue 394 ASP Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 140 HIS Chi-restraints excluded: chain e residue 205 MET Chi-restraints excluded: chain e residue 259 ASP Chi-restraints excluded: chain e residue 381 TRP Chi-restraints excluded: chain e residue 394 ASP Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 23 LEU Chi-restraints excluded: chain f residue 44 LYS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 153 SER Chi-restraints excluded: chain f residue 205 MET Chi-restraints excluded: chain f residue 264 LEU Chi-restraints excluded: chain f residue 277 VAL Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 381 TRP Chi-restraints excluded: chain f residue 394 ASP Chi-restraints excluded: chain f residue 411 ASP Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 233 ASP Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 327 MET Chi-restraints excluded: chain g residue 341 MET Chi-restraints excluded: chain g residue 381 TRP Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 8 ASN Chi-restraints excluded: chain h residue 21 MET Chi-restraints excluded: chain h residue 56 GLU Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 140 HIS Chi-restraints excluded: chain h residue 162 LEU Chi-restraints excluded: chain h residue 259 ASP Chi-restraints excluded: chain h residue 333 GLU Chi-restraints excluded: chain h residue 340 ASN Chi-restraints excluded: chain h residue 381 TRP Chi-restraints excluded: chain h residue 394 ASP Chi-restraints excluded: chain h residue 408 THR Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 91 LEU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 226 GLU Chi-restraints excluded: chain i residue 264 LEU Chi-restraints excluded: chain i residue 373 THR Chi-restraints excluded: chain i residue 379 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 465 optimal weight: 10.0000 chunk 623 optimal weight: 2.9990 chunk 179 optimal weight: 0.0770 chunk 539 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 162 optimal weight: 8.9990 chunk 586 optimal weight: 0.6980 chunk 245 optimal weight: 7.9990 chunk 602 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 overall best weight: 2.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 292 ASN ** o 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 292 ASN ** j 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 193 GLN b 220 GLN c 172 GLN c 189 GLN d 193 GLN ** e 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 374 GLN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.077594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.059242 restraints weight = 154387.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.061370 restraints weight = 73254.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.062791 restraints weight = 44906.774| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 60822 Z= 0.238 Angle : 0.656 12.668 82008 Z= 0.308 Chirality : 0.043 0.227 9324 Planarity : 0.004 0.073 10620 Dihedral : 4.683 46.734 8395 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.27 % Allowed : 30.59 % Favored : 66.14 % 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: 0.68 (0.10), residues: 7506 helix: 1.34 (0.09), residues: 3240 sheet: 0.01 (0.15), residues: 1134 loop : -0.23 (0.11), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.009 TRP l 381 HIS 0.004 0.001 HIS q 140 PHE 0.027 0.001 PHE e 62 TYR 0.027 0.001 TYR p 332 ARG 0.011 0.000 ARG p 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15364.28 seconds wall clock time: 268 minutes 49.28 seconds (16129.28 seconds total)