Starting phenix.real_space_refine on Wed May 15 01:45:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wux_37863/05_2024/8wux_37863_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wux_37863/05_2024/8wux_37863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wux_37863/05_2024/8wux_37863.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wux_37863/05_2024/8wux_37863.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wux_37863/05_2024/8wux_37863_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wux_37863/05_2024/8wux_37863_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 7 8.98 5 P 42 5.49 5 Mg 14 5.21 5 S 154 5.16 5 C 38262 2.51 5 N 10521 2.21 5 O 12026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A ASP 172": "OD1" <-> "OD2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A ASP 432": "OD1" <-> "OD2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H ASP 52": "OD1" <-> "OD2" Residue "H GLU 59": "OE1" <-> "OE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 178": "OE1" <-> "OE2" Residue "H ASP 196": "OD1" <-> "OD2" Residue "H TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 391": "OE1" <-> "OE2" Residue "H ASP 427": "OD1" <-> "OD2" Residue "H PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 461": "OE1" <-> "OE2" Residue "H GLU 467": "OE1" <-> "OE2" Residue "H GLU 494": "OE1" <-> "OE2" Residue "a ASP 9": "OD1" <-> "OD2" Residue "a GLU 17": "OE1" <-> "OE2" Residue "a GLU 20": "OE1" <-> "OE2" Residue "a GLU 35": "OE1" <-> "OE2" Residue "a GLU 41": "OE1" <-> "OE2" Residue "a ASP 47": "OD1" <-> "OD2" Residue "a GLU 78": "OE1" <-> "OE2" Residue "a GLU 89": "OE1" <-> "OE2" Residue "a ASP 90": "OD1" <-> "OD2" Residue "B TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 21": "OD1" <-> "OD2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 253": "OD1" <-> "OD2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B GLU 304": "OE1" <-> "OE2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B ASP 328": "OD1" <-> "OD2" Residue "B TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 367": "OE1" <-> "OE2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B ASP 432": "OD1" <-> "OD2" Residue "B TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I ASP 52": "OD1" <-> "OD2" Residue "I ASP 87": "OD1" <-> "OD2" Residue "I GLU 179": "OE1" <-> "OE2" Residue "I GLU 388": "OE1" <-> "OE2" Residue "I PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 461": "OE1" <-> "OE2" Residue "b GLU 17": "OE1" <-> "OE2" Residue "b GLU 18": "OE1" <-> "OE2" Residue "b GLU 35": "OE1" <-> "OE2" Residue "b GLU 41": "OE1" <-> "OE2" Residue "b ASP 65": "OD1" <-> "OD2" Residue "b GLU 76": "OE1" <-> "OE2" Residue "b ASP 80": "OD1" <-> "OD2" Residue "b GLU 89": "OE1" <-> "OE2" Residue "C ASP 52": "OD1" <-> "OD2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 253": "OD1" <-> "OD2" Residue "C ASP 328": "OD1" <-> "OD2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C GLU 391": "OE1" <-> "OE2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 527": "OE1" <-> "OE2" Residue "J ASP 52": "OD1" <-> "OD2" Residue "J GLU 76": "OE1" <-> "OE2" Residue "J ASP 155": "OD1" <-> "OD2" Residue "J GLU 388": "OE1" <-> "OE2" Residue "J GLU 391": "OE1" <-> "OE2" Residue "J GLU 397": "OE1" <-> "OE2" Residue "J PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 461": "OE1" <-> "OE2" Residue "J GLU 475": "OE1" <-> "OE2" Residue "J GLU 494": "OE1" <-> "OE2" Residue "c ASP 9": "OD1" <-> "OD2" Residue "c GLU 17": "OE1" <-> "OE2" Residue "c GLU 20": "OE1" <-> "OE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 76": "OE1" <-> "OE2" Residue "c GLU 82": "OE1" <-> "OE2" Residue "c GLU 89": "OE1" <-> "OE2" Residue "c ASP 90": "OD1" <-> "OD2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "D TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D ASP 87": "OD1" <-> "OD2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 328": "OD1" <-> "OD2" Residue "D GLU 386": "OE1" <-> "OE2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D GLU 408": "OE1" <-> "OE2" Residue "D GLU 461": "OE1" <-> "OE2" Residue "D TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 467": "OE1" <-> "OE2" Residue "K GLU 10": "OE1" <-> "OE2" Residue "K ASP 52": "OD1" <-> "OD2" Residue "K GLU 76": "OE1" <-> "OE2" Residue "K PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 397": "OE1" <-> "OE2" Residue "K GLU 461": "OE1" <-> "OE2" Residue "K GLU 467": "OE1" <-> "OE2" Residue "K GLU 494": "OE1" <-> "OE2" Residue "d ASP 9": "OD1" <-> "OD2" Residue "d GLU 17": "OE1" <-> "OE2" Residue "d GLU 18": "OE1" <-> "OE2" Residue "d GLU 35": "OE1" <-> "OE2" Residue "d GLU 41": "OE1" <-> "OE2" Residue "d ASP 65": "OD1" <-> "OD2" Residue "d PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 76": "OE1" <-> "OE2" Residue "d ASP 80": "OD1" <-> "OD2" Residue "d GLU 82": "OE1" <-> "OE2" Residue "d ASP 90": "OD1" <-> "OD2" Residue "d GLU 91": "OE1" <-> "OE2" Residue "E TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E ASP 87": "OD1" <-> "OD2" Residue "E ASP 155": "OD1" <-> "OD2" Residue "E ASP 172": "OD1" <-> "OD2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 303": "OE1" <-> "OE2" Residue "E TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 388": "OE1" <-> "OE2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "E ASP 432": "OD1" <-> "OD2" Residue "E TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 467": "OE1" <-> "OE2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L ASP 52": "OD1" <-> "OD2" Residue "L GLU 59": "OE1" <-> "OE2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "L ASP 155": "OD1" <-> "OD2" Residue "L ASP 172": "OD1" <-> "OD2" Residue "L GLU 179": "OE1" <-> "OE2" Residue "L TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 397": "OE1" <-> "OE2" Residue "L PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 461": "OE1" <-> "OE2" Residue "L GLU 494": "OE1" <-> "OE2" Residue "e GLU 20": "OE1" <-> "OE2" Residue "e GLU 41": "OE1" <-> "OE2" Residue "e ASP 65": "OD1" <-> "OD2" Residue "e GLU 76": "OE1" <-> "OE2" Residue "e ASP 80": "OD1" <-> "OD2" Residue "e GLU 89": "OE1" <-> "OE2" Residue "e ASP 90": "OD1" <-> "OD2" Residue "e GLU 91": "OE1" <-> "OE2" Residue "F GLU 76": "OE1" <-> "OE2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "F GLU 145": "OE1" <-> "OE2" Residue "F GLU 179": "OE1" <-> "OE2" Residue "F PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 310": "OE1" <-> "OE2" Residue "F ASP 328": "OD1" <-> "OD2" Residue "F ASP 432": "OD1" <-> "OD2" Residue "F ASP 441": "OD1" <-> "OD2" Residue "F GLU 467": "OE1" <-> "OE2" Residue "F GLU 494": "OE1" <-> "OE2" Residue "F GLU 527": "OE1" <-> "OE2" Residue "M GLU 10": "OE1" <-> "OE2" Residue "M ASP 52": "OD1" <-> "OD2" Residue "M GLU 59": "OE1" <-> "OE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M ASP 155": "OD1" <-> "OD2" Residue "M GLU 178": "OE1" <-> "OE2" Residue "M TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 391": "OE1" <-> "OE2" Residue "M GLU 397": "OE1" <-> "OE2" Residue "M GLU 467": "OE1" <-> "OE2" Residue "M GLU 494": "OE1" <-> "OE2" Residue "f GLU 17": "OE1" <-> "OE2" Residue "f GLU 89": "OE1" <-> "OE2" Residue "f GLU 91": "OE1" <-> "OE2" Residue "G TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 76": "OE1" <-> "OE2" Residue "G GLU 178": "OE1" <-> "OE2" Residue "G TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "G TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 287": "OD1" <-> "OD2" Residue "G TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 328": "OD1" <-> "OD2" Residue "G GLU 367": "OE1" <-> "OE2" Residue "G GLU 391": "OE1" <-> "OE2" Residue "G TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 467": "OE1" <-> "OE2" Residue "N GLU 10": "OE1" <-> "OE2" Residue "N ASP 52": "OD1" <-> "OD2" Residue "N GLU 76": "OE1" <-> "OE2" Residue "N ASP 155": "OD1" <-> "OD2" Residue "N GLU 179": "OE1" <-> "OE2" Residue "N GLU 388": "OE1" <-> "OE2" Residue "N GLU 397": "OE1" <-> "OE2" Residue "N GLU 461": "OE1" <-> "OE2" Residue "N GLU 467": "OE1" <-> "OE2" Residue "N GLU 530": "OE1" <-> "OE2" Residue "g ASP 9": "OD1" <-> "OD2" Residue "g GLU 20": "OE1" <-> "OE2" Residue "g ASP 31": "OD1" <-> "OD2" Residue "g GLU 35": "OE1" <-> "OE2" Residue "g GLU 41": "OE1" <-> "OE2" Residue "g ASP 80": "OD1" <-> "OD2" Residue "g GLU 82": "OE1" <-> "OE2" Residue "g GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 61026 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "H" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "a" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "B" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "I" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "b" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "C" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "J" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "c" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "D" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "K" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "d" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "E" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "L" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "e" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "F" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "M" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "f" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "G" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3954 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "N" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3968 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "g" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 24.15, per 1000 atoms: 0.40 Number of scatterers: 61026 At special positions: 0 Unit cell: (166.944, 169.2, 221.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 7 19.00 S 154 16.00 P 42 15.00 Mg 14 11.99 O 12026 8.00 N 10521 7.00 C 38262 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: 18.91 Conformation dependent library (CDL) restraints added in 8.1 seconds 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14700 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 302 helices and 109 sheets defined 50.0% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.73 Creating SS restraints... Processing helix chain 'A' and resid 9 through 30 removed outlier: 3.703A pdb=" N ALA A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N THR A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 removed outlier: 3.810A pdb=" N GLU A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 84 removed outlier: 3.616A pdb=" N GLU A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 109 Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 141 through 151 Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 230 through 243 Proline residue: A 235 - end of helix removed outlier: 3.510A pdb=" N ASN A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ARG A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.994A pdb=" N THR A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.699A pdb=" N LYS A 286 " --> pdb=" O GLN A 283 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP A 287 " --> pdb=" O ARG A 284 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 294 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 339 through 358 removed outlier: 3.520A pdb=" N ARG A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N SER A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 373 removed outlier: 3.551A pdb=" N LYS A 371 " --> pdb=" O ARG A 368 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 372 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 373 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 409 removed outlier: 3.631A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 427 removed outlier: 3.519A pdb=" N GLU A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA A 425 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 447 Processing helix chain 'A' and resid 449 through 457 Processing helix chain 'A' and resid 462 through 475 removed outlier: 4.201A pdb=" N LYS A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 495 No H-bonds generated for 'chain 'A' and resid 492 through 495' Processing helix chain 'A' and resid 501 through 520 removed outlier: 3.763A pdb=" N THR A 520 " --> pdb=" O GLY A 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 30 removed outlier: 3.637A pdb=" N ALA H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL H 29 " --> pdb=" O ASN H 25 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 59 removed outlier: 3.644A pdb=" N GLU H 59 " --> pdb=" O THR H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 85 removed outlier: 3.618A pdb=" N GLY H 70 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 108 Processing helix chain 'H' and resid 113 through 134 Processing helix chain 'H' and resid 141 through 151 Processing helix chain 'H' and resid 156 through 169 Processing helix chain 'H' and resid 230 through 243 Proline residue: H 235 - end of helix removed outlier: 3.623A pdb=" N VAL H 241 " --> pdb=" O LEU H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 267 removed outlier: 3.675A pdb=" N VAL H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE H 267 " --> pdb=" O VAL H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 295 removed outlier: 4.296A pdb=" N GLN H 290 " --> pdb=" O ASP H 287 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP H 291 " --> pdb=" O TYR H 288 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU H 295 " --> pdb=" O ILE H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 305 No H-bonds generated for 'chain 'H' and resid 303 through 305' Processing helix chain 'H' and resid 309 through 311 No H-bonds generated for 'chain 'H' and resid 309 through 311' Processing helix chain 'H' and resid 339 through 355 removed outlier: 4.124A pdb=" N GLN H 348 " --> pdb=" O ALA H 344 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE H 349 " --> pdb=" O ARG H 345 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU H 354 " --> pdb=" O LYS H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 364 removed outlier: 3.923A pdb=" N LYS H 364 " --> pdb=" O TYR H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 373 removed outlier: 3.915A pdb=" N LEU H 372 " --> pdb=" O ARG H 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 386 through 409 removed outlier: 3.551A pdb=" N ALA H 394 " --> pdb=" O LYS H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 427 removed outlier: 4.192A pdb=" N ALA H 425 " --> pdb=" O ARG H 421 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU H 426 " --> pdb=" O ALA H 422 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP H 427 " --> pdb=" O SER H 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 447 Processing helix chain 'H' and resid 449 through 458 Processing helix chain 'H' and resid 462 through 475 removed outlier: 4.012A pdb=" N LYS H 474 " --> pdb=" O LEU H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 492 through 495 No H-bonds generated for 'chain 'H' and resid 492 through 495' Processing helix chain 'H' and resid 501 through 520 removed outlier: 3.544A pdb=" N THR H 520 " --> pdb=" O GLY H 516 " (cutoff:3.500A) Processing helix chain 'a' and resid 31 through 33 No H-bonds generated for 'chain 'a' and resid 31 through 33' Processing helix chain 'B' and resid 9 through 30 removed outlier: 3.648A pdb=" N ALA B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N THR B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 removed outlier: 3.783A pdb=" N GLU B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 84 removed outlier: 3.501A pdb=" N GLY B 70 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 109 Processing helix chain 'B' and resid 113 through 134 Processing helix chain 'B' and resid 141 through 151 Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 230 through 243 Proline residue: B 235 - end of helix removed outlier: 3.609A pdb=" N ASN B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 268 removed outlier: 4.046A pdb=" N THR B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 296 removed outlier: 4.347A pdb=" N ASP B 287 " --> pdb=" O ARG B 284 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 289 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 294 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 341 through 358 removed outlier: 3.847A pdb=" N GLU B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 373 removed outlier: 4.357A pdb=" N ARG B 368 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 372 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER B 373 " --> pdb=" O ALA B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 409 removed outlier: 3.695A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 427 removed outlier: 3.526A pdb=" N GLU B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASP B 427 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 447 Processing helix chain 'B' and resid 449 through 457 Processing helix chain 'B' and resid 462 through 475 removed outlier: 4.304A pdb=" N LYS B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 495 No H-bonds generated for 'chain 'B' and resid 492 through 495' Processing helix chain 'B' and resid 501 through 520 removed outlier: 3.782A pdb=" N THR B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 30 removed outlier: 3.588A pdb=" N ALA I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL I 29 " --> pdb=" O ASN I 25 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N THR I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 59 removed outlier: 3.626A pdb=" N GLU I 59 " --> pdb=" O THR I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 85 removed outlier: 3.643A pdb=" N GLY I 70 " --> pdb=" O TYR I 66 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 108 Processing helix chain 'I' and resid 113 through 134 Processing helix chain 'I' and resid 141 through 151 Processing helix chain 'I' and resid 156 through 169 Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 230 through 243 Proline residue: I 235 - end of helix Processing helix chain 'I' and resid 259 through 267 removed outlier: 4.669A pdb=" N VAL I 264 " --> pdb=" O ALA I 260 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE I 267 " --> pdb=" O VAL I 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 295 removed outlier: 3.927A pdb=" N GLN I 290 " --> pdb=" O ASP I 287 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP I 291 " --> pdb=" O TYR I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 305 No H-bonds generated for 'chain 'I' and resid 303 through 305' Processing helix chain 'I' and resid 314 through 316 No H-bonds generated for 'chain 'I' and resid 314 through 316' Processing helix chain 'I' and resid 339 through 355 removed outlier: 3.880A pdb=" N GLU I 347 " --> pdb=" O GLN I 343 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN I 348 " --> pdb=" O ALA I 344 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE I 349 " --> pdb=" O ARG I 345 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE I 353 " --> pdb=" O ILE I 349 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU I 354 " --> pdb=" O LYS I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 386 through 409 removed outlier: 3.503A pdb=" N ARG I 395 " --> pdb=" O GLU I 391 " (cutoff:3.500A) Processing helix chain 'I' and resid 417 through 427 removed outlier: 4.251A pdb=" N ALA I 425 " --> pdb=" O ARG I 421 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU I 426 " --> pdb=" O ALA I 422 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP I 427 " --> pdb=" O SER I 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 434 through 447 Processing helix chain 'I' and resid 449 through 458 Processing helix chain 'I' and resid 462 through 475 removed outlier: 4.173A pdb=" N LYS I 474 " --> pdb=" O LEU I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 492 through 495 No H-bonds generated for 'chain 'I' and resid 492 through 495' Processing helix chain 'I' and resid 501 through 519 Processing helix chain 'b' and resid 31 through 33 No H-bonds generated for 'chain 'b' and resid 31 through 33' Processing helix chain 'b' and resid 89 through 91 No H-bonds generated for 'chain 'b' and resid 89 through 91' Processing helix chain 'C' and resid 9 through 30 removed outlier: 3.689A pdb=" N ALA C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 59 removed outlier: 3.723A pdb=" N GLU C 59 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 84 removed outlier: 3.535A pdb=" N GLY C 70 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU C 76 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 109 Processing helix chain 'C' and resid 113 through 134 Processing helix chain 'C' and resid 141 through 151 Processing helix chain 'C' and resid 156 through 169 Processing helix chain 'C' and resid 230 through 243 Proline residue: C 235 - end of helix removed outlier: 3.838A pdb=" N ARG C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 268 removed outlier: 4.509A pdb=" N THR C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 295 removed outlier: 4.403A pdb=" N ASP C 287 " --> pdb=" O ARG C 284 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU C 289 " --> pdb=" O LYS C 286 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 294 " --> pdb=" O ASP C 291 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 295 " --> pdb=" O ILE C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 311 No H-bonds generated for 'chain 'C' and resid 309 through 311' Processing helix chain 'C' and resid 341 through 358 removed outlier: 3.687A pdb=" N ARG C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU C 347 " --> pdb=" O GLN C 343 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER C 358 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 373 removed outlier: 4.081A pdb=" N LEU C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 372 " --> pdb=" O ARG C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 409 removed outlier: 3.831A pdb=" N GLU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 427 removed outlier: 3.536A pdb=" N GLU C 424 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP C 427 " --> pdb=" O SER C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 447 Processing helix chain 'C' and resid 449 through 457 Processing helix chain 'C' and resid 462 through 475 removed outlier: 4.194A pdb=" N LYS C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 495 No H-bonds generated for 'chain 'C' and resid 492 through 495' Processing helix chain 'C' and resid 501 through 520 removed outlier: 3.806A pdb=" N THR C 520 " --> pdb=" O GLY C 516 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 30 removed outlier: 3.594A pdb=" N ALA J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL J 29 " --> pdb=" O ASN J 25 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N THR J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 59 removed outlier: 3.697A pdb=" N GLU J 59 " --> pdb=" O THR J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 85 removed outlier: 3.663A pdb=" N GLY J 70 " --> pdb=" O TYR J 66 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 108 Processing helix chain 'J' and resid 113 through 134 Processing helix chain 'J' and resid 141 through 151 Processing helix chain 'J' and resid 156 through 169 Processing helix chain 'J' and resid 230 through 243 Proline residue: J 235 - end of helix Processing helix chain 'J' and resid 259 through 265 removed outlier: 3.918A pdb=" N VAL J 263 " --> pdb=" O LEU J 259 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N VAL J 264 " --> pdb=" O ALA J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 295 Processing helix chain 'J' and resid 303 through 305 No H-bonds generated for 'chain 'J' and resid 303 through 305' Processing helix chain 'J' and resid 309 through 311 No H-bonds generated for 'chain 'J' and resid 309 through 311' Processing helix chain 'J' and resid 339 through 355 removed outlier: 3.829A pdb=" N GLN J 348 " --> pdb=" O ALA J 344 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE J 349 " --> pdb=" O ARG J 345 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE J 353 " --> pdb=" O ILE J 349 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU J 354 " --> pdb=" O LYS J 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 Processing helix chain 'J' and resid 386 through 409 removed outlier: 3.768A pdb=" N GLU J 391 " --> pdb=" O ALA J 387 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA J 394 " --> pdb=" O LYS J 390 " (cutoff:3.500A) Processing helix chain 'J' and resid 417 through 427 removed outlier: 4.240A pdb=" N ALA J 425 " --> pdb=" O ARG J 421 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU J 426 " --> pdb=" O ALA J 422 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP J 427 " --> pdb=" O SER J 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 434 through 447 Processing helix chain 'J' and resid 449 through 458 Processing helix chain 'J' and resid 462 through 475 removed outlier: 4.075A pdb=" N LYS J 474 " --> pdb=" O LEU J 470 " (cutoff:3.500A) Processing helix chain 'J' and resid 492 through 495 No H-bonds generated for 'chain 'J' and resid 492 through 495' Processing helix chain 'J' and resid 501 through 519 Processing helix chain 'c' and resid 31 through 33 No H-bonds generated for 'chain 'c' and resid 31 through 33' Processing helix chain 'D' and resid 9 through 30 removed outlier: 3.660A pdb=" N ALA D 26 " --> pdb=" O LYS D 22 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 removed outlier: 3.804A pdb=" N GLU D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 84 removed outlier: 3.641A pdb=" N MET D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY D 70 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU D 76 " --> pdb=" O GLN D 72 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 109 Processing helix chain 'D' and resid 113 through 134 Processing helix chain 'D' and resid 141 through 151 Processing helix chain 'D' and resid 156 through 169 Processing helix chain 'D' and resid 230 through 243 Proline residue: D 235 - end of helix removed outlier: 3.739A pdb=" N VAL D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG D 242 " --> pdb=" O GLU D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 268 removed outlier: 3.805A pdb=" N THR D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 296 removed outlier: 3.510A pdb=" N ARG D 285 " --> pdb=" O GLY D 282 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP D 287 " --> pdb=" O ARG D 284 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 289 " --> pdb=" O LYS D 286 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN D 290 " --> pdb=" O ASP D 287 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR D 296 " --> pdb=" O ALA D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 358 removed outlier: 4.083A pdb=" N LYS D 350 " --> pdb=" O ILE D 346 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG D 351 " --> pdb=" O GLU D 347 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU D 354 " --> pdb=" O LYS D 350 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLU D 355 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N SER D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 373 Processing helix chain 'D' and resid 386 through 409 removed outlier: 3.764A pdb=" N GLU D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 427 removed outlier: 3.540A pdb=" N GLU D 424 " --> pdb=" O VAL D 420 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA D 425 " --> pdb=" O ARG D 421 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP D 427 " --> pdb=" O SER D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 457 removed outlier: 3.776A pdb=" N ARG D 448 " --> pdb=" O LYS D 444 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR D 449 " --> pdb=" O LYS D 445 " (cutoff:3.500A) Proline residue: D 450 - end of helix Processing helix chain 'D' and resid 462 through 475 removed outlier: 4.291A pdb=" N LYS D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 495 No H-bonds generated for 'chain 'D' and resid 492 through 495' Processing helix chain 'D' and resid 501 through 520 removed outlier: 3.769A pdb=" N THR D 520 " --> pdb=" O GLY D 516 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 30 removed outlier: 3.573A pdb=" N ALA K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL K 29 " --> pdb=" O ASN K 25 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N THR K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.608A pdb=" N GLU K 59 " --> pdb=" O THR K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 85 removed outlier: 3.597A pdb=" N GLY K 70 " --> pdb=" O TYR K 66 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER K 82 " --> pdb=" O ALA K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 109 Processing helix chain 'K' and resid 113 through 134 Processing helix chain 'K' and resid 141 through 151 Processing helix chain 'K' and resid 156 through 169 Processing helix chain 'K' and resid 202 through 204 No H-bonds generated for 'chain 'K' and resid 202 through 204' Processing helix chain 'K' and resid 230 through 243 Proline residue: K 235 - end of helix Processing helix chain 'K' and resid 259 through 267 removed outlier: 4.499A pdb=" N VAL K 264 " --> pdb=" O ALA K 260 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE K 267 " --> pdb=" O VAL K 263 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 295 removed outlier: 3.674A pdb=" N GLN K 290 " --> pdb=" O ASP K 287 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE K 292 " --> pdb=" O LEU K 289 " (cutoff:3.500A) Processing helix chain 'K' and resid 309 through 311 No H-bonds generated for 'chain 'K' and resid 309 through 311' Processing helix chain 'K' and resid 339 through 355 removed outlier: 4.514A pdb=" N LEU K 354 " --> pdb=" O LYS K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 364 Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 386 through 409 removed outlier: 3.697A pdb=" N GLU K 391 " --> pdb=" O ALA K 387 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA K 394 " --> pdb=" O LYS K 390 " (cutoff:3.500A) Processing helix chain 'K' and resid 417 through 427 removed outlier: 4.203A pdb=" N ALA K 425 " --> pdb=" O ARG K 421 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU K 426 " --> pdb=" O ALA K 422 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP K 427 " --> pdb=" O SER K 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 447 Processing helix chain 'K' and resid 449 through 458 Processing helix chain 'K' and resid 462 through 475 removed outlier: 4.066A pdb=" N LYS K 474 " --> pdb=" O LEU K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 492 through 495 No H-bonds generated for 'chain 'K' and resid 492 through 495' Processing helix chain 'K' and resid 501 through 519 Processing helix chain 'd' and resid 31 through 33 No H-bonds generated for 'chain 'd' and resid 31 through 33' Processing helix chain 'd' and resid 89 through 91 No H-bonds generated for 'chain 'd' and resid 89 through 91' Processing helix chain 'E' and resid 9 through 30 removed outlier: 3.727A pdb=" N ALA E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL E 27 " --> pdb=" O LEU E 23 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL E 29 " --> pdb=" O ASN E 25 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THR E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 removed outlier: 3.947A pdb=" N GLU E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 84 removed outlier: 3.672A pdb=" N GLU E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 109 Processing helix chain 'E' and resid 113 through 134 Processing helix chain 'E' and resid 141 through 151 Processing helix chain 'E' and resid 156 through 172 removed outlier: 6.168A pdb=" N LYS E 171 " --> pdb=" O GLU E 167 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASP E 172 " --> pdb=" O ALA E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 243 Proline residue: E 235 - end of helix removed outlier: 3.570A pdb=" N ARG E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 268 removed outlier: 3.569A pdb=" N THR E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL E 263 " --> pdb=" O LEU E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 296 removed outlier: 4.683A pdb=" N ASP E 287 " --> pdb=" O ARG E 284 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU E 289 " --> pdb=" O LYS E 286 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE E 294 " --> pdb=" O ASP E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 342 through 358 removed outlier: 5.095A pdb=" N SER E 358 " --> pdb=" O LEU E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 373 removed outlier: 3.733A pdb=" N LEU E 369 " --> pdb=" O LEU E 365 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 372 " --> pdb=" O ARG E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 409 removed outlier: 3.674A pdb=" N GLU E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 427 removed outlier: 3.514A pdb=" N GLU E 424 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA E 425 " --> pdb=" O ARG E 421 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP E 427 " --> pdb=" O SER E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 447 Processing helix chain 'E' and resid 449 through 457 Processing helix chain 'E' and resid 462 through 475 removed outlier: 4.281A pdb=" N LYS E 474 " --> pdb=" O LEU E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 495 No H-bonds generated for 'chain 'E' and resid 492 through 495' Processing helix chain 'E' and resid 501 through 520 removed outlier: 3.796A pdb=" N THR E 520 " --> pdb=" O GLY E 516 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 30 removed outlier: 3.601A pdb=" N ALA L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL L 29 " --> pdb=" O ASN L 25 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 59 removed outlier: 3.699A pdb=" N GLU L 59 " --> pdb=" O THR L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 85 removed outlier: 3.653A pdb=" N GLY L 70 " --> pdb=" O TYR L 66 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER L 82 " --> pdb=" O ALA L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 109 Processing helix chain 'L' and resid 113 through 134 Processing helix chain 'L' and resid 141 through 151 Processing helix chain 'L' and resid 156 through 167 Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 231 through 243 Proline residue: L 235 - end of helix removed outlier: 4.890A pdb=" N GLU L 238 " --> pdb=" O PRO L 235 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 268 removed outlier: 4.148A pdb=" N ILE L 267 " --> pdb=" O VAL L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 296 removed outlier: 3.508A pdb=" N ALA L 293 " --> pdb=" O GLN L 290 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR L 296 " --> pdb=" O ALA L 293 " (cutoff:3.500A) Processing helix chain 'L' and resid 303 through 305 No H-bonds generated for 'chain 'L' and resid 303 through 305' Processing helix chain 'L' and resid 339 through 355 removed outlier: 4.075A pdb=" N LEU L 354 " --> pdb=" O LYS L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 364 removed outlier: 3.776A pdb=" N LYS L 364 " --> pdb=" O TYR L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 367 through 373 removed outlier: 3.626A pdb=" N LEU L 372 " --> pdb=" O ARG L 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 386 through 409 removed outlier: 3.719A pdb=" N GLU L 391 " --> pdb=" O ALA L 387 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA L 394 " --> pdb=" O LYS L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 417 through 427 removed outlier: 4.260A pdb=" N ALA L 425 " --> pdb=" O ARG L 421 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU L 426 " --> pdb=" O ALA L 422 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP L 427 " --> pdb=" O SER L 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 434 through 447 Processing helix chain 'L' and resid 449 through 458 Processing helix chain 'L' and resid 462 through 475 removed outlier: 4.089A pdb=" N LYS L 474 " --> pdb=" O LEU L 470 " (cutoff:3.500A) Processing helix chain 'L' and resid 492 through 495 No H-bonds generated for 'chain 'L' and resid 492 through 495' Processing helix chain 'L' and resid 501 through 519 Processing helix chain 'F' and resid 9 through 30 removed outlier: 3.721A pdb=" N ALA F 26 " --> pdb=" O LYS F 22 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N THR F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 59 removed outlier: 3.804A pdb=" N GLU F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 84 removed outlier: 3.705A pdb=" N GLY F 70 " --> pdb=" O TYR F 66 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU F 76 " --> pdb=" O GLN F 72 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 109 removed outlier: 3.520A pdb=" N ARG F 105 " --> pdb=" O ASN F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 134 Processing helix chain 'F' and resid 141 through 151 Processing helix chain 'F' and resid 156 through 169 Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 231 through 243 Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 256 through 268 removed outlier: 3.948A pdb=" N THR F 261 " --> pdb=" O GLU F 257 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU F 262 " --> pdb=" O ALA F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 295 removed outlier: 3.798A pdb=" N ASP F 287 " --> pdb=" O ARG F 284 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU F 289 " --> pdb=" O LYS F 286 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN F 290 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU F 295 " --> pdb=" O ILE F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 339 through 358 removed outlier: 3.521A pdb=" N GLU F 347 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER F 358 " --> pdb=" O LEU F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 373 removed outlier: 3.746A pdb=" N LEU F 372 " --> pdb=" O ARG F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 409 removed outlier: 3.706A pdb=" N GLU F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 428 removed outlier: 4.205A pdb=" N ALA F 425 " --> pdb=" O ARG F 421 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP F 427 " --> pdb=" O SER F 423 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN F 428 " --> pdb=" O GLU F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 447 Processing helix chain 'F' and resid 449 through 457 Processing helix chain 'F' and resid 462 through 475 removed outlier: 4.271A pdb=" N LYS F 474 " --> pdb=" O LEU F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 495 No H-bonds generated for 'chain 'F' and resid 492 through 495' Processing helix chain 'F' and resid 501 through 520 removed outlier: 3.826A pdb=" N THR F 520 " --> pdb=" O GLY F 516 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 30 removed outlier: 3.670A pdb=" N ALA M 26 " --> pdb=" O LYS M 22 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL M 29 " --> pdb=" O ASN M 25 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 59 removed outlier: 3.741A pdb=" N GLU M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 85 removed outlier: 3.751A pdb=" N GLY M 70 " --> pdb=" O TYR M 66 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER M 82 " --> pdb=" O ALA M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 109 Processing helix chain 'M' and resid 113 through 134 Processing helix chain 'M' and resid 141 through 151 Processing helix chain 'M' and resid 156 through 169 Processing helix chain 'M' and resid 202 through 204 No H-bonds generated for 'chain 'M' and resid 202 through 204' Processing helix chain 'M' and resid 230 through 243 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 259 through 267 removed outlier: 3.755A pdb=" N VAL M 263 " --> pdb=" O LEU M 259 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N VAL M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE M 267 " --> pdb=" O VAL M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 285 through 295 Processing helix chain 'M' and resid 303 through 305 No H-bonds generated for 'chain 'M' and resid 303 through 305' Processing helix chain 'M' and resid 339 through 355 removed outlier: 3.526A pdb=" N ILE M 346 " --> pdb=" O ILE M 342 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU M 347 " --> pdb=" O GLN M 343 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN M 348 " --> pdb=" O ALA M 344 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU M 354 " --> pdb=" O LYS M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 373 removed outlier: 3.692A pdb=" N LYS M 364 " --> pdb=" O TYR M 360 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLU M 367 " --> pdb=" O GLU M 363 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG M 368 " --> pdb=" O LYS M 364 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU M 369 " --> pdb=" O LEU M 365 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA M 370 " --> pdb=" O GLN M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 386 through 409 removed outlier: 3.816A pdb=" N GLU M 391 " --> pdb=" O ALA M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 417 through 427 removed outlier: 4.257A pdb=" N ALA M 425 " --> pdb=" O ARG M 421 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU M 426 " --> pdb=" O ALA M 422 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP M 427 " --> pdb=" O SER M 423 " (cutoff:3.500A) Processing helix chain 'M' and resid 434 through 447 Processing helix chain 'M' and resid 449 through 458 Processing helix chain 'M' and resid 462 through 475 removed outlier: 3.997A pdb=" N LYS M 474 " --> pdb=" O LEU M 470 " (cutoff:3.500A) Processing helix chain 'M' and resid 492 through 495 No H-bonds generated for 'chain 'M' and resid 492 through 495' Processing helix chain 'M' and resid 501 through 519 Processing helix chain 'f' and resid 31 through 33 No H-bonds generated for 'chain 'f' and resid 31 through 33' Processing helix chain 'f' and resid 89 through 91 No H-bonds generated for 'chain 'f' and resid 89 through 91' Processing helix chain 'G' and resid 9 through 30 removed outlier: 3.628A pdb=" N ALA G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL G 29 " --> pdb=" O ASN G 25 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N THR G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 59 removed outlier: 3.757A pdb=" N GLU G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 84 removed outlier: 3.649A pdb=" N GLY G 70 " --> pdb=" O TYR G 66 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU G 76 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 109 Processing helix chain 'G' and resid 113 through 134 Processing helix chain 'G' and resid 141 through 151 Processing helix chain 'G' and resid 156 through 169 Processing helix chain 'G' and resid 230 through 243 Proline residue: G 235 - end of helix removed outlier: 3.559A pdb=" N ARG G 242 " --> pdb=" O GLU G 238 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA G 243 " --> pdb=" O ASN G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 268 removed outlier: 3.996A pdb=" N THR G 261 " --> pdb=" O GLU G 257 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU G 262 " --> pdb=" O ALA G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 296 removed outlier: 3.568A pdb=" N ARG G 285 " --> pdb=" O GLY G 282 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU G 289 " --> pdb=" O LYS G 286 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE G 294 " --> pdb=" O ASP G 291 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU G 295 " --> pdb=" O ILE G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 311 No H-bonds generated for 'chain 'G' and resid 309 through 311' Processing helix chain 'G' and resid 314 through 316 No H-bonds generated for 'chain 'G' and resid 314 through 316' Processing helix chain 'G' and resid 341 through 358 removed outlier: 5.372A pdb=" N SER G 358 " --> pdb=" O LEU G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 373 removed outlier: 3.757A pdb=" N LEU G 369 " --> pdb=" O LEU G 365 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU G 372 " --> pdb=" O ARG G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 409 removed outlier: 3.749A pdb=" N GLU G 391 " --> pdb=" O ALA G 387 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU G 408 " --> pdb=" O LYS G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 428 removed outlier: 3.511A pdb=" N GLU G 424 " --> pdb=" O VAL G 420 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA G 425 " --> pdb=" O ARG G 421 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU G 426 " --> pdb=" O ALA G 422 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP G 427 " --> pdb=" O SER G 423 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASN G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 447 Processing helix chain 'G' and resid 449 through 457 Processing helix chain 'G' and resid 462 through 475 removed outlier: 4.280A pdb=" N LYS G 474 " --> pdb=" O LEU G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 492 through 495 No H-bonds generated for 'chain 'G' and resid 492 through 495' Processing helix chain 'G' and resid 501 through 520 removed outlier: 3.794A pdb=" N THR G 520 " --> pdb=" O GLY G 516 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 30 removed outlier: 3.591A pdb=" N ALA N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL N 29 " --> pdb=" O ASN N 25 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N THR N 30 " --> pdb=" O ALA N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 54 through 59 removed outlier: 3.656A pdb=" N GLU N 59 " --> pdb=" O THR N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 85 removed outlier: 3.623A pdb=" N GLY N 70 " --> pdb=" O TYR N 66 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER N 82 " --> pdb=" O ALA N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 109 Processing helix chain 'N' and resid 113 through 134 Processing helix chain 'N' and resid 141 through 151 Processing helix chain 'N' and resid 156 through 169 Processing helix chain 'N' and resid 202 through 204 No H-bonds generated for 'chain 'N' and resid 202 through 204' Processing helix chain 'N' and resid 230 through 243 Proline residue: N 235 - end of helix removed outlier: 3.613A pdb=" N ASN N 239 " --> pdb=" O PRO N 235 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 268 removed outlier: 5.009A pdb=" N VAL N 264 " --> pdb=" O ALA N 260 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE N 267 " --> pdb=" O VAL N 263 " (cutoff:3.500A) Processing helix chain 'N' and resid 282 through 296 removed outlier: 4.164A pdb=" N THR N 296 " --> pdb=" O ALA N 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 303 through 305 No H-bonds generated for 'chain 'N' and resid 303 through 305' Processing helix chain 'N' and resid 339 through 355 removed outlier: 4.044A pdb=" N GLU N 347 " --> pdb=" O GLN N 343 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN N 348 " --> pdb=" O ALA N 344 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE N 349 " --> pdb=" O ARG N 345 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU N 354 " --> pdb=" O LYS N 350 " (cutoff:3.500A) Processing helix chain 'N' and resid 359 through 364 removed outlier: 3.768A pdb=" N LYS N 364 " --> pdb=" O TYR N 360 " (cutoff:3.500A) Processing helix chain 'N' and resid 368 through 373 Processing helix chain 'N' and resid 386 through 409 removed outlier: 3.748A pdb=" N GLU N 391 " --> pdb=" O ALA N 387 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA N 394 " --> pdb=" O LYS N 390 " (cutoff:3.500A) Processing helix chain 'N' and resid 417 through 427 removed outlier: 4.262A pdb=" N ALA N 425 " --> pdb=" O ARG N 421 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU N 426 " --> pdb=" O ALA N 422 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP N 427 " --> pdb=" O SER N 423 " (cutoff:3.500A) Processing helix chain 'N' and resid 434 through 447 Processing helix chain 'N' and resid 449 through 458 Processing helix chain 'N' and resid 462 through 475 removed outlier: 4.321A pdb=" N LYS N 474 " --> pdb=" O LEU N 470 " (cutoff:3.500A) Processing helix chain 'N' and resid 492 through 495 No H-bonds generated for 'chain 'N' and resid 492 through 495' Processing helix chain 'N' and resid 501 through 520 removed outlier: 3.696A pdb=" N THR N 520 " --> pdb=" O GLY N 516 " (cutoff:3.500A) Processing helix chain 'g' and resid 31 through 33 No H-bonds generated for 'chain 'g' and resid 31 through 33' Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 Processing sheet with id= B, first strand: chain 'A' and resid 38 through 40 Processing sheet with id= C, first strand: chain 'A' and resid 174 through 179 Processing sheet with id= D, first strand: chain 'A' and resid 193 through 195 Processing sheet with id= E, first strand: chain 'A' and resid 219 through 222 Processing sheet with id= F, first strand: chain 'A' and resid 411 through 413 Processing sheet with id= G, first strand: chain 'A' and resid 480 through 483 Processing sheet with id= H, first strand: chain 'H' and resid 4 through 8 Processing sheet with id= I, first strand: chain 'H' and resid 38 through 40 Processing sheet with id= J, first strand: chain 'H' and resid 175 through 180 removed outlier: 6.034A pdb=" N ALA H 377 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLU H 178 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE H 379 " --> pdb=" O GLU H 178 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N SER H 180 " --> pdb=" O ILE H 379 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL H 381 " --> pdb=" O SER H 180 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL H 190 " --> pdb=" O VAL H 376 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 192 through 195 Processing sheet with id= L, first strand: chain 'H' and resid 219 through 222 removed outlier: 7.184A pdb=" N CYS H 274 " --> pdb=" O ILE H 249 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 411 through 413 Processing sheet with id= N, first strand: chain 'H' and resid 480 through 483 removed outlier: 3.542A pdb=" N ASP H 488 " --> pdb=" O ASP H 483 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'a' and resid 85 through 88 removed outlier: 6.129A pdb=" N LYS a 14 " --> pdb=" O VAL a 42 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL a 42 " --> pdb=" O LYS a 14 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA a 94 " --> pdb=" O VAL a 68 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 4 through 8 Processing sheet with id= Q, first strand: chain 'B' and resid 38 through 40 Processing sheet with id= R, first strand: chain 'B' and resid 174 through 179 removed outlier: 3.535A pdb=" N VAL B 376 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 193 through 195 Processing sheet with id= T, first strand: chain 'B' and resid 219 through 222 removed outlier: 3.561A pdb=" N ALA B 251 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 411 through 413 Processing sheet with id= V, first strand: chain 'B' and resid 480 through 483 Processing sheet with id= W, first strand: chain 'I' and resid 4 through 8 Processing sheet with id= X, first strand: chain 'I' and resid 38 through 40 Processing sheet with id= Y, first strand: chain 'I' and resid 175 through 179 removed outlier: 6.124A pdb=" N ALA I 377 " --> pdb=" O THR I 176 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLU I 178 " --> pdb=" O ALA I 377 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE I 379 " --> pdb=" O GLU I 178 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 193 through 195 removed outlier: 4.272A pdb=" N VAL I 323 " --> pdb=" O LEU I 215 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU I 215 " --> pdb=" O VAL I 323 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 218 through 222 removed outlier: 7.898A pdb=" N LEU I 221 " --> pdb=" O PRO I 246 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU I 248 " --> pdb=" O LEU I 221 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N CYS I 274 " --> pdb=" O ILE I 249 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ALA I 251 " --> pdb=" O CYS I 274 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL I 276 " --> pdb=" O ALA I 251 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'I' and resid 411 through 413 Processing sheet with id= AC, first strand: chain 'I' and resid 480 through 483 removed outlier: 3.798A pdb=" N ASP I 488 " --> pdb=" O ASP I 483 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'b' and resid 85 through 88 removed outlier: 3.934A pdb=" N ALA b 44 " --> pdb=" O VAL b 12 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS b 14 " --> pdb=" O VAL b 42 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VAL b 42 " --> pdb=" O LYS b 14 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'b' and resid 77 through 79 Processing sheet with id= AF, first strand: chain 'C' and resid 4 through 8 Processing sheet with id= AG, first strand: chain 'C' and resid 38 through 40 Processing sheet with id= AH, first strand: chain 'C' and resid 174 through 179 removed outlier: 3.509A pdb=" N VAL C 376 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 193 through 195 removed outlier: 3.530A pdb=" N ASN C 329 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 219 through 222 Processing sheet with id= AK, first strand: chain 'C' and resid 411 through 413 Processing sheet with id= AL, first strand: chain 'C' and resid 480 through 483 Processing sheet with id= AM, first strand: chain 'J' and resid 4 through 8 Processing sheet with id= AN, first strand: chain 'J' and resid 38 through 40 Processing sheet with id= AO, first strand: chain 'J' and resid 175 through 179 removed outlier: 6.483A pdb=" N ALA J 377 " --> pdb=" O THR J 176 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLU J 178 " --> pdb=" O ALA J 377 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE J 379 " --> pdb=" O GLU J 178 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'J' and resid 193 through 195 removed outlier: 3.501A pdb=" N ILE J 332 " --> pdb=" O MET J 193 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL J 323 " --> pdb=" O LEU J 215 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA J 213 " --> pdb=" O VAL J 325 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'J' and resid 219 through 222 removed outlier: 7.251A pdb=" N CYS J 274 " --> pdb=" O ILE J 249 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ALA J 251 " --> pdb=" O CYS J 274 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL J 276 " --> pdb=" O ALA J 251 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'J' and resid 411 through 413 Processing sheet with id= AS, first strand: chain 'J' and resid 480 through 483 Processing sheet with id= AT, first strand: chain 'c' and resid 85 through 88 removed outlier: 3.746A pdb=" N ALA c 44 " --> pdb=" O VAL c 12 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS c 14 " --> pdb=" O VAL c 42 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL c 42 " --> pdb=" O LYS c 14 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'c' and resid 77 through 79 Processing sheet with id= AV, first strand: chain 'D' and resid 4 through 8 Processing sheet with id= AW, first strand: chain 'D' and resid 38 through 40 Processing sheet with id= AX, first strand: chain 'D' and resid 174 through 179 Processing sheet with id= AY, first strand: chain 'D' and resid 193 through 195 removed outlier: 3.532A pdb=" N ASN D 329 " --> pdb=" O ASP D 326 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'D' and resid 219 through 222 Processing sheet with id= BA, first strand: chain 'D' and resid 411 through 413 Processing sheet with id= BB, first strand: chain 'D' and resid 480 through 483 Processing sheet with id= BC, first strand: chain 'K' and resid 4 through 8 Processing sheet with id= BD, first strand: chain 'K' and resid 38 through 40 Processing sheet with id= BE, first strand: chain 'K' and resid 175 through 179 removed outlier: 6.194A pdb=" N ALA K 377 " --> pdb=" O THR K 176 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLU K 178 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ILE K 379 " --> pdb=" O GLU K 178 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'K' and resid 193 through 195 removed outlier: 3.989A pdb=" N MET K 193 " --> pdb=" O ILE K 332 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE K 332 " --> pdb=" O MET K 193 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR K 330 " --> pdb=" O PHE K 195 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL K 323 " --> pdb=" O LEU K 215 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'K' and resid 219 through 222 removed outlier: 6.905A pdb=" N CYS K 274 " --> pdb=" O ILE K 249 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'K' and resid 411 through 413 Processing sheet with id= BI, first strand: chain 'K' and resid 480 through 483 removed outlier: 3.819A pdb=" N ASP K 488 " --> pdb=" O ASP K 483 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'd' and resid 85 through 88 removed outlier: 6.371A pdb=" N LYS d 14 " --> pdb=" O VAL d 42 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL d 42 " --> pdb=" O LYS d 14 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'E' and resid 4 through 8 Processing sheet with id= BL, first strand: chain 'E' and resid 38 through 40 Processing sheet with id= BM, first strand: chain 'E' and resid 174 through 179 Processing sheet with id= BN, first strand: chain 'E' and resid 193 through 195 removed outlier: 3.501A pdb=" N LEU E 215 " --> pdb=" O VAL E 323 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'E' and resid 219 through 222 Processing sheet with id= BP, first strand: chain 'E' and resid 411 through 413 Processing sheet with id= BQ, first strand: chain 'E' and resid 480 through 483 Processing sheet with id= BR, first strand: chain 'L' and resid 4 through 8 Processing sheet with id= BS, first strand: chain 'L' and resid 38 through 40 Processing sheet with id= BT, first strand: chain 'L' and resid 175 through 179 removed outlier: 6.155A pdb=" N ALA L 377 " --> pdb=" O THR L 176 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU L 178 " --> pdb=" O ALA L 377 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE L 379 " --> pdb=" O GLU L 178 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'L' and resid 193 through 195 removed outlier: 3.505A pdb=" N ILE L 332 " --> pdb=" O MET L 193 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'L' and resid 219 through 222 removed outlier: 6.561A pdb=" N CYS L 274 " --> pdb=" O ILE L 249 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ALA L 251 " --> pdb=" O CYS L 274 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL L 276 " --> pdb=" O ALA L 251 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'L' and resid 411 through 413 Processing sheet with id= BX, first strand: chain 'L' and resid 480 through 483 removed outlier: 3.840A pdb=" N ASP L 488 " --> pdb=" O ASP L 483 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'e' and resid 75 through 79 removed outlier: 9.015A pdb=" N LYS e 83 " --> pdb=" O ARG e 15 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG e 15 " --> pdb=" O LYS e 83 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LYS e 14 " --> pdb=" O VAL e 42 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL e 42 " --> pdb=" O LYS e 14 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA e 94 " --> pdb=" O VAL e 68 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= CA, first strand: chain 'F' and resid 38 through 40 Processing sheet with id= CB, first strand: chain 'F' and resid 174 through 179 Processing sheet with id= CC, first strand: chain 'F' and resid 193 through 195 removed outlier: 3.597A pdb=" N ASN F 329 " --> pdb=" O ASP F 326 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL F 323 " --> pdb=" O LEU F 215 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU F 215 " --> pdb=" O VAL F 323 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'F' and resid 219 through 222 removed outlier: 3.529A pdb=" N ALA F 251 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'F' and resid 411 through 413 Processing sheet with id= CF, first strand: chain 'F' and resid 480 through 483 Processing sheet with id= CG, first strand: chain 'M' and resid 4 through 8 Processing sheet with id= CH, first strand: chain 'M' and resid 38 through 40 Processing sheet with id= CI, first strand: chain 'M' and resid 176 through 179 Processing sheet with id= CJ, first strand: chain 'M' and resid 193 through 195 removed outlier: 3.604A pdb=" N MET M 193 " --> pdb=" O ILE M 332 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'M' and resid 219 through 222 removed outlier: 7.658A pdb=" N CYS M 274 " --> pdb=" O ILE M 249 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N ALA M 251 " --> pdb=" O CYS M 274 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL M 276 " --> pdb=" O ALA M 251 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'M' and resid 411 through 413 Processing sheet with id= CM, first strand: chain 'M' and resid 480 through 483 removed outlier: 3.510A pdb=" N ASP M 488 " --> pdb=" O ASP M 483 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'f' and resid 85 through 88 removed outlier: 3.745A pdb=" N ALA f 44 " --> pdb=" O VAL f 12 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS f 14 " --> pdb=" O VAL f 42 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL f 42 " --> pdb=" O LYS f 14 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA f 94 " --> pdb=" O VAL f 68 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'f' and resid 77 through 79 Processing sheet with id= CP, first strand: chain 'G' and resid 4 through 8 Processing sheet with id= CQ, first strand: chain 'G' and resid 38 through 40 Processing sheet with id= CR, first strand: chain 'G' and resid 174 through 179 Processing sheet with id= CS, first strand: chain 'G' and resid 193 through 195 removed outlier: 3.594A pdb=" N ASN G 329 " --> pdb=" O ASP G 326 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'G' and resid 219 through 222 Processing sheet with id= CU, first strand: chain 'G' and resid 411 through 413 Processing sheet with id= CV, first strand: chain 'G' and resid 480 through 483 Processing sheet with id= CW, first strand: chain 'N' and resid 4 through 8 Processing sheet with id= CX, first strand: chain 'N' and resid 38 through 40 Processing sheet with id= CY, first strand: chain 'N' and resid 175 through 178 removed outlier: 6.213A pdb=" N ALA N 377 " --> pdb=" O THR N 176 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLU N 178 " --> pdb=" O ALA N 377 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE N 379 " --> pdb=" O GLU N 178 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'N' and resid 193 through 195 removed outlier: 3.645A pdb=" N THR N 330 " --> pdb=" O PHE N 195 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA N 213 " --> pdb=" O VAL N 325 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'N' and resid 219 through 222 Processing sheet with id= DB, first strand: chain 'N' and resid 411 through 413 Processing sheet with id= DC, first strand: chain 'N' and resid 480 through 483 removed outlier: 3.502A pdb=" N ASP N 488 " --> pdb=" O ASP N 483 " (cutoff:3.500A) Processing sheet with id= DD, first strand: chain 'g' and resid 85 through 88 removed outlier: 6.232A pdb=" N LYS g 14 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL g 42 " --> pdb=" O LYS g 14 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA g 94 " --> pdb=" O VAL g 68 " (cutoff:3.500A) Processing sheet with id= DE, first strand: chain 'g' and resid 77 through 79 3069 hydrogen bonds defined for protein. 8502 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.62 Time building geometry restraints manager: 20.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 19469 1.34 - 1.46: 7678 1.46 - 1.58: 34109 1.58 - 1.70: 57 1.70 - 1.82: 294 Bond restraints: 61607 Sorted by residual: bond pdb=" CB GLU c 76 " pdb=" CG GLU c 76 " ideal model delta sigma weight residual 1.520 1.584 -0.064 3.00e-02 1.11e+03 4.50e+00 bond pdb=" CA ASN d 70 " pdb=" CB ASN d 70 " ideal model delta sigma weight residual 1.527 1.550 -0.024 1.15e-02 7.56e+03 4.24e+00 bond pdb=" N ASP g 80 " pdb=" CA ASP g 80 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.29e-02 6.01e+03 2.58e+00 bond pdb=" C ARG A 284 " pdb=" O ARG A 284 " ideal model delta sigma weight residual 1.236 1.213 0.024 1.47e-02 4.63e+03 2.57e+00 bond pdb=" C LEU A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.36e-02 5.41e+03 2.56e+00 ... (remaining 61602 not shown) Histogram of bond angle deviations from ideal: 96.40 - 103.98: 738 103.98 - 111.56: 28580 111.56 - 119.14: 23552 119.14 - 126.72: 29942 126.72 - 134.30: 446 Bond angle restraints: 83258 Sorted by residual: angle pdb=" CA GLU c 76 " pdb=" CB GLU c 76 " pdb=" CG GLU c 76 " ideal model delta sigma weight residual 114.10 125.74 -11.64 2.00e+00 2.50e-01 3.39e+01 angle pdb=" C THR I 206 " pdb=" N ASN I 207 " pdb=" CA ASN I 207 " ideal model delta sigma weight residual 120.09 127.21 -7.12 1.25e+00 6.40e-01 3.24e+01 angle pdb=" CA LYS D 231 " pdb=" CB LYS D 231 " pdb=" CG LYS D 231 " ideal model delta sigma weight residual 114.10 123.67 -9.57 2.00e+00 2.50e-01 2.29e+01 angle pdb=" CB GLU c 76 " pdb=" CG GLU c 76 " pdb=" CD GLU c 76 " ideal model delta sigma weight residual 112.60 120.29 -7.69 1.70e+00 3.46e-01 2.05e+01 angle pdb=" CA LYS G 231 " pdb=" CB LYS G 231 " pdb=" CG LYS G 231 " ideal model delta sigma weight residual 114.10 122.87 -8.77 2.00e+00 2.50e-01 1.92e+01 ... (remaining 83253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 34422 17.87 - 35.73: 2890 35.73 - 53.60: 758 53.60 - 71.47: 215 71.47 - 89.33: 152 Dihedral angle restraints: 38437 sinusoidal: 15561 harmonic: 22876 Sorted by residual: dihedral pdb=" CA ILE c 86 " pdb=" C ILE c 86 " pdb=" N MET c 87 " pdb=" CA MET c 87 " ideal model delta harmonic sigma weight residual 180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA TYR C 223 " pdb=" C TYR C 223 " pdb=" N GLU C 224 " pdb=" CA GLU C 224 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ARG A 285 " pdb=" C ARG A 285 " pdb=" N LYS A 286 " pdb=" CA LYS A 286 " ideal model delta harmonic sigma weight residual 180.00 -159.81 -20.19 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 38434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 7320 0.040 - 0.081: 1896 0.081 - 0.121: 704 0.121 - 0.162: 84 0.162 - 0.202: 6 Chirality restraints: 10010 Sorted by residual: chirality pdb=" CA GLU d 17 " pdb=" N GLU d 17 " pdb=" C GLU d 17 " pdb=" CB GLU d 17 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLU c 76 " pdb=" N GLU c 76 " pdb=" C GLU c 76 " pdb=" CB GLU c 76 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CB ILE G 307 " pdb=" CA ILE G 307 " pdb=" CG1 ILE G 307 " pdb=" CG2 ILE G 307 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 10007 not shown) Planarity restraints: 10668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU c 76 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" CD GLU c 76 " -0.070 2.00e-02 2.50e+03 pdb=" OE1 GLU c 76 " 0.026 2.00e-02 2.50e+03 pdb=" OE2 GLU c 76 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU d 17 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" CD GLU d 17 " -0.058 2.00e-02 2.50e+03 pdb=" OE1 GLU d 17 " 0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU d 17 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN d 70 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C ASN d 70 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN d 70 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS d 71 " -0.013 2.00e-02 2.50e+03 ... (remaining 10665 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.64: 790 2.64 - 3.27: 66185 3.27 - 3.89: 120050 3.89 - 4.52: 162295 4.52 - 5.14: 251372 Nonbonded interactions: 600692 Sorted by model distance: nonbonded pdb="MG MG H 601 " pdb=" O1G ANP H 603 " model vdw 2.017 2.170 nonbonded pdb="MG MG J 601 " pdb=" O1G ANP J 603 " model vdw 2.036 2.170 nonbonded pdb="MG MG M 601 " pdb=" O1G ANP M 603 " model vdw 2.037 2.170 nonbonded pdb="MG MG N 601 " pdb=" O1G ANP N 603 " model vdw 2.043 2.170 nonbonded pdb="MG MG I 601 " pdb=" O1G ANP I 603 " model vdw 2.049 2.170 ... (remaining 600687 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 529 or resid 602)) selection = (chain 'B' and (resid 3 through 529 or resid 602)) selection = (chain 'C' and (resid 3 through 529 or resid 602)) selection = (chain 'D' and (resid 3 through 529 or resid 602)) selection = (chain 'E' and (resid 3 through 529 or resid 602)) selection = (chain 'F' and (resid 3 through 529 or resid 602)) selection = (chain 'G' and (resid 3 through 529 or resid 602)) selection = (chain 'H' and (resid 3 through 529 or resid 603)) selection = (chain 'I' and (resid 3 through 529 or resid 603)) selection = (chain 'J' and (resid 3 through 529 or resid 603)) selection = (chain 'K' and (resid 3 through 529 or resid 603)) selection = (chain 'L' and (resid 3 through 529 or resid 603)) selection = (chain 'M' and (resid 3 through 529 or resid 603)) selection = (chain 'N' and (resid 3 through 529 or resid 603)) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.200 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: 0.060 Extract box with map and model: 27.550 Check model and map are aligned: 0.400 Set scattering table: 0.420 Process input model: 130.840 Find NCS groups from input model: 3.910 Set up NCS constraints: 0.600 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 181.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 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 : 0.003 0.064 61607 Z= 0.182 Angle : 0.634 12.525 83258 Z= 0.345 Chirality : 0.042 0.202 10010 Planarity : 0.004 0.050 10668 Dihedral : 16.056 89.332 23737 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.39 % Favored : 97.54 % Rotamer: Outliers : 1.06 % Allowed : 15.10 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.09), residues: 8008 helix: 1.14 (0.08), residues: 3722 sheet: 0.09 (0.16), residues: 1090 loop : 0.22 (0.11), residues: 3196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 44 HIS 0.003 0.000 HIS H 266 PHE 0.016 0.001 PHE F 281 TYR 0.018 0.001 TYR C 223 ARG 0.012 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 532 time to evaluate : 5.183 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: H 189 THR cc_start: 0.9164 (p) cc_final: 0.8876 (m) REVERT: B 223 TYR cc_start: 0.8417 (t80) cc_final: 0.7859 (t80) REVERT: I 395 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8572 (mtm110) REVERT: C 114 MET cc_start: 0.9280 (tpp) cc_final: 0.8988 (tpp) REVERT: C 223 TYR cc_start: 0.7756 (t80) cc_final: 0.7541 (t80) REVERT: c 69 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: c 84 TYR cc_start: 0.8510 (m-80) cc_final: 0.8270 (m-80) REVERT: c 85 LEU cc_start: 0.9031 (pt) cc_final: 0.8829 (pt) REVERT: D 114 MET cc_start: 0.9305 (tpp) cc_final: 0.9053 (tpt) REVERT: D 172 ASP cc_start: 0.7682 (p0) cc_final: 0.7433 (p0) REVERT: D 223 TYR cc_start: 0.8414 (t80) cc_final: 0.8146 (t80) REVERT: D 368 ARG cc_start: 0.8232 (ttp80) cc_final: 0.7923 (ttp80) REVERT: K 348 GLN cc_start: 0.6328 (OUTLIER) cc_final: 0.6099 (pt0) REVERT: K 395 ARG cc_start: 0.8486 (ttp80) cc_final: 0.7990 (ttp80) REVERT: d 69 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7213 (m-80) REVERT: E 229 ASN cc_start: 0.8095 (m110) cc_final: 0.7528 (p0) REVERT: L 121 ASP cc_start: 0.8640 (m-30) cc_final: 0.8308 (m-30) REVERT: L 316 MET cc_start: 0.4363 (ppp) cc_final: 0.3981 (pmm) REVERT: F 199 TYR cc_start: 0.7064 (OUTLIER) cc_final: 0.6626 (t80) REVERT: M 395 ARG cc_start: 0.8540 (ttp80) cc_final: 0.7820 (ttp80) REVERT: f 56 ILE cc_start: 0.9389 (mp) cc_final: 0.9170 (mp) REVERT: f 69 PHE cc_start: 0.8406 (m-80) cc_final: 0.7908 (m-80) REVERT: f 84 TYR cc_start: 0.8182 (m-80) cc_final: 0.7824 (m-80) outliers start: 68 outliers final: 49 residues processed: 588 average time/residue: 1.3443 time to fit residues: 1020.5702 Evaluate side-chains 521 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 468 time to evaluate : 5.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain a residue 32 THR Chi-restraints excluded: chain a residue 72 TYR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 90 ASP Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 348 GLN Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain d residue 75 THR Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain e residue 69 PHE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 352 GLN Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 289 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 667 optimal weight: 0.7980 chunk 599 optimal weight: 0.9990 chunk 332 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 404 optimal weight: 1.9990 chunk 320 optimal weight: 0.0970 chunk 619 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 376 optimal weight: 8.9990 chunk 461 optimal weight: 4.9990 chunk 718 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 55 GLN c 55 GLN D 366 GLN ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 55 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 61607 Z= 0.184 Angle : 0.580 9.550 83258 Z= 0.300 Chirality : 0.044 0.179 10010 Planarity : 0.004 0.050 10668 Dihedral : 10.043 63.528 9050 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.47 % Favored : 97.47 % Rotamer: Outliers : 2.77 % Allowed : 13.79 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.09), residues: 8008 helix: 1.43 (0.08), residues: 3858 sheet: 0.26 (0.16), residues: 1051 loop : 0.08 (0.11), residues: 3099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 44 HIS 0.002 0.001 HIS G 266 PHE 0.016 0.001 PHE G 195 TYR 0.018 0.001 TYR c 72 ARG 0.015 0.000 ARG G 284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 514 time to evaluate : 5.136 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 199 TYR cc_start: 0.7179 (OUTLIER) cc_final: 0.6895 (t80) REVERT: A 225 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8990 (mppt) REVERT: H 189 THR cc_start: 0.9150 (p) cc_final: 0.8822 (m) REVERT: B 223 TYR cc_start: 0.8357 (t80) cc_final: 0.7860 (t80) REVERT: B 303 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8178 (pt0) REVERT: B 345 ARG cc_start: 0.9147 (tpt-90) cc_final: 0.8945 (tpt-90) REVERT: I 143 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: I 475 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: C 199 TYR cc_start: 0.7524 (OUTLIER) cc_final: 0.7303 (t80) REVERT: C 223 TYR cc_start: 0.7726 (t80) cc_final: 0.7363 (t80) REVERT: C 234 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9270 (mp) REVERT: J 143 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: J 193 MET cc_start: 0.3022 (mmt) cc_final: 0.0673 (pmm) REVERT: J 475 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: c 5 ARG cc_start: 0.8187 (ptt90) cc_final: 0.7920 (ptm160) REVERT: c 69 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: c 84 TYR cc_start: 0.8455 (m-80) cc_final: 0.8097 (m-80) REVERT: c 87 MET cc_start: 0.6628 (tpt) cc_final: 0.6230 (tpt) REVERT: D 172 ASP cc_start: 0.7592 (p0) cc_final: 0.7295 (p0) REVERT: D 223 TYR cc_start: 0.8451 (t80) cc_final: 0.8069 (t80) REVERT: D 272 ARG cc_start: 0.8696 (mtm180) cc_final: 0.7965 (ptt-90) REVERT: K 348 GLN cc_start: 0.6296 (OUTLIER) cc_final: 0.6082 (pt0) REVERT: K 395 ARG cc_start: 0.8557 (ttp80) cc_final: 0.8020 (ttp80) REVERT: d 69 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7658 (m-80) REVERT: d 93 LEU cc_start: 0.8492 (mp) cc_final: 0.7966 (mp) REVERT: E 52 ASP cc_start: 0.9184 (OUTLIER) cc_final: 0.8889 (m-30) REVERT: E 199 TYR cc_start: 0.7462 (OUTLIER) cc_final: 0.6858 (t80) REVERT: E 272 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8321 (ptt-90) REVERT: L 193 MET cc_start: 0.4583 (ppp) cc_final: 0.4218 (mmm) REVERT: L 316 MET cc_start: 0.4346 (ppp) cc_final: 0.4015 (pmm) REVERT: F 199 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6679 (t80) REVERT: F 225 LYS cc_start: 0.8898 (mtmm) cc_final: 0.8615 (mppt) REVERT: M 143 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: M 391 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8209 (pm20) REVERT: f 87 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.5834 (tmt) REVERT: G 52 ASP cc_start: 0.9231 (OUTLIER) cc_final: 0.8839 (m-30) REVERT: G 199 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.6192 (t80) REVERT: G 284 ARG cc_start: 0.8653 (tmm160) cc_final: 0.8033 (tmm160) REVERT: G 345 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8650 (tpp80) REVERT: N 193 MET cc_start: 0.5124 (mpt) cc_final: 0.4296 (ppp) REVERT: N 395 ARG cc_start: 0.8550 (ttp80) cc_final: 0.7700 (ttt90) outliers start: 178 outliers final: 60 residues processed: 653 average time/residue: 1.2965 time to fit residues: 1103.9395 Evaluate side-chains 544 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 463 time to evaluate : 5.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain a residue 72 TYR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 475 GLU Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 52 SER Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 475 GLU Chi-restraints excluded: chain c residue 15 ARG Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 348 GLN Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 52 SER Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain e residue 57 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 391 GLU Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain f residue 87 MET Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 352 GLN Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 90 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 399 optimal weight: 8.9990 chunk 222 optimal weight: 20.0000 chunk 597 optimal weight: 7.9990 chunk 489 optimal weight: 0.9980 chunk 198 optimal weight: 20.0000 chunk 719 optimal weight: 0.2980 chunk 777 optimal weight: 0.0000 chunk 640 optimal weight: 40.0000 chunk 713 optimal weight: 20.0000 chunk 245 optimal weight: 7.9990 chunk 577 optimal weight: 4.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 348 GLN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN f 19 GLN ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 55 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 61607 Z= 0.324 Angle : 0.592 10.806 83258 Z= 0.300 Chirality : 0.045 0.188 10010 Planarity : 0.004 0.056 10668 Dihedral : 9.305 59.780 9019 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 3.22 % Allowed : 14.13 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.09), residues: 8008 helix: 1.49 (0.08), residues: 3874 sheet: 0.06 (0.17), residues: 938 loop : 0.06 (0.11), residues: 3196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 44 HIS 0.003 0.001 HIS J 401 PHE 0.013 0.001 PHE A 195 TYR 0.016 0.001 TYR a 84 ARG 0.007 0.000 ARG G 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 478 time to evaluate : 5.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 TYR cc_start: 0.7162 (OUTLIER) cc_final: 0.6750 (t80) REVERT: A 225 LYS cc_start: 0.9259 (mmmm) cc_final: 0.8998 (mppt) REVERT: A 345 ARG cc_start: 0.8817 (mtp-110) cc_final: 0.8489 (ttm110) REVERT: H 395 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8281 (ttp80) REVERT: a 82 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7214 (tm-30) REVERT: B 223 TYR cc_start: 0.8473 (t80) cc_final: 0.8032 (t80) REVERT: B 226 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8053 (mmmt) REVERT: B 303 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8185 (pt0) REVERT: I 5 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8657 (ttmt) REVERT: I 143 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: I 475 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: b 84 TYR cc_start: 0.7214 (m-10) cc_final: 0.6953 (m-10) REVERT: C 199 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.7267 (t80) REVERT: C 223 TYR cc_start: 0.7929 (t80) cc_final: 0.7663 (t80) REVERT: J 143 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: J 201 SER cc_start: 0.1152 (OUTLIER) cc_final: 0.0930 (p) REVERT: J 211 MET cc_start: 0.6444 (mpt) cc_final: 0.5978 (tpt) REVERT: c 5 ARG cc_start: 0.8303 (ptt90) cc_final: 0.8073 (ptm160) REVERT: c 69 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7770 (m-80) REVERT: c 84 TYR cc_start: 0.8393 (m-80) cc_final: 0.8080 (m-80) REVERT: c 87 MET cc_start: 0.6558 (tpt) cc_final: 0.6338 (tpt) REVERT: D 172 ASP cc_start: 0.7482 (p0) cc_final: 0.7248 (p0) REVERT: d 69 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: d 84 TYR cc_start: 0.7811 (m-80) cc_final: 0.7376 (m-80) REVERT: E 199 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.6899 (t80) REVERT: E 272 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8250 (ptt-90) REVERT: L 143 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: L 211 MET cc_start: 0.4525 (OUTLIER) cc_final: 0.4296 (tmt) REVERT: L 316 MET cc_start: 0.4389 (ppp) cc_final: 0.4135 (pmm) REVERT: e 84 TYR cc_start: 0.7145 (m-80) cc_final: 0.6833 (m-10) REVERT: F 199 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.6643 (t80) REVERT: F 225 LYS cc_start: 0.8840 (mtmm) cc_final: 0.8543 (mppt) REVERT: M 143 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: f 51 LEU cc_start: 0.8001 (mt) cc_final: 0.7668 (mp) REVERT: G 199 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.6732 (t80) REVERT: G 284 ARG cc_start: 0.8541 (tmm160) cc_final: 0.8188 (tmm160) REVERT: G 345 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8317 (mmm160) REVERT: N 193 MET cc_start: 0.5050 (mpt) cc_final: 0.4257 (ppp) REVERT: N 379 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8391 (mm) outliers start: 207 outliers final: 90 residues processed: 631 average time/residue: 1.2940 time to fit residues: 1066.6502 Evaluate side-chains 557 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 445 time to evaluate : 5.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 32 THR Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain a residue 72 TYR Chi-restraints excluded: chain a residue 82 GLU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 475 GLU Chi-restraints excluded: chain b residue 25 SER Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 52 SER Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 58 SER Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 316 MET Chi-restraints excluded: chain K residue 348 GLN Chi-restraints excluded: chain K residue 356 THR Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 52 SER Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 68 VAL Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 211 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain e residue 57 VAL Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 72 TYR Chi-restraints excluded: chain e residue 92 VAL Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 379 ILE Chi-restraints excluded: chain g residue 57 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 710 optimal weight: 5.9990 chunk 541 optimal weight: 30.0000 chunk 373 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 343 optimal weight: 2.9990 chunk 483 optimal weight: 20.0000 chunk 722 optimal weight: 6.9990 chunk 764 optimal weight: 8.9990 chunk 377 optimal weight: 3.9990 chunk 684 optimal weight: 0.7980 chunk 206 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 GLN D 366 GLN ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 ASN G 283 GLN ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 55 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 61607 Z= 0.273 Angle : 0.578 10.507 83258 Z= 0.290 Chirality : 0.044 0.173 10010 Planarity : 0.004 0.057 10668 Dihedral : 8.450 57.931 9014 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.57 % Favored : 97.35 % Rotamer: Outliers : 3.21 % Allowed : 14.94 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.09), residues: 8008 helix: 1.53 (0.08), residues: 3904 sheet: -0.04 (0.16), residues: 1009 loop : -0.06 (0.11), residues: 3095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 44 HIS 0.002 0.001 HIS J 401 PHE 0.013 0.001 PHE A 195 TYR 0.019 0.001 TYR d 72 ARG 0.007 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 476 time to evaluate : 5.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7600 (p0) cc_final: 0.7379 (p0) REVERT: A 199 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.6679 (t80) REVERT: A 225 LYS cc_start: 0.9277 (mmmm) cc_final: 0.9000 (mppt) REVERT: A 226 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8339 (mtpp) REVERT: A 231 LYS cc_start: 0.9320 (mppt) cc_final: 0.9106 (tptt) REVERT: A 272 ARG cc_start: 0.8143 (mtm110) cc_final: 0.7928 (mtm110) REVERT: H 143 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7458 (mt-10) REVERT: H 189 THR cc_start: 0.9076 (p) cc_final: 0.8693 (m) REVERT: H 193 MET cc_start: 0.3299 (mmt) cc_final: 0.1181 (pmm) REVERT: H 395 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7832 (ttt90) REVERT: a 93 LEU cc_start: 0.8916 (tp) cc_final: 0.8688 (tt) REVERT: B 223 TYR cc_start: 0.8562 (t80) cc_final: 0.8213 (t80) REVERT: B 225 LYS cc_start: 0.8902 (mtmm) cc_final: 0.7689 (mppt) REVERT: B 226 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8108 (mmmt) REVERT: B 303 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8221 (mp0) REVERT: I 143 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: I 379 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8373 (mm) REVERT: I 475 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: b 15 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6119 (mtp-110) REVERT: b 84 TYR cc_start: 0.7247 (m-10) cc_final: 0.6940 (m-10) REVERT: C 199 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.7261 (t80) REVERT: C 223 TYR cc_start: 0.8115 (t80) cc_final: 0.7547 (t80) REVERT: C 285 ARG cc_start: 0.8106 (mpt180) cc_final: 0.7870 (mpt90) REVERT: J 143 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: J 201 SER cc_start: 0.1142 (OUTLIER) cc_final: 0.0911 (p) REVERT: J 475 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: c 5 ARG cc_start: 0.8315 (ptt90) cc_final: 0.7999 (ptm160) REVERT: c 69 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: c 87 MET cc_start: 0.6737 (tpt) cc_final: 0.5848 (tpt) REVERT: D 223 TYR cc_start: 0.8276 (t80) cc_final: 0.8004 (t80) REVERT: d 69 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.8025 (m-80) REVERT: d 91 GLU cc_start: 0.8577 (pt0) cc_final: 0.8216 (pp20) REVERT: E 229 ASN cc_start: 0.8089 (m110) cc_final: 0.7613 (p0) REVERT: E 272 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8238 (ptt-90) REVERT: L 143 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7470 (mt-10) REVERT: L 193 MET cc_start: 0.5746 (pmm) cc_final: 0.5493 (mmm) REVERT: L 211 MET cc_start: 0.4768 (OUTLIER) cc_final: 0.4528 (tmt) REVERT: L 316 MET cc_start: 0.4290 (ppp) cc_final: 0.4063 (pmm) REVERT: e 84 TYR cc_start: 0.7185 (m-80) cc_final: 0.6965 (m-10) REVERT: F 199 TYR cc_start: 0.7098 (OUTLIER) cc_final: 0.6592 (t80) REVERT: F 225 LYS cc_start: 0.8836 (mtmm) cc_final: 0.8579 (mppt) REVERT: M 143 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: M 391 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8155 (pm20) REVERT: f 84 TYR cc_start: 0.8125 (m-80) cc_final: 0.7904 (m-80) REVERT: G 59 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8804 (mp0) REVERT: G 172 ASP cc_start: 0.7408 (p0) cc_final: 0.7058 (p0) REVERT: G 199 TYR cc_start: 0.6950 (OUTLIER) cc_final: 0.6716 (t80) REVERT: G 327 LYS cc_start: 0.9140 (mmmt) cc_final: 0.8884 (tppp) REVERT: G 345 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8685 (tpp80) REVERT: N 193 MET cc_start: 0.5141 (mpt) cc_final: 0.4295 (ppp) REVERT: N 379 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8376 (mm) outliers start: 206 outliers final: 88 residues processed: 632 average time/residue: 1.3051 time to fit residues: 1075.2836 Evaluate side-chains 565 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 451 time to evaluate : 5.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 32 THR Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain a residue 72 TYR Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 379 ILE Chi-restraints excluded: chain I residue 475 GLU Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 25 SER Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 58 SER Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 475 GLU Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 316 MET Chi-restraints excluded: chain K residue 356 THR Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 52 SER Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 211 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain e residue 57 VAL Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 72 TYR Chi-restraints excluded: chain e residue 92 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 391 GLU Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 379 ILE Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 85 LEU Chi-restraints excluded: chain g residue 90 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 636 optimal weight: 40.0000 chunk 434 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 569 optimal weight: 7.9990 chunk 315 optimal weight: 20.0000 chunk 652 optimal weight: 7.9990 chunk 528 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 390 optimal weight: 1.9990 chunk 686 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 55 GLN ** f 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 61607 Z= 0.334 Angle : 0.600 10.377 83258 Z= 0.300 Chirality : 0.045 0.183 10010 Planarity : 0.004 0.064 10668 Dihedral : 8.015 59.958 9006 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.14 % Rotamer: Outliers : 3.32 % Allowed : 15.38 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.09), residues: 8008 helix: 1.54 (0.08), residues: 3910 sheet: -0.12 (0.16), residues: 1039 loop : -0.17 (0.11), residues: 3059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 44 HIS 0.003 0.001 HIS J 401 PHE 0.012 0.001 PHE A 195 TYR 0.013 0.001 TYR F 223 ARG 0.006 0.000 ARG G 285 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 473 time to evaluate : 5.104 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 172 ASP cc_start: 0.7536 (p0) cc_final: 0.7286 (p0) REVERT: A 199 TYR cc_start: 0.7184 (OUTLIER) cc_final: 0.6810 (t80) REVERT: A 223 TYR cc_start: 0.7701 (t80) cc_final: 0.7488 (t80) REVERT: A 225 LYS cc_start: 0.9282 (mmmm) cc_final: 0.9003 (mppt) REVERT: A 226 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8347 (mtpp) REVERT: A 231 LYS cc_start: 0.9335 (mppt) cc_final: 0.9128 (tptt) REVERT: H 143 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: H 189 THR cc_start: 0.9078 (p) cc_final: 0.8673 (m) REVERT: a 93 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8714 (tt) REVERT: B 223 TYR cc_start: 0.8618 (t80) cc_final: 0.8288 (t80) REVERT: B 226 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8087 (mmmt) REVERT: B 272 ARG cc_start: 0.8352 (mtm180) cc_final: 0.8072 (mtm180) REVERT: B 303 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8253 (pt0) REVERT: B 330 THR cc_start: 0.8772 (m) cc_final: 0.8364 (p) REVERT: B 391 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7603 (tp30) REVERT: I 5 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8670 (ttmt) REVERT: I 143 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: I 379 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8349 (mm) REVERT: I 475 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: b 15 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6161 (mtp-110) REVERT: b 84 TYR cc_start: 0.7335 (m-10) cc_final: 0.7028 (m-10) REVERT: C 199 TYR cc_start: 0.7497 (OUTLIER) cc_final: 0.7237 (t80) REVERT: C 223 TYR cc_start: 0.8400 (t80) cc_final: 0.7638 (t80) REVERT: J 143 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7614 (mt-10) REVERT: J 201 SER cc_start: 0.1109 (OUTLIER) cc_final: 0.0903 (p) REVERT: J 211 MET cc_start: 0.6468 (mpt) cc_final: 0.5924 (tpt) REVERT: J 475 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: c 5 ARG cc_start: 0.8291 (ptt90) cc_final: 0.7999 (ptm160) REVERT: c 69 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7544 (m-80) REVERT: c 87 MET cc_start: 0.6323 (tpt) cc_final: 0.6003 (tpt) REVERT: D 223 TYR cc_start: 0.8313 (t80) cc_final: 0.8050 (t80) REVERT: D 226 LYS cc_start: 0.8855 (mmmm) cc_final: 0.8505 (mmmm) REVERT: D 284 ARG cc_start: 0.8445 (mmm160) cc_final: 0.7374 (mmm160) REVERT: d 69 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8243 (m-80) REVERT: d 86 ILE cc_start: 0.9196 (mp) cc_final: 0.8980 (mp) REVERT: d 87 MET cc_start: 0.7181 (mmm) cc_final: 0.6913 (tpt) REVERT: E 229 ASN cc_start: 0.8108 (m110) cc_final: 0.7390 (p0) REVERT: E 231 LYS cc_start: 0.8999 (pptt) cc_final: 0.8534 (pptt) REVERT: E 272 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8171 (ptt-90) REVERT: L 143 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7522 (mt-10) REVERT: L 193 MET cc_start: 0.5650 (pmm) cc_final: 0.5439 (mmm) REVERT: L 211 MET cc_start: 0.4673 (OUTLIER) cc_final: 0.4408 (tmt) REVERT: L 316 MET cc_start: 0.4381 (ppp) cc_final: 0.4136 (pmm) REVERT: e 65 ASP cc_start: 0.6052 (OUTLIER) cc_final: 0.5825 (p0) REVERT: F 199 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.6572 (t80) REVERT: F 225 LYS cc_start: 0.8810 (mtmm) cc_final: 0.8556 (mppt) REVERT: F 272 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8037 (ptt-90) REVERT: M 143 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: M 391 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8265 (pm20) REVERT: G 59 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.8760 (mp0) REVERT: G 172 ASP cc_start: 0.7445 (p0) cc_final: 0.7100 (p0) REVERT: G 199 TYR cc_start: 0.6987 (OUTLIER) cc_final: 0.6609 (t80) REVERT: G 214 VAL cc_start: 0.9185 (OUTLIER) cc_final: 0.8947 (t) REVERT: G 345 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8691 (tpp80) REVERT: N 193 MET cc_start: 0.5087 (mpt) cc_final: 0.4282 (ppp) REVERT: N 379 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8371 (mm) REVERT: N 475 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8052 (mp0) outliers start: 213 outliers final: 103 residues processed: 638 average time/residue: 1.3178 time to fit residues: 1092.4648 Evaluate side-chains 589 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 454 time to evaluate : 5.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 32 THR Chi-restraints excluded: chain a residue 72 TYR Chi-restraints excluded: chain a residue 93 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 379 ILE Chi-restraints excluded: chain I residue 475 GLU Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 25 SER Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 475 GLU Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 316 MET Chi-restraints excluded: chain K residue 356 THR Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 52 SER Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 68 VAL Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 211 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain e residue 57 VAL Chi-restraints excluded: chain e residue 65 ASP Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 72 TYR Chi-restraints excluded: chain e residue 92 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 272 ARG Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 391 GLU Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 69 PHE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 326 ASP Chi-restraints excluded: chain N residue 379 ILE Chi-restraints excluded: chain N residue 475 GLU Chi-restraints excluded: chain g residue 23 THR Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 85 LEU Chi-restraints excluded: chain g residue 90 ASP Chi-restraints excluded: chain g residue 93 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 257 optimal weight: 5.9990 chunk 688 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 448 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 765 optimal weight: 30.0000 chunk 635 optimal weight: 7.9990 chunk 354 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 253 optimal weight: 9.9990 chunk 401 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN ** f 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 61607 Z= 0.211 Angle : 0.573 13.039 83258 Z= 0.285 Chirality : 0.043 0.165 10010 Planarity : 0.003 0.059 10668 Dihedral : 7.237 59.803 9005 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.63 % Favored : 97.29 % Rotamer: Outliers : 2.84 % Allowed : 16.31 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.09), residues: 8008 helix: 1.63 (0.08), residues: 3910 sheet: -0.09 (0.15), residues: 1118 loop : -0.13 (0.11), residues: 2980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 44 HIS 0.002 0.000 HIS J 266 PHE 0.012 0.001 PHE A 195 TYR 0.022 0.001 TYR d 72 ARG 0.009 0.000 ARG D 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 481 time to evaluate : 5.346 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 172 ASP cc_start: 0.7608 (p0) cc_final: 0.7316 (p0) REVERT: A 199 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.6733 (t80) REVERT: A 225 LYS cc_start: 0.9316 (mmmm) cc_final: 0.9031 (mppt) REVERT: A 226 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8318 (mtpp) REVERT: A 231 LYS cc_start: 0.9339 (mppt) cc_final: 0.9130 (tptt) REVERT: A 345 ARG cc_start: 0.8831 (mtp-110) cc_final: 0.8388 (ttm110) REVERT: H 143 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7462 (mt-10) REVERT: H 193 MET cc_start: 0.3137 (mmt) cc_final: 0.1187 (pmm) REVERT: H 196 ASP cc_start: 0.6737 (OUTLIER) cc_final: 0.6530 (t70) REVERT: a 93 LEU cc_start: 0.8877 (tp) cc_final: 0.8667 (tt) REVERT: B 223 TYR cc_start: 0.8658 (t80) cc_final: 0.8188 (t80) REVERT: B 225 LYS cc_start: 0.8887 (mtmm) cc_final: 0.7513 (mppt) REVERT: B 226 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7990 (mmmt) REVERT: B 272 ARG cc_start: 0.8339 (mtm180) cc_final: 0.8055 (mtm180) REVERT: B 303 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8279 (mp0) REVERT: I 5 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8652 (ttmt) REVERT: I 143 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7639 (mt-10) REVERT: I 379 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8365 (mm) REVERT: I 475 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: b 15 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.5982 (mtp-110) REVERT: b 84 TYR cc_start: 0.7279 (m-10) cc_final: 0.6934 (m-10) REVERT: C 199 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.7201 (t80) REVERT: C 223 TYR cc_start: 0.8510 (t80) cc_final: 0.7911 (t80) REVERT: C 330 THR cc_start: 0.8569 (m) cc_final: 0.8329 (p) REVERT: J 143 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: J 211 MET cc_start: 0.6341 (mpt) cc_final: 0.5792 (tpt) REVERT: J 475 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: c 5 ARG cc_start: 0.8262 (ptt90) cc_final: 0.8015 (ptm160) REVERT: c 87 MET cc_start: 0.6422 (tpt) cc_final: 0.6206 (tpt) REVERT: D 223 TYR cc_start: 0.8297 (t80) cc_final: 0.8041 (t80) REVERT: D 226 LYS cc_start: 0.8876 (mmmm) cc_final: 0.8513 (mmmm) REVERT: D 272 ARG cc_start: 0.8657 (mtm180) cc_final: 0.7940 (ptt-90) REVERT: D 284 ARG cc_start: 0.8424 (mmm160) cc_final: 0.7451 (mmm160) REVERT: D 288 TYR cc_start: 0.8978 (m-10) cc_final: 0.8303 (m-10) REVERT: K 412 VAL cc_start: 0.9563 (OUTLIER) cc_final: 0.9355 (m) REVERT: d 5 ARG cc_start: 0.7984 (ptt90) cc_final: 0.7635 (ptm160) REVERT: d 69 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8289 (m-80) REVERT: d 86 ILE cc_start: 0.9228 (mp) cc_final: 0.8992 (mp) REVERT: E 229 ASN cc_start: 0.8165 (m110) cc_final: 0.7684 (p0) REVERT: E 272 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8184 (ptt-90) REVERT: E 285 ARG cc_start: 0.8825 (ttm-80) cc_final: 0.8479 (ttm-80) REVERT: E 368 ARG cc_start: 0.8313 (ttt180) cc_final: 0.7895 (mtp-110) REVERT: L 143 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: L 211 MET cc_start: 0.4751 (OUTLIER) cc_final: 0.4489 (tmt) REVERT: L 316 MET cc_start: 0.4339 (ppp) cc_final: 0.4113 (pmm) REVERT: e 65 ASP cc_start: 0.6028 (OUTLIER) cc_final: 0.5776 (p0) REVERT: F 225 LYS cc_start: 0.8816 (mtmm) cc_final: 0.8562 (mppt) REVERT: F 349 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7709 (tp) REVERT: M 143 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: M 211 MET cc_start: 0.3353 (tmt) cc_final: 0.3093 (tmm) REVERT: M 391 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8224 (pm20) REVERT: G 52 ASP cc_start: 0.9226 (OUTLIER) cc_final: 0.8910 (m-30) REVERT: G 59 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8788 (mp0) REVERT: G 172 ASP cc_start: 0.7315 (p0) cc_final: 0.6945 (p0) REVERT: G 214 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8995 (t) REVERT: G 229 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8120 (t0) REVERT: G 303 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8164 (mp0) REVERT: G 345 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8767 (mtp85) REVERT: N 193 MET cc_start: 0.5103 (mpt) cc_final: 0.4290 (ppp) REVERT: N 379 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8353 (mm) REVERT: N 475 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8061 (mp0) outliers start: 182 outliers final: 87 residues processed: 620 average time/residue: 1.3872 time to fit residues: 1124.0466 Evaluate side-chains 580 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 463 time to evaluate : 5.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 196 ASP Chi-restraints excluded: chain H residue 326 ASP Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 32 THR Chi-restraints excluded: chain a residue 72 TYR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 379 ILE Chi-restraints excluded: chain I residue 475 GLU Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 25 SER Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 58 SER Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 475 GLU Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 316 MET Chi-restraints excluded: chain K residue 356 THR Chi-restraints excluded: chain K residue 412 VAL Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 58 SER Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 211 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 32 THR Chi-restraints excluded: chain e residue 57 VAL Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain e residue 65 ASP Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 391 GLU Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 229 ASN Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 271 ILE Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 379 ILE Chi-restraints excluded: chain N residue 475 GLU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 90 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 737 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 436 optimal weight: 0.9980 chunk 558 optimal weight: 9.9990 chunk 433 optimal weight: 0.7980 chunk 644 optimal weight: 9.9990 chunk 427 optimal weight: 2.9990 chunk 762 optimal weight: 10.0000 chunk 477 optimal weight: 7.9990 chunk 464 optimal weight: 2.9990 chunk 351 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 70 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 55 GLN ** f 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 GLN ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 61607 Z= 0.244 Angle : 0.581 13.626 83258 Z= 0.289 Chirality : 0.044 0.165 10010 Planarity : 0.003 0.066 10668 Dihedral : 6.715 59.384 9001 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.15 % Rotamer: Outliers : 2.94 % Allowed : 16.54 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.09), residues: 8008 helix: 1.68 (0.08), residues: 3908 sheet: -0.10 (0.15), residues: 1123 loop : -0.14 (0.11), residues: 2977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 44 HIS 0.002 0.000 HIS J 266 PHE 0.012 0.001 PHE L 195 TYR 0.020 0.001 TYR A 223 ARG 0.010 0.000 ARG G 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 482 time to evaluate : 5.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7489 (p0) cc_final: 0.7179 (p0) REVERT: A 199 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.6815 (t80) REVERT: A 223 TYR cc_start: 0.7706 (t80) cc_final: 0.7433 (t80) REVERT: A 225 LYS cc_start: 0.9315 (mmmm) cc_final: 0.9000 (mppt) REVERT: A 226 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8220 (tttp) REVERT: A 231 LYS cc_start: 0.9343 (mppt) cc_final: 0.9130 (tptt) REVERT: A 345 ARG cc_start: 0.8820 (mtp-110) cc_final: 0.8336 (ttm110) REVERT: H 143 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: H 395 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8270 (ttp80) REVERT: B 223 TYR cc_start: 0.8717 (t80) cc_final: 0.8273 (t80) REVERT: B 225 LYS cc_start: 0.8895 (mtmm) cc_final: 0.7506 (mppt) REVERT: B 226 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8134 (mmmt) REVERT: B 272 ARG cc_start: 0.8365 (mtm180) cc_final: 0.8018 (mtm180) REVERT: B 303 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8294 (mp0) REVERT: B 330 THR cc_start: 0.8864 (m) cc_final: 0.8457 (p) REVERT: I 5 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8662 (ttmt) REVERT: I 143 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: I 475 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: b 15 ARG cc_start: 0.6702 (OUTLIER) cc_final: 0.5959 (mtp-110) REVERT: b 84 TYR cc_start: 0.7246 (m-10) cc_final: 0.6854 (m-10) REVERT: C 199 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.7215 (t80) REVERT: C 223 TYR cc_start: 0.8420 (t80) cc_final: 0.7688 (t80) REVERT: C 285 ARG cc_start: 0.8198 (mpt180) cc_final: 0.7936 (mpt180) REVERT: C 330 THR cc_start: 0.8552 (m) cc_final: 0.8286 (p) REVERT: J 143 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: J 475 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: c 5 ARG cc_start: 0.8262 (ptt90) cc_final: 0.7971 (ptm160) REVERT: c 87 MET cc_start: 0.6334 (tpt) cc_final: 0.6021 (tpt) REVERT: D 223 TYR cc_start: 0.8303 (t80) cc_final: 0.8055 (t80) REVERT: D 226 LYS cc_start: 0.8857 (mmmm) cc_final: 0.8485 (mmmm) REVERT: d 5 ARG cc_start: 0.7970 (ptt90) cc_final: 0.7595 (ptm160) REVERT: d 69 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: d 86 ILE cc_start: 0.9242 (mp) cc_final: 0.9014 (mp) REVERT: d 87 MET cc_start: 0.7252 (tpt) cc_final: 0.6941 (tpt) REVERT: E 229 ASN cc_start: 0.8183 (m110) cc_final: 0.7681 (p0) REVERT: E 272 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8132 (ptt-90) REVERT: E 368 ARG cc_start: 0.8331 (ttt180) cc_final: 0.7849 (mtp-110) REVERT: L 143 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7502 (mt-10) REVERT: L 193 MET cc_start: 0.3549 (mmm) cc_final: 0.1012 (pp-130) REVERT: L 211 MET cc_start: 0.4744 (OUTLIER) cc_final: 0.4499 (tmt) REVERT: e 65 ASP cc_start: 0.6010 (OUTLIER) cc_final: 0.5763 (p0) REVERT: e 84 TYR cc_start: 0.7136 (m-10) cc_final: 0.6589 (m-10) REVERT: F 225 LYS cc_start: 0.8837 (mtmm) cc_final: 0.8590 (mppt) REVERT: F 272 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7950 (ptt-90) REVERT: M 143 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7524 (mt-10) REVERT: M 211 MET cc_start: 0.3659 (tmt) cc_final: 0.3421 (tmm) REVERT: M 391 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8260 (pm20) REVERT: f 5 ARG cc_start: 0.8270 (ptm160) cc_final: 0.7841 (ptm160) REVERT: f 84 TYR cc_start: 0.7978 (m-80) cc_final: 0.7600 (m-80) REVERT: G 52 ASP cc_start: 0.9261 (OUTLIER) cc_final: 0.8969 (m-30) REVERT: G 59 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8768 (mp0) REVERT: G 172 ASP cc_start: 0.7294 (p0) cc_final: 0.6930 (p0) REVERT: G 214 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8985 (t) REVERT: G 303 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8160 (mp0) REVERT: G 316 MET cc_start: 0.8931 (ptp) cc_final: 0.8615 (pmm) REVERT: G 345 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8745 (mtp85) REVERT: N 193 MET cc_start: 0.5057 (mpt) cc_final: 0.4224 (ppp) REVERT: N 379 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8345 (mm) REVERT: N 475 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8069 (mp0) outliers start: 189 outliers final: 94 residues processed: 624 average time/residue: 1.3471 time to fit residues: 1093.0831 Evaluate side-chains 578 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 457 time to evaluate : 5.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 326 ASP Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 32 THR Chi-restraints excluded: chain a residue 70 ASN Chi-restraints excluded: chain a residue 72 TYR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 475 GLU Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 25 SER Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 475 GLU Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain c residue 79 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 316 MET Chi-restraints excluded: chain K residue 356 THR Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 211 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 57 VAL Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain e residue 65 ASP Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 72 TYR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 272 ARG Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 391 GLU Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 271 ILE Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 379 ILE Chi-restraints excluded: chain N residue 475 GLU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 57 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 471 optimal weight: 8.9990 chunk 304 optimal weight: 3.9990 chunk 455 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 484 optimal weight: 9.9990 chunk 519 optimal weight: 10.0000 chunk 376 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 599 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 GLN ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 61607 Z= 0.409 Angle : 0.641 14.251 83258 Z= 0.319 Chirality : 0.046 0.256 10010 Planarity : 0.004 0.059 10668 Dihedral : 6.789 59.877 8999 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 2.85 % Allowed : 16.70 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.09), residues: 8008 helix: 1.56 (0.08), residues: 3914 sheet: -0.16 (0.15), residues: 1233 loop : -0.22 (0.11), residues: 2861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 44 HIS 0.003 0.001 HIS J 401 PHE 0.014 0.001 PHE G 281 TYR 0.025 0.002 TYR d 72 ARG 0.011 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 460 time to evaluate : 5.233 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 172 ASP cc_start: 0.7508 (p0) cc_final: 0.7269 (p0) REVERT: A 225 LYS cc_start: 0.9296 (mmmm) cc_final: 0.8988 (mppt) REVERT: A 226 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8263 (tttp) REVERT: A 231 LYS cc_start: 0.9348 (mppt) cc_final: 0.9125 (tptt) REVERT: A 345 ARG cc_start: 0.8800 (mtp-110) cc_final: 0.8332 (ttm110) REVERT: H 143 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7419 (mt-10) REVERT: H 395 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8135 (ttp80) REVERT: B 225 LYS cc_start: 0.8886 (mtmm) cc_final: 0.7504 (mppt) REVERT: B 226 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8223 (mmmt) REVERT: B 272 ARG cc_start: 0.8365 (mtm180) cc_final: 0.7981 (mtm180) REVERT: B 303 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8328 (mp0) REVERT: B 391 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7639 (tp30) REVERT: I 5 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8654 (ttmt) REVERT: I 143 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: I 326 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7297 (p0) REVERT: I 379 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8369 (mm) REVERT: I 475 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: b 15 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.5978 (mtp-110) REVERT: b 82 GLU cc_start: 0.7045 (mp0) cc_final: 0.6754 (mp0) REVERT: b 84 TYR cc_start: 0.7282 (m-10) cc_final: 0.6950 (m-10) REVERT: C 199 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.7180 (t80) REVERT: C 223 TYR cc_start: 0.8410 (t80) cc_final: 0.7579 (t80) REVERT: C 285 ARG cc_start: 0.8204 (mpt180) cc_final: 0.7928 (mpt180) REVERT: C 330 THR cc_start: 0.8574 (m) cc_final: 0.8358 (p) REVERT: J 143 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: J 211 MET cc_start: 0.6154 (mpt) cc_final: 0.5455 (tpt) REVERT: J 475 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: c 5 ARG cc_start: 0.8320 (ptt90) cc_final: 0.8035 (ptm160) REVERT: c 21 GLN cc_start: 0.8399 (tt0) cc_final: 0.8140 (pm20) REVERT: D 223 TYR cc_start: 0.8393 (t80) cc_final: 0.8094 (t80) REVERT: D 226 LYS cc_start: 0.8867 (mmmm) cc_final: 0.8526 (mmmm) REVERT: d 5 ARG cc_start: 0.8081 (ptt90) cc_final: 0.7731 (ptm160) REVERT: d 69 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8420 (m-80) REVERT: d 87 MET cc_start: 0.7160 (tpt) cc_final: 0.6914 (tpt) REVERT: E 229 ASN cc_start: 0.8165 (m110) cc_final: 0.7681 (p0) REVERT: E 272 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8148 (ptt-90) REVERT: E 285 ARG cc_start: 0.8792 (ttm-80) cc_final: 0.8450 (ttm-80) REVERT: E 368 ARG cc_start: 0.8342 (ttt180) cc_final: 0.8067 (mtp180) REVERT: L 143 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7541 (mt-10) REVERT: L 193 MET cc_start: 0.3622 (mmm) cc_final: 0.1027 (pmm) REVERT: L 211 MET cc_start: 0.4586 (OUTLIER) cc_final: 0.4358 (tmt) REVERT: e 65 ASP cc_start: 0.6420 (p0) cc_final: 0.6205 (p0) REVERT: F 193 MET cc_start: 0.8899 (mmm) cc_final: 0.8655 (tpp) REVERT: F 199 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.6618 (t80) REVERT: F 225 LYS cc_start: 0.8803 (mtmm) cc_final: 0.8570 (mppt) REVERT: F 272 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7956 (ptt-90) REVERT: M 143 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: M 211 MET cc_start: 0.3604 (tmt) cc_final: 0.3363 (tmm) REVERT: M 391 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8282 (pm20) REVERT: f 84 TYR cc_start: 0.8110 (m-80) cc_final: 0.7879 (m-80) REVERT: G 172 ASP cc_start: 0.7291 (p0) cc_final: 0.6928 (p0) REVERT: G 214 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8968 (t) REVERT: G 229 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.7734 (p0) REVERT: G 288 TYR cc_start: 0.8998 (m-80) cc_final: 0.8795 (m-80) REVERT: G 345 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8728 (mmm160) REVERT: N 193 MET cc_start: 0.5075 (mpt) cc_final: 0.4176 (ppp) REVERT: N 379 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8344 (mm) REVERT: N 475 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8063 (mp0) outliers start: 183 outliers final: 100 residues processed: 600 average time/residue: 1.3516 time to fit residues: 1050.6541 Evaluate side-chains 585 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 457 time to evaluate : 5.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 326 ASP Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 32 THR Chi-restraints excluded: chain a residue 84 TYR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 267 ILE Chi-restraints excluded: chain I residue 326 ASP Chi-restraints excluded: chain I residue 379 ILE Chi-restraints excluded: chain I residue 475 GLU Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 25 SER Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 58 SER Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 475 GLU Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 316 MET Chi-restraints excluded: chain K residue 356 THR Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 211 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 57 VAL Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 72 TYR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 272 ARG Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 391 GLU Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 229 ASN Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 271 ILE Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 326 ASP Chi-restraints excluded: chain N residue 379 ILE Chi-restraints excluded: chain N residue 475 GLU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 57 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 693 optimal weight: 1.9990 chunk 730 optimal weight: 2.9990 chunk 666 optimal weight: 9.9990 chunk 710 optimal weight: 4.9990 chunk 427 optimal weight: 4.9990 chunk 309 optimal weight: 30.0000 chunk 557 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 chunk 641 optimal weight: 2.9990 chunk 671 optimal weight: 8.9990 chunk 707 optimal weight: 0.4980 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 70 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 55 GLN E 283 GLN ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 GLN ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 61607 Z= 0.309 Angle : 0.620 14.731 83258 Z= 0.306 Chirality : 0.045 0.236 10010 Planarity : 0.004 0.054 10668 Dihedral : 6.641 59.807 8996 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.72 % Favored : 97.20 % Rotamer: Outliers : 2.55 % Allowed : 17.35 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.09), residues: 8008 helix: 1.61 (0.08), residues: 3921 sheet: -0.13 (0.15), residues: 1198 loop : -0.27 (0.11), residues: 2889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 44 HIS 0.003 0.000 HIS J 266 PHE 0.013 0.001 PHE G 281 TYR 0.018 0.001 TYR e 84 ARG 0.011 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 465 time to evaluate : 5.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7459 (p0) cc_final: 0.7179 (p0) REVERT: A 225 LYS cc_start: 0.9296 (mmmm) cc_final: 0.8980 (mppt) REVERT: A 226 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8212 (tttp) REVERT: A 231 LYS cc_start: 0.9355 (mppt) cc_final: 0.9133 (tptt) REVERT: A 345 ARG cc_start: 0.8790 (mtp-110) cc_final: 0.8306 (ttm110) REVERT: H 143 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7419 (mt-10) REVERT: H 326 ASP cc_start: 0.6874 (OUTLIER) cc_final: 0.6644 (p0) REVERT: H 395 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8160 (ttp80) REVERT: B 226 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8250 (mmmt) REVERT: B 391 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7591 (tp30) REVERT: I 5 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8665 (ttmt) REVERT: I 143 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7389 (mt-10) REVERT: I 379 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8319 (mm) REVERT: I 395 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8294 (ttp80) REVERT: I 475 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: b 15 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.5954 (mtp-110) REVERT: b 84 TYR cc_start: 0.7264 (m-10) cc_final: 0.6845 (m-10) REVERT: C 199 TYR cc_start: 0.7437 (OUTLIER) cc_final: 0.7182 (t80) REVERT: C 223 TYR cc_start: 0.8437 (t80) cc_final: 0.7510 (t80) REVERT: C 272 ARG cc_start: 0.8551 (mtm180) cc_final: 0.8109 (mtm180) REVERT: C 285 ARG cc_start: 0.8223 (mpt180) cc_final: 0.7960 (mpt180) REVERT: C 330 THR cc_start: 0.8548 (m) cc_final: 0.8301 (p) REVERT: J 143 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: J 211 MET cc_start: 0.6281 (mpt) cc_final: 0.5505 (tpt) REVERT: J 475 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: c 5 ARG cc_start: 0.8324 (ptt90) cc_final: 0.8036 (ptm160) REVERT: c 21 GLN cc_start: 0.8377 (tt0) cc_final: 0.8095 (pm20) REVERT: D 223 TYR cc_start: 0.8454 (t80) cc_final: 0.8134 (t80) REVERT: D 226 LYS cc_start: 0.8861 (mmmm) cc_final: 0.8523 (mmmm) REVERT: d 5 ARG cc_start: 0.8089 (ptt90) cc_final: 0.7756 (ptm160) REVERT: d 69 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8385 (m-80) REVERT: d 87 MET cc_start: 0.7078 (tpt) cc_final: 0.6815 (tpt) REVERT: E 52 ASP cc_start: 0.9232 (OUTLIER) cc_final: 0.9024 (m-30) REVERT: E 229 ASN cc_start: 0.8142 (m110) cc_final: 0.7626 (p0) REVERT: E 272 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8166 (ptt-90) REVERT: E 285 ARG cc_start: 0.8783 (ttm-80) cc_final: 0.8461 (ttm-80) REVERT: E 368 ARG cc_start: 0.8338 (ttt180) cc_final: 0.8013 (mtp180) REVERT: L 143 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: L 193 MET cc_start: 0.3782 (mmm) cc_final: 0.1234 (pmm) REVERT: L 211 MET cc_start: 0.4600 (OUTLIER) cc_final: 0.4362 (tmt) REVERT: e 82 GLU cc_start: 0.7496 (pm20) cc_final: 0.7273 (pm20) REVERT: F 193 MET cc_start: 0.8837 (mmm) cc_final: 0.8536 (tpp) REVERT: F 199 TYR cc_start: 0.7386 (OUTLIER) cc_final: 0.6691 (t80) REVERT: F 225 LYS cc_start: 0.8812 (mtmm) cc_final: 0.8586 (mppt) REVERT: F 272 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7947 (ptt-90) REVERT: F 350 LYS cc_start: 0.8957 (pmmt) cc_final: 0.8745 (mppt) REVERT: M 143 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: M 211 MET cc_start: 0.3702 (tmt) cc_final: 0.3465 (tmm) REVERT: M 391 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8247 (pm20) REVERT: f 5 ARG cc_start: 0.8336 (ptm160) cc_final: 0.7893 (ptm160) REVERT: f 67 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8507 (m) REVERT: f 84 TYR cc_start: 0.8166 (m-80) cc_final: 0.7869 (m-80) REVERT: G 52 ASP cc_start: 0.9261 (OUTLIER) cc_final: 0.9046 (m-30) REVERT: G 172 ASP cc_start: 0.7285 (p0) cc_final: 0.6934 (p0) REVERT: G 214 VAL cc_start: 0.9192 (OUTLIER) cc_final: 0.8978 (t) REVERT: G 229 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.7770 (p0) REVERT: G 288 TYR cc_start: 0.9016 (m-80) cc_final: 0.8801 (m-80) REVERT: G 316 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8588 (pmm) REVERT: G 345 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8741 (mtp85) REVERT: N 143 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: N 193 MET cc_start: 0.5077 (mpt) cc_final: 0.4193 (ppp) REVERT: N 379 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8337 (mm) REVERT: N 475 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8037 (mp0) outliers start: 164 outliers final: 102 residues processed: 592 average time/residue: 1.3756 time to fit residues: 1058.8450 Evaluate side-chains 588 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 453 time to evaluate : 5.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 326 ASP Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 32 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 267 ILE Chi-restraints excluded: chain I residue 379 ILE Chi-restraints excluded: chain I residue 395 ARG Chi-restraints excluded: chain I residue 475 GLU Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 25 SER Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 475 GLU Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 316 MET Chi-restraints excluded: chain K residue 356 THR Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 211 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 57 VAL Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 72 TYR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 272 ARG Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 391 GLU Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 51 LEU Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 229 ASN Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 271 ILE Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 326 ASP Chi-restraints excluded: chain N residue 379 ILE Chi-restraints excluded: chain N residue 475 GLU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 57 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 466 optimal weight: 2.9990 chunk 751 optimal weight: 30.0000 chunk 458 optimal weight: 0.9980 chunk 356 optimal weight: 0.8980 chunk 522 optimal weight: 20.0000 chunk 788 optimal weight: 5.9990 chunk 725 optimal weight: 0.1980 chunk 627 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 484 optimal weight: 20.0000 chunk 384 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN H 239 ASN ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 70 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 55 GLN ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 ASN ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 61607 Z= 0.186 Angle : 0.600 15.112 83258 Z= 0.294 Chirality : 0.044 0.238 10010 Planarity : 0.003 0.045 10668 Dihedral : 6.308 59.825 8996 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 2.13 % Allowed : 17.85 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.09), residues: 8008 helix: 1.75 (0.08), residues: 3915 sheet: -0.03 (0.15), residues: 1120 loop : -0.28 (0.11), residues: 2973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 44 HIS 0.002 0.000 HIS J 266 PHE 0.012 0.001 PHE A 195 TYR 0.017 0.001 TYR F 223 ARG 0.011 0.000 ARG G 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16016 Ramachandran restraints generated. 8008 Oldfield, 0 Emsley, 8008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 467 time to evaluate : 5.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7424 (p0) cc_final: 0.7120 (p0) REVERT: A 181 LYS cc_start: 0.8954 (mmpt) cc_final: 0.8709 (tppt) REVERT: A 225 LYS cc_start: 0.9301 (mmmm) cc_final: 0.9020 (mppt) REVERT: A 226 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8193 (tttp) REVERT: A 231 LYS cc_start: 0.9340 (mppt) cc_final: 0.9134 (tptt) REVERT: A 272 ARG cc_start: 0.8338 (mtm180) cc_final: 0.8028 (mtm110) REVERT: A 345 ARG cc_start: 0.8848 (mtp-110) cc_final: 0.8422 (ttm110) REVERT: H 143 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: H 193 MET cc_start: 0.3816 (mmt) cc_final: 0.1748 (ppp) REVERT: H 211 MET cc_start: 0.4525 (OUTLIER) cc_final: 0.3391 (mtp) REVERT: B 226 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8177 (mmmt) REVERT: I 395 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8284 (ttp80) REVERT: I 475 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: b 15 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.6027 (mtp-110) REVERT: b 84 TYR cc_start: 0.7286 (m-10) cc_final: 0.6769 (m-80) REVERT: C 223 TYR cc_start: 0.8444 (t80) cc_final: 0.7497 (t80) REVERT: C 225 LYS cc_start: 0.8671 (mppt) cc_final: 0.8370 (mppt) REVERT: J 143 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: J 211 MET cc_start: 0.6254 (mpt) cc_final: 0.5438 (tpt) REVERT: J 475 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: c 5 ARG cc_start: 0.8277 (ptt90) cc_final: 0.7995 (ptm160) REVERT: c 21 GLN cc_start: 0.8370 (tt0) cc_final: 0.8110 (pm20) REVERT: c 87 MET cc_start: 0.6338 (tpt) cc_final: 0.6085 (tpt) REVERT: D 223 TYR cc_start: 0.8436 (t80) cc_final: 0.8113 (t80) REVERT: D 226 LYS cc_start: 0.8864 (mmmm) cc_final: 0.8522 (mmmm) REVERT: D 272 ARG cc_start: 0.8684 (mtm180) cc_final: 0.7963 (ptt-90) REVERT: D 285 ARG cc_start: 0.8632 (mmm-85) cc_final: 0.8283 (mmm-85) REVERT: d 5 ARG cc_start: 0.8004 (ptt90) cc_final: 0.7667 (ptm160) REVERT: d 69 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8346 (m-80) REVERT: d 84 TYR cc_start: 0.7961 (m-80) cc_final: 0.7687 (m-80) REVERT: d 87 MET cc_start: 0.7118 (tpt) cc_final: 0.6839 (tpt) REVERT: E 229 ASN cc_start: 0.8153 (m110) cc_final: 0.7645 (p0) REVERT: E 272 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8144 (ptt-90) REVERT: E 285 ARG cc_start: 0.8725 (ttm-80) cc_final: 0.8429 (ttm-80) REVERT: E 368 ARG cc_start: 0.8352 (ttt180) cc_final: 0.7890 (mtp-110) REVERT: L 143 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: L 193 MET cc_start: 0.3887 (mmm) cc_final: 0.1321 (pmm) REVERT: L 211 MET cc_start: 0.4645 (OUTLIER) cc_final: 0.4393 (tmt) REVERT: e 84 TYR cc_start: 0.7166 (m-10) cc_final: 0.6698 (m-10) REVERT: F 193 MET cc_start: 0.8832 (mmm) cc_final: 0.8596 (tpp) REVERT: F 225 LYS cc_start: 0.8846 (mtmm) cc_final: 0.8645 (mppt) REVERT: M 143 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: M 211 MET cc_start: 0.3652 (tmt) cc_final: 0.3409 (tmm) REVERT: M 391 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8218 (pm20) REVERT: f 5 ARG cc_start: 0.8370 (ptm160) cc_final: 0.7849 (ptm160) REVERT: f 67 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8507 (m) REVERT: f 69 PHE cc_start: 0.8558 (m-80) cc_final: 0.8246 (m-80) REVERT: f 84 TYR cc_start: 0.8156 (m-80) cc_final: 0.7893 (m-80) REVERT: f 87 MET cc_start: 0.6412 (ttt) cc_final: 0.5959 (tmt) REVERT: f 92 VAL cc_start: 0.7561 (t) cc_final: 0.6996 (t) REVERT: G 172 ASP cc_start: 0.7164 (p0) cc_final: 0.6771 (p0) REVERT: G 214 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8991 (t) REVERT: G 272 ARG cc_start: 0.8704 (mtm180) cc_final: 0.7983 (ptt-90) REVERT: G 316 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8577 (pmm) REVERT: G 345 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8678 (mmm160) REVERT: N 143 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: N 193 MET cc_start: 0.5019 (mpt) cc_final: 0.4185 (ppp) REVERT: N 475 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8056 (mp0) outliers start: 137 outliers final: 81 residues processed: 573 average time/residue: 1.3605 time to fit residues: 1008.4226 Evaluate side-chains 552 residues out of total 6419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 450 time to evaluate : 5.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain H residue 326 ASP Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 32 THR Chi-restraints excluded: chain a residue 70 ASN Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain I residue 267 ILE Chi-restraints excluded: chain I residue 395 ARG Chi-restraints excluded: chain I residue 475 GLU Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 25 SER Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 72 TYR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 475 GLU Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 69 PHE Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 316 MET Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 69 PHE Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 211 MET Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 57 VAL Chi-restraints excluded: chain e residue 58 SER Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 72 TYR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 143 GLU Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 391 GLU Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 58 SER Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain G residue 345 ARG Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 271 ILE Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 326 ASP Chi-restraints excluded: chain N residue 475 GLU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 57 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 498 optimal weight: 0.9980 chunk 668 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 578 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 628 optimal weight: 2.9990 chunk 263 optimal weight: 7.9990 chunk 645 optimal weight: 8.9990 chunk 79 optimal weight: 30.0000 chunk 115 optimal weight: 0.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 70 ASN ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 ASN ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.129357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.069103 restraints weight = 117563.449| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.73 r_work: 0.2738 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 61607 Z= 0.374 Angle : 0.647 14.837 83258 Z= 0.319 Chirality : 0.046 0.266 10010 Planarity : 0.004 0.044 10668 Dihedral : 6.328 59.776 8990 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.81 % Favored : 97.12 % Rotamer: Outliers : 1.99 % Allowed : 18.15 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.09), residues: 8008 helix: 1.69 (0.08), residues: 3921 sheet: -0.15 (0.15), residues: 1198 loop : -0.29 (0.11), residues: 2889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 44 HIS 0.003 0.001 HIS J 401 PHE 0.018 0.001 PHE a 69 TYR 0.026 0.002 TYR C 288 ARG 0.012 0.000 ARG A 285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19500.27 seconds wall clock time: 338 minutes 55.16 seconds (20335.16 seconds total)