Starting phenix.real_space_refine on Fri Feb 23 11:23:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9t_34581/02_2024/8h9t_34581_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9t_34581/02_2024/8h9t_34581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9t_34581/02_2024/8h9t_34581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9t_34581/02_2024/8h9t_34581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9t_34581/02_2024/8h9t_34581_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9t_34581/02_2024/8h9t_34581_updated.pdb" } resolution = 2.77 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= 0.009 sd= 1.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 161 5.16 5 C 24416 2.51 5 N 6479 2.21 5 O 7181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 7": "OE1" <-> "OE2" Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 49": "OE1" <-> "OE2" Residue "K TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 83": "OD1" <-> "OD2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K GLU 137": "OE1" <-> "OE2" Residue "K TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 169": "OE1" <-> "OE2" Residue "K GLU 171": "OE1" <-> "OE2" Residue "L ASP 62": "OD1" <-> "OD2" Residue "L GLU 72": "OE1" <-> "OE2" Residue "L PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 11": "OD1" <-> "OD2" Residue "M PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M GLU 35": "OE1" <-> "OE2" Residue "M GLU 93": "OE1" <-> "OE2" Residue "M GLU 119": "OE1" <-> "OE2" Residue "M PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 128": "OD1" <-> "OD2" Residue "6 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 38": "NH1" <-> "NH2" Residue "7 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 38": "NH1" <-> "NH2" Residue "8 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 38": "NH1" <-> "NH2" Residue "1 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 38": "NH1" <-> "NH2" Residue "3 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 38": "NH1" <-> "NH2" Residue "4 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 38": "NH1" <-> "NH2" Residue "5 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 124": "OD1" <-> "OD2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "I PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 203": "OE1" <-> "OE2" Residue "R ARG 45": "NH1" <-> "NH2" Residue "R TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "C ASP 194": "OD1" <-> "OD2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 333": "OD1" <-> "OD2" Residue "C GLU 355": "OE1" <-> "OE2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 494": "OD1" <-> "OD2" Residue "C PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 509": "OE1" <-> "OE2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 222": "OD1" <-> "OD2" Residue "A ASP 224": "OD1" <-> "OD2" Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 373": "NH1" <-> "NH2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 222": "OD1" <-> "OD2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 494": "OD1" <-> "OD2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E ASP 213": "OD1" <-> "OD2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "E PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 248": "OD1" <-> "OD2" Residue "E PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 322": "OD1" <-> "OD2" Residue "E ASP 352": "OD1" <-> "OD2" Residue "E ASP 355": "OD1" <-> "OD2" Residue "E ASP 362": "OD1" <-> "OD2" Residue "E ASP 389": "OD1" <-> "OD2" Residue "E ASP 397": "OD1" <-> "OD2" Residue "E PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 29": "OD1" <-> "OD2" Residue "F GLU 40": "OE1" <-> "OE2" Residue "F GLU 58": "OE1" <-> "OE2" Residue "F ASP 67": "OD1" <-> "OD2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "F TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 244": "OE1" <-> "OE2" Residue "F TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "F ASP 248": "OD1" <-> "OD2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 277": "NH1" <-> "NH2" Residue "F GLU 297": "OE1" <-> "OE2" Residue "F TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 340": "NH1" <-> "NH2" Residue "F TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 425": "OE1" <-> "OE2" Residue "F GLU 451": "OE1" <-> "OE2" Residue "F TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 468": "OE1" <-> "OE2" Residue "F ASP 474": "OD1" <-> "OD2" Residue "F GLU 478": "OE1" <-> "OE2" Residue "F GLU 479": "OE1" <-> "OE2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "O ARG 6": "NH1" <-> "NH2" Residue "O GLU 15": "OE1" <-> "OE2" Residue "O GLU 36": "OE1" <-> "OE2" Residue "O GLU 48": "OE1" <-> "OE2" Residue "O GLU 91": "OE1" <-> "OE2" Residue "O PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 128": "OE1" <-> "OE2" Residue "O ASP 155": "OD1" <-> "OD2" Residue "O TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 172": "OD1" <-> "OD2" Residue "D PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 132": "OE1" <-> "OE2" Residue "D PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D ASP 198": "OD1" <-> "OD2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 244": "OE1" <-> "OE2" Residue "D TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "D PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 277": "NH1" <-> "NH2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 318": "OD1" <-> "OD2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "D ASP 362": "OD1" <-> "OD2" Residue "D TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 451": "OE1" <-> "OE2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "D TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 468": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38255 Number of models: 1 Model: "" Number of chains: 32 Chain: "K" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1573 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1259 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 144} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "6" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "7" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "8" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "1" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "2" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "3" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "4" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "5" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 975 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 344 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "R" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 39} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 422 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 8, 'TRANS': 42} Chain: "C" Number of atoms: 3745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3745 Classifications: {'peptide': 491} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 472} Chain breaks: 2 Chain: "A" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3639 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 458} Chain breaks: 1 Chain: "B" Number of atoms: 3714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3714 Classifications: {'peptide': 487} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 468} Chain breaks: 1 Chain: "E" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3522 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 441} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3562 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 444} Chain: "G" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2103 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 5, 'TRANS': 265} Chain: "O" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1437 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "D" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3344 Classifications: {'peptide': 442} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 416} Chain breaks: 2 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.02, per 1000 atoms: 0.52 Number of scatterers: 38255 At special positions: 0 Unit cell: (139.43, 130.67, 241.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 161 16.00 P 13 15.00 Mg 5 11.99 O 7181 8.00 N 6479 7.00 C 24416 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: 16.52 Conformation dependent library (CDL) restraints added in 7.9 seconds 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9124 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 183 helices and 28 sheets defined 53.2% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.69 Creating SS restraints... Processing helix chain 'K' and resid 19 through 28 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 33 through 47 Processing helix chain 'K' and resid 55 through 183 Proline residue: K 76 - end of helix removed outlier: 3.710A pdb=" N ALA K 99 " --> pdb=" O GLU K 95 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER K 100 " --> pdb=" O ALA K 96 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N HIS K 122 " --> pdb=" O VAL K 118 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR K 123 " --> pdb=" O GLN K 119 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU K 124 " --> pdb=" O LYS K 120 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE K 125 " --> pdb=" O ARG K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 207 Processing helix chain 'L' and resid 41 through 54 removed outlier: 4.172A pdb=" N ARG L 48 " --> pdb=" O VAL L 44 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU L 49 " --> pdb=" O ASP L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 82 removed outlier: 3.999A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 17 No H-bonds generated for 'chain 'M' and resid 14 through 17' Processing helix chain 'M' and resid 24 through 43 Processing helix chain 'M' and resid 54 through 57 No H-bonds generated for 'chain 'M' and resid 54 through 57' Processing helix chain 'M' and resid 65 through 74 Processing helix chain 'M' and resid 86 through 123 Processing helix chain 'M' and resid 127 through 129 No H-bonds generated for 'chain 'M' and resid 127 through 129' Processing helix chain 'M' and resid 132 through 138 Processing helix chain 'M' and resid 140 through 142 No H-bonds generated for 'chain 'M' and resid 140 through 142' Processing helix chain '6' and resid 2 through 38 removed outlier: 3.979A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL 6 18 " --> pdb=" O ALA 6 14 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ALA 6 19 " --> pdb=" O THR 6 15 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLY 6 20 " --> pdb=" O VAL 6 16 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER 6 21 " --> pdb=" O GLY 6 17 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 73 Processing helix chain '7' and resid 2 through 38 removed outlier: 3.979A pdb=" N GLY 7 17 " --> pdb=" O ALA 7 13 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL 7 18 " --> pdb=" O ALA 7 14 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA 7 19 " --> pdb=" O THR 7 15 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLY 7 20 " --> pdb=" O VAL 7 16 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER 7 21 " --> pdb=" O GLY 7 17 " (cutoff:3.500A) Processing helix chain '7' and resid 43 through 73 Processing helix chain '8' and resid 2 through 38 removed outlier: 3.979A pdb=" N GLY 8 17 " --> pdb=" O ALA 8 13 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL 8 18 " --> pdb=" O ALA 8 14 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ALA 8 19 " --> pdb=" O THR 8 15 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLY 8 20 " --> pdb=" O VAL 8 16 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER 8 21 " --> pdb=" O GLY 8 17 " (cutoff:3.500A) Processing helix chain '8' and resid 43 through 73 Processing helix chain '1' and resid 2 through 38 removed outlier: 3.979A pdb=" N GLY 1 17 " --> pdb=" O ALA 1 13 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL 1 18 " --> pdb=" O ALA 1 14 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ALA 1 19 " --> pdb=" O THR 1 15 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLY 1 20 " --> pdb=" O VAL 1 16 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER 1 21 " --> pdb=" O GLY 1 17 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 73 Processing helix chain '2' and resid 2 through 38 removed outlier: 3.980A pdb=" N GLY 2 17 " --> pdb=" O ALA 2 13 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL 2 18 " --> pdb=" O ALA 2 14 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA 2 19 " --> pdb=" O THR 2 15 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLY 2 20 " --> pdb=" O VAL 2 16 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER 2 21 " --> pdb=" O GLY 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 73 Processing helix chain '3' and resid 2 through 38 removed outlier: 3.979A pdb=" N GLY 3 17 " --> pdb=" O ALA 3 13 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL 3 18 " --> pdb=" O ALA 3 14 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA 3 19 " --> pdb=" O THR 3 15 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLY 3 20 " --> pdb=" O VAL 3 16 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER 3 21 " --> pdb=" O GLY 3 17 " (cutoff:3.500A) Processing helix chain '3' and resid 43 through 73 Processing helix chain '4' and resid 2 through 38 removed outlier: 3.979A pdb=" N GLY 4 17 " --> pdb=" O ALA 4 13 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL 4 18 " --> pdb=" O ALA 4 14 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ALA 4 19 " --> pdb=" O THR 4 15 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLY 4 20 " --> pdb=" O VAL 4 16 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER 4 21 " --> pdb=" O GLY 4 17 " (cutoff:3.500A) Processing helix chain '4' and resid 43 through 73 Processing helix chain '5' and resid 2 through 38 removed outlier: 3.979A pdb=" N GLY 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL 5 18 " --> pdb=" O ALA 5 14 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA 5 19 " --> pdb=" O THR 5 15 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLY 5 20 " --> pdb=" O VAL 5 16 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER 5 21 " --> pdb=" O GLY 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 43 through 73 Processing helix chain 'H' and resid 106 through 121 Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'I' and resid 4 through 7 No H-bonds generated for 'chain 'I' and resid 4 through 7' Processing helix chain 'I' and resid 12 through 25 Processing helix chain 'I' and resid 29 through 39 removed outlier: 4.212A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASN I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 9 Processing helix chain 'N' and resid 20 through 24 Processing helix chain 'N' and resid 27 through 30 Processing helix chain 'N' and resid 41 through 60 removed outlier: 3.664A pdb=" N THR N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N MET N 60 " --> pdb=" O GLN N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 86 removed outlier: 4.807A pdb=" N TRP N 68 " --> pdb=" O LYS N 64 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER N 69 " --> pdb=" O GLY N 65 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU N 70 " --> pdb=" O ARG N 66 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N MET N 71 " --> pdb=" O THR N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 118 Proline residue: N 107 - end of helix Processing helix chain 'N' and resid 121 through 127 Processing helix chain 'N' and resid 135 through 183 Proline residue: N 139 - end of helix Proline residue: N 153 - end of helix removed outlier: 4.838A pdb=" N ALA N 162 " --> pdb=" O ARG N 159 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE N 164 " --> pdb=" O THR N 161 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA N 166 " --> pdb=" O ASN N 163 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR N 183 " --> pdb=" O ALA N 180 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 225 Processing helix chain 'P' and resid 14 through 19 removed outlier: 3.651A pdb=" N LYS P 19 " --> pdb=" O PRO P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 40 Processing helix chain 'R' and resid 26 through 31 Processing helix chain 'R' and resid 36 through 54 Processing helix chain 'R' and resid 63 through 80 removed outlier: 4.624A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 87 No H-bonds generated for 'chain 'R' and resid 85 through 87' Processing helix chain 'S' and resid 28 through 36 Processing helix chain 'S' and resid 45 through 61 Processing helix chain 'S' and resid 63 through 66 Processing helix chain 'S' and resid 69 through 94 Processing helix chain 'T' and resid 9 through 44 Proline residue: T 35 - end of helix Processing helix chain 'Q' and resid 2 through 4 No H-bonds generated for 'chain 'Q' and resid 2 through 4' Processing helix chain 'Q' and resid 9 through 21 Proline residue: Q 15 - end of helix Processing helix chain 'Q' and resid 23 through 29 Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 190 removed outlier: 3.734A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ARG C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 240 through 259 Proline residue: C 247 - end of helix removed outlier: 4.034A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 284 Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 298 through 308 removed outlier: 4.446A pdb=" N ARG C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 337 through 345 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 375 through 378 Processing helix chain 'C' and resid 381 through 399 removed outlier: 4.391A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 428 Processing helix chain 'C' and resid 438 through 449 Processing helix chain 'C' and resid 458 through 475 removed outlier: 4.758A pdb=" N THR C 462 " --> pdb=" O SER C 459 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN C 475 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 486 Processing helix chain 'C' and resid 491 through 507 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 191 removed outlier: 4.381A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 240 through 260 Proline residue: A 247 - end of helix removed outlier: 3.910A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 284 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 296 through 306 removed outlier: 4.226A pdb=" N PHE A 299 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG A 304 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.844A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 458 through 474 removed outlier: 4.912A pdb=" N THR A 462 " --> pdb=" O SER A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 486 Processing helix chain 'A' and resid 491 through 506 Processing helix chain 'B' and resid 8 through 10 No H-bonds generated for 'chain 'B' and resid 8 through 10' Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 190 removed outlier: 3.836A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ARG B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 226 through 228 No H-bonds generated for 'chain 'B' and resid 226 through 228' Processing helix chain 'B' and resid 240 through 259 Proline residue: B 247 - end of helix removed outlier: 4.008A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 284 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 298 through 306 removed outlier: 4.009A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 345 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 375 through 378 Processing helix chain 'B' and resid 381 through 399 removed outlier: 3.989A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 427 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 458 through 474 removed outlier: 4.628A pdb=" N THR B 462 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 486 Processing helix chain 'B' and resid 491 through 507 Processing helix chain 'E' and resid 126 through 128 No H-bonds generated for 'chain 'E' and resid 126 through 128' Processing helix chain 'E' and resid 141 through 146 Processing helix chain 'E' and resid 166 through 178 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 229 through 250 removed outlier: 4.966A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE E 246 " --> pdb=" O VAL E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 274 Processing helix chain 'E' and resid 281 through 283 No H-bonds generated for 'chain 'E' and resid 281 through 283' Processing helix chain 'E' and resid 288 through 298 removed outlier: 3.706A pdb=" N MET E 295 " --> pdb=" O ASP E 291 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ARG E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 318 No H-bonds generated for 'chain 'E' and resid 316 through 318' Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 340 through 344 Processing helix chain 'E' and resid 363 through 393 removed outlier: 7.441A pdb=" N SER E 368 " --> pdb=" O ASN E 364 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N GLU E 369 " --> pdb=" O ILE E 365 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N HIS E 370 " --> pdb=" O VAL E 366 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE E 393 " --> pdb=" O ASP E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 416 Processing helix chain 'E' and resid 422 through 425 Processing helix chain 'E' and resid 437 through 449 Processing helix chain 'E' and resid 458 through 460 No H-bonds generated for 'chain 'E' and resid 458 through 460' Processing helix chain 'E' and resid 466 through 476 Processing helix chain 'F' and resid 91 through 93 No H-bonds generated for 'chain 'F' and resid 91 through 93' Processing helix chain 'F' and resid 126 through 128 No H-bonds generated for 'chain 'F' and resid 126 through 128' Processing helix chain 'F' and resid 141 through 146 Processing helix chain 'F' and resid 165 through 179 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 229 through 248 removed outlier: 5.112A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 272 Processing helix chain 'F' and resid 288 through 296 Processing helix chain 'F' and resid 316 through 318 No H-bonds generated for 'chain 'F' and resid 316 through 318' Processing helix chain 'F' and resid 323 through 331 removed outlier: 4.408A pdb=" N ALA F 330 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N HIS F 331 " --> pdb=" O THR F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 345 removed outlier: 3.667A pdb=" N LEU F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 366 No H-bonds generated for 'chain 'F' and resid 363 through 366' Processing helix chain 'F' and resid 368 through 394 removed outlier: 4.452A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 398 No H-bonds generated for 'chain 'F' and resid 396 through 398' Processing helix chain 'F' and resid 401 through 417 Processing helix chain 'F' and resid 422 through 428 removed outlier: 3.798A pdb=" N GLU F 425 " --> pdb=" O GLN F 422 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL F 426 " --> pdb=" O VAL F 423 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR F 428 " --> pdb=" O GLU F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 449 Processing helix chain 'F' and resid 457 through 459 No H-bonds generated for 'chain 'F' and resid 457 through 459' Processing helix chain 'F' and resid 466 through 479 Processing helix chain 'G' and resid 3 through 54 removed outlier: 3.853A pdb=" N ARG G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 3.732A pdb=" N LEU G 49 " --> pdb=" O GLY G 45 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 98 Processing helix chain 'G' and resid 110 through 120 removed outlier: 4.591A pdb=" N ARG G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N THR G 119 " --> pdb=" O ILE G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 149 Processing helix chain 'G' and resid 181 through 186 Processing helix chain 'G' and resid 188 through 192 Processing helix chain 'G' and resid 198 through 221 Processing helix chain 'G' and resid 225 through 270 Processing helix chain 'O' and resid 13 through 28 removed outlier: 3.911A pdb=" N LYS O 28 " --> pdb=" O SER O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 46 Processing helix chain 'O' and resid 49 through 56 Processing helix chain 'O' and resid 62 through 75 Processing helix chain 'O' and resid 80 through 91 Processing helix chain 'O' and resid 95 through 112 removed outlier: 4.543A pdb=" N GLN O 99 " --> pdb=" O SER O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 141 removed outlier: 3.897A pdb=" N SER O 140 " --> pdb=" O THR O 136 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE O 141 " --> pdb=" O VAL O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 175 through 187 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 165 through 178 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 229 through 248 removed outlier: 4.900A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 274 removed outlier: 4.206A pdb=" N LEU D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 323 through 331 removed outlier: 4.579A pdb=" N ALA D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N HIS D 331 " --> pdb=" O THR D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 344 Processing helix chain 'D' and resid 368 through 383 Processing helix chain 'D' and resid 404 through 416 Processing helix chain 'D' and resid 437 through 448 Processing helix chain 'D' and resid 457 through 459 No H-bonds generated for 'chain 'D' and resid 457 through 459' Processing helix chain 'D' and resid 466 through 479 Processing sheet with id= A, first strand: chain 'H' and resid 43 through 47 removed outlier: 6.983A pdb=" N HIS H 66 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL H 36 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL H 64 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL H 38 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N LEU H 62 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 54 through 57 Processing sheet with id= C, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.716A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ALA C 93 " --> pdb=" O MET C 52 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N GLU C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR C 91 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.999A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 349 through 352 removed outlier: 6.746A pdb=" N LEU C 166 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU C 352 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE C 168 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 8.748A pdb=" N ILE C 230 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N HIS C 263 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ILE C 202 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU C 265 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL C 204 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE C 267 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE C 206 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASP C 269 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER C 320 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE C 266 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N THR C 322 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N TYR C 268 " --> pdb=" O THR C 322 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.808A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.026A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 349 through 352 removed outlier: 7.015A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 229 through 234 removed outlier: 6.618A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER A 320 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE A 266 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR A 322 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N TYR A 268 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU A 324 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.346A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.004A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 107 through 109 removed outlier: 8.096A pdb=" N VAL B 108 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL B 231 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS B 201 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL B 232 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N TYR B 203 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA B 234 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA B 205 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N SER B 320 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ILE B 266 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR B 322 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N TYR B 268 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B 324 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 349 through 352 removed outlier: 7.105A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 13 through 15 removed outlier: 6.653A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR E 60 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLN E 27 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ILE E 16 " --> pdb=" O GLN E 27 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 86 through 89 removed outlier: 3.994A pdb=" N GLN E 115 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 334 through 336 removed outlier: 8.496A pdb=" N ILE E 155 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER E 309 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU E 157 " --> pdb=" O SER E 309 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLN E 311 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 13 through 15 removed outlier: 6.728A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA F 18 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLN F 27 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE F 16 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 86 through 89 removed outlier: 4.228A pdb=" N GLN F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 157 through 159 Processing sheet with id= U, first strand: chain 'F' and resid 218 through 223 removed outlier: 7.085A pdb=" N SER F 184 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N VAL F 221 " --> pdb=" O SER F 184 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE F 186 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLY F 223 " --> pdb=" O PHE F 186 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLY F 188 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER F 306 " --> pdb=" O VAL F 254 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU F 256 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR F 308 " --> pdb=" O LEU F 256 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE F 258 " --> pdb=" O THR F 308 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL F 310 " --> pdb=" O ILE F 258 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 170 through 179 removed outlier: 6.557A pdb=" N LYS G 172 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N PHE G 165 " --> pdb=" O LYS G 172 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU G 174 " --> pdb=" O ASN G 163 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN G 163 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS G 176 " --> pdb=" O ILE G 161 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE G 161 " --> pdb=" O LYS G 176 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE G 178 " --> pdb=" O SER G 159 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER G 159 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU G 67 " --> pdb=" O SER G 159 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE G 161 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE G 69 " --> pdb=" O ILE G 161 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N ASN G 163 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N VAL G 71 " --> pdb=" O ASN G 163 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N PHE G 165 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N MET G 104 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N GLY G 70 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL G 106 " --> pdb=" O GLY G 70 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL G 126 " --> pdb=" O GLY G 107 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'O' and resid 147 through 150 Processing sheet with id= X, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.687A pdb=" N ARG D 62 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N HIS D 55 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N THR D 60 " --> pdb=" O HIS D 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 18 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLN D 27 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE D 16 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 86 through 89 removed outlier: 3.943A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 134 through 136 removed outlier: 4.468A pdb=" N GLU D 134 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR D 149 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 157 through 159 Processing sheet with id= AB, first strand: chain 'D' and resid 218 through 223 removed outlier: 7.131A pdb=" N SER D 184 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N VAL D 221 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE D 186 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLY D 223 " --> pdb=" O PHE D 186 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLY D 188 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER D 306 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N LEU D 256 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR D 308 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE D 258 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL D 310 " --> pdb=" O ILE D 258 " (cutoff:3.500A) 2013 hydrogen bonds defined for protein. 5670 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: 14.78 Time building geometry restraints manager: 17.66 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: 11943 1.34 - 1.46: 6678 1.46 - 1.58: 19938 1.58 - 1.70: 21 1.70 - 1.82: 303 Bond restraints: 38883 Sorted by residual: bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.459 -0.122 1.10e-02 8.26e+03 1.24e+02 bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 601 " ideal model delta sigma weight residual 1.337 1.456 -0.119 1.10e-02 8.26e+03 1.16e+02 bond pdb=" C6 ATP C 601 " pdb=" N6 ATP C 601 " ideal model delta sigma weight residual 1.337 1.455 -0.118 1.10e-02 8.26e+03 1.15e+02 bond pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 1.374 1.280 0.094 1.00e-02 1.00e+04 8.86e+01 bond pdb=" C4 ATP C 601 " pdb=" N9 ATP C 601 " ideal model delta sigma weight residual 1.374 1.280 0.094 1.00e-02 1.00e+04 8.77e+01 ... (remaining 38878 not shown) Histogram of bond angle deviations from ideal: 96.05 - 104.29: 637 104.29 - 112.52: 20802 112.52 - 120.75: 19452 120.75 - 128.99: 11584 128.99 - 137.22: 138 Bond angle restraints: 52613 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 123.51 16.36 1.00e+00 1.00e+00 2.68e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 123.51 16.36 1.00e+00 1.00e+00 2.68e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 120.93 15.90 1.00e+00 1.00e+00 2.53e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 122.53 14.30 1.00e+00 1.00e+00 2.05e+02 ... (remaining 52608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.71: 22983 32.71 - 65.42: 516 65.42 - 98.13: 77 98.13 - 130.84: 1 130.84 - 163.55: 1 Dihedral angle restraints: 23578 sinusoidal: 9323 harmonic: 14255 Sorted by residual: dihedral pdb=" O1B ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PB ADP F 501 " pdb=" PA ADP F 501 " ideal model delta sinusoidal sigma weight residual 300.00 136.45 163.55 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 61.42 -121.42 1 2.00e+01 2.50e-03 3.65e+01 dihedral pdb=" CA VAL T 5 " pdb=" C VAL T 5 " pdb=" N GLN T 6 " pdb=" CA GLN T 6 " ideal model delta harmonic sigma weight residual -180.00 -152.52 -27.48 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 23575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 4434 0.052 - 0.104: 1386 0.104 - 0.156: 265 0.156 - 0.208: 49 0.208 - 0.260: 6 Chirality restraints: 6140 Sorted by residual: chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.42 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ILE P 5 " pdb=" N ILE P 5 " pdb=" C ILE P 5 " pdb=" CB ILE P 5 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.45 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 6137 not shown) Planarity restraints: 6703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 3 38 " -0.561 9.50e-02 1.11e+02 2.51e-01 3.86e+01 pdb=" NE ARG 3 38 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG 3 38 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG 3 38 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG 3 38 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 6 38 " 0.359 9.50e-02 1.11e+02 1.61e-01 1.58e+01 pdb=" NE ARG 6 38 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG 6 38 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG 6 38 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG 6 38 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 188 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C GLY E 188 " 0.055 2.00e-02 2.50e+03 pdb=" O GLY E 188 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL E 189 " -0.019 2.00e-02 2.50e+03 ... (remaining 6700 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 128 2.39 - 3.02: 24137 3.02 - 3.65: 58067 3.65 - 4.27: 91190 4.27 - 4.90: 150566 Nonbonded interactions: 324088 Sorted by model distance: nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 602 " model vdw 1.767 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 602 " model vdw 1.991 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 602 " model vdw 2.017 2.170 nonbonded pdb=" O3G ATP A 601 " pdb="MG MG A 602 " model vdw 2.186 2.170 nonbonded pdb=" O LEU S 77 " pdb=" OG1 THR S 80 " model vdw 2.204 2.440 ... (remaining 324083 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' } ncs_group { reference = (chain 'A' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = (chain 'B' and (resid 24 through 508 or resid 601 through 602)) selection = (chain 'C' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) } ncs_group { reference = (chain 'D' and (resid 12 through 318 or (resid 319 and (name N or name CA or nam \ e C or name O or name CB )) or resid 320 through 403 or (resid 404 and (name N o \ r name CA or name C or name O or name CB )) or resid 405 through 477)) selection = (chain 'E' and (resid 12 through 384 or resid 403 through 420 or resid 431 throu \ gh 477)) selection = (chain 'F' and (resid 12 through 318 or (resid 319 and (name N or name CA or nam \ e C or name O or name CB )) or resid 320 through 384 or resid 403 or (resid 404 \ and (name N or name CA or name C or name O or name CB )) or resid 405 through 42 \ 0 or resid 431 through 477)) } 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: 5.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 29.980 Check model and map are aligned: 0.690 Set scattering table: 0.360 Process input model: 106.140 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.144 38883 Z= 0.513 Angle : 0.832 19.456 52613 Z= 0.518 Chirality : 0.051 0.260 6140 Planarity : 0.006 0.251 6703 Dihedral : 14.481 163.552 14454 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.81 % Favored : 95.09 % Rotamer: Outliers : 0.05 % Allowed : 4.86 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % 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: -2.81 (0.10), residues: 4931 helix: -1.36 (0.09), residues: 2614 sheet: -1.93 (0.19), residues: 571 loop : -2.39 (0.13), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 53 HIS 0.009 0.001 HIS N 127 PHE 0.021 0.002 PHE D 262 TYR 0.022 0.002 TYR O 170 ARG 0.004 0.000 ARG O 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 898 time to evaluate : 4.677 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: K 29 THR cc_start: 0.6220 (OUTLIER) cc_final: 0.5776 (t) REVERT: L 87 MET cc_start: 0.8145 (mpp) cc_final: 0.7680 (mpp) REVERT: L 104 GLU cc_start: 0.7699 (pt0) cc_final: 0.7461 (pp20) REVERT: M 33 TRP cc_start: 0.8523 (m100) cc_final: 0.8257 (m-10) REVERT: 6 75 MET cc_start: 0.5799 (mmt) cc_final: 0.5461 (tpp) REVERT: 2 75 MET cc_start: 0.4741 (mmt) cc_final: 0.4156 (tpp) REVERT: 3 65 LEU cc_start: 0.8868 (tt) cc_final: 0.8627 (tm) REVERT: 3 73 PHE cc_start: 0.8475 (m-80) cc_final: 0.8180 (m-80) REVERT: 4 73 PHE cc_start: 0.5194 (m-80) cc_final: 0.4259 (t80) REVERT: H 15 GLN cc_start: 0.5456 (tp40) cc_final: 0.5001 (tt0) REVERT: H 34 ARG cc_start: 0.7743 (ptm-80) cc_final: 0.7523 (mtm110) REVERT: H 111 ASN cc_start: 0.7613 (m110) cc_final: 0.7330 (m110) REVERT: I 44 LYS cc_start: 0.8855 (mttt) cc_final: 0.8584 (mttm) REVERT: N 140 MET cc_start: 0.6712 (pmm) cc_final: 0.6461 (pmm) REVERT: R 87 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7929 (tm-30) REVERT: S 54 LYS cc_start: 0.8822 (tppt) cc_final: 0.8572 (tppt) REVERT: S 86 PHE cc_start: 0.9026 (t80) cc_final: 0.8796 (t80) REVERT: T 5 VAL cc_start: 0.4955 (m) cc_final: 0.4286 (m) REVERT: T 36 ARG cc_start: 0.7644 (mpp80) cc_final: 0.7236 (mpp80) REVERT: C 26 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7479 (mp0) REVERT: C 67 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7889 (mt-10) REVERT: C 140 ILE cc_start: 0.8924 (tt) cc_final: 0.8722 (tp) REVERT: C 195 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7399 (tm-30) REVERT: C 453 LEU cc_start: 0.7893 (mm) cc_final: 0.7601 (mm) REVERT: C 463 LYS cc_start: 0.8641 (ttpt) cc_final: 0.8340 (ttmt) REVERT: C 475 GLN cc_start: 0.7550 (mm110) cc_final: 0.7326 (mm-40) REVERT: C 484 ARG cc_start: 0.6336 (ttp80) cc_final: 0.5792 (ttm-80) REVERT: C 499 GLU cc_start: 0.8123 (tp30) cc_final: 0.7801 (tp30) REVERT: C 503 ASN cc_start: 0.5809 (m-40) cc_final: 0.5572 (m-40) REVERT: A 96 ASP cc_start: 0.8366 (p0) cc_final: 0.7977 (p0) REVERT: A 362 ARG cc_start: 0.7519 (mtt180) cc_final: 0.6518 (mtt90) REVERT: A 391 LYS cc_start: 0.7213 (ttpt) cc_final: 0.6986 (tttp) REVERT: A 415 GLN cc_start: 0.6244 (pt0) cc_final: 0.6015 (pm20) REVERT: B 328 GLU cc_start: 0.7950 (tt0) cc_final: 0.7686 (tt0) REVERT: B 355 GLU cc_start: 0.7477 (mp0) cc_final: 0.7076 (mp0) REVERT: E 205 GLU cc_start: 0.8249 (tt0) cc_final: 0.7773 (pt0) REVERT: F 217 LYS cc_start: 0.8053 (ptpp) cc_final: 0.7460 (mttp) REVERT: F 408 SER cc_start: 0.7586 (m) cc_final: 0.7259 (p) REVERT: F 422 GLN cc_start: 0.7777 (tp40) cc_final: 0.7570 (tm-30) REVERT: G 130 GLU cc_start: 0.7740 (tp30) cc_final: 0.6888 (tm-30) REVERT: G 260 LYS cc_start: 0.8604 (tttt) cc_final: 0.8264 (tttp) REVERT: O 33 GLU cc_start: 0.7149 (pt0) cc_final: 0.6560 (pm20) REVERT: O 37 LYS cc_start: 0.7202 (tttt) cc_final: 0.6444 (tppt) REVERT: D 64 ILE cc_start: 0.8428 (mt) cc_final: 0.8119 (pt) REVERT: D 180 HIS cc_start: 0.7621 (t-90) cc_final: 0.7223 (t-90) REVERT: D 259 ASP cc_start: 0.8597 (t0) cc_final: 0.8210 (t0) REVERT: D 462 MET cc_start: 0.5221 (mmt) cc_final: 0.4858 (mmt) outliers start: 2 outliers final: 6 residues processed: 899 average time/residue: 1.5618 time to fit residues: 1688.1177 Evaluate side-chains 636 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 629 time to evaluate : 4.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain L residue 49 GLU Chi-restraints excluded: chain 3 residue 39 ASN Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 393 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 412 optimal weight: 0.2980 chunk 369 optimal weight: 1.9990 chunk 205 optimal weight: 0.5980 chunk 126 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 382 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 284 optimal weight: 0.7980 chunk 443 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 88 GLN K 103 HIS K 114 GLN ** K 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 ASN 6 45 GLN 8 45 GLN 2 39 ASN 2 45 GLN 4 39 ASN 4 45 GLN H 32 ASN H 111 ASN N 4 ASN N 46 GLN N 47 GLN N 61 HIS N 101 ASN N 163 ASN N 210 GLN N 225 ASN P 8 ASN ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 GLN C 396 GLN A 163 GLN ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 GLN B 432 GLN B 476 HIS E 378 GLN E 419 GLN F 133 GLN F 224 GLN F 266 GLN O 84 ASN O 92 ASN D 175 ASN D 210 ASN D 364 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38883 Z= 0.226 Angle : 0.610 9.196 52613 Z= 0.314 Chirality : 0.044 0.282 6140 Planarity : 0.004 0.046 6703 Dihedral : 7.279 144.531 5498 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.33 % Favored : 96.65 % Rotamer: Outliers : 3.40 % Allowed : 15.06 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % 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: -1.18 (0.11), residues: 4931 helix: 0.01 (0.10), residues: 2649 sheet: -1.40 (0.20), residues: 555 loop : -1.69 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 53 HIS 0.009 0.001 HIS K 180 PHE 0.032 0.002 PHE L 82 TYR 0.025 0.002 TYR Q 47 ARG 0.009 0.000 ARG H 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 721 time to evaluate : 4.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 150 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7951 (tm-30) REVERT: L 49 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7624 (pm20) REVERT: L 50 TYR cc_start: 0.6483 (t80) cc_final: 0.5744 (t80) REVERT: L 87 MET cc_start: 0.8068 (mpp) cc_final: 0.7411 (mpp) REVERT: L 104 GLU cc_start: 0.7803 (pt0) cc_final: 0.7494 (pp20) REVERT: M 23 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7702 (pm20) REVERT: M 33 TRP cc_start: 0.8508 (m100) cc_final: 0.8275 (m-10) REVERT: 8 66 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7550 (pp-130) REVERT: 2 75 MET cc_start: 0.4760 (mmt) cc_final: 0.4180 (mpp) REVERT: 4 73 PHE cc_start: 0.5187 (m-80) cc_final: 0.4277 (t80) REVERT: 5 51 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7503 (mp) REVERT: 5 75 MET cc_start: 0.5299 (OUTLIER) cc_final: 0.4995 (mpm) REVERT: H 15 GLN cc_start: 0.5273 (tp40) cc_final: 0.4354 (mt0) REVERT: H 32 ASN cc_start: 0.5764 (t0) cc_final: 0.5548 (t0) REVERT: H 59 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7300 (ptt180) REVERT: I 44 LYS cc_start: 0.8834 (mttt) cc_final: 0.8583 (mttm) REVERT: N 140 MET cc_start: 0.6651 (pmm) cc_final: 0.6431 (pmm) REVERT: S 54 LYS cc_start: 0.8816 (tppt) cc_final: 0.8579 (tppt) REVERT: T 40 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8096 (mm-30) REVERT: C 26 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7486 (mp0) REVERT: C 67 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7825 (mt-10) REVERT: C 146 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.6823 (tmm) REVERT: C 195 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7115 (tp30) REVERT: C 390 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7019 (tpp) REVERT: C 465 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: C 475 GLN cc_start: 0.7504 (mm110) cc_final: 0.7279 (mm-40) REVERT: C 484 ARG cc_start: 0.6389 (ttp80) cc_final: 0.5803 (ttm-80) REVERT: C 499 GLU cc_start: 0.8091 (tp30) cc_final: 0.7688 (tm-30) REVERT: A 96 ASP cc_start: 0.8346 (p0) cc_final: 0.7989 (p0) REVERT: A 218 LYS cc_start: 0.7848 (tttp) cc_final: 0.7591 (tttt) REVERT: A 362 ARG cc_start: 0.7508 (mtt180) cc_final: 0.6512 (mtt90) REVERT: A 391 LYS cc_start: 0.7256 (ttpt) cc_final: 0.7043 (tttp) REVERT: A 482 THR cc_start: 0.7069 (p) cc_final: 0.6840 (t) REVERT: B 195 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7574 (mt-10) REVERT: B 496 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6391 (tmtm) REVERT: B 500 ILE cc_start: 0.8019 (mt) cc_final: 0.7696 (mp) REVERT: E 195 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: E 205 GLU cc_start: 0.8218 (tt0) cc_final: 0.7720 (pt0) REVERT: E 234 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.6342 (mmt90) REVERT: E 390 ILE cc_start: 0.6131 (OUTLIER) cc_final: 0.5874 (mp) REVERT: E 445 GLN cc_start: 0.7677 (tt0) cc_final: 0.7473 (tt0) REVERT: E 476 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.7040 (mt) REVERT: F 30 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7366 (pt0) REVERT: F 171 GLU cc_start: 0.7495 (tp30) cc_final: 0.7200 (tp30) REVERT: F 217 LYS cc_start: 0.7877 (ptpp) cc_final: 0.7315 (mttp) REVERT: F 248 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8123 (m-30) REVERT: F 249 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7935 (mt0) REVERT: F 380 ILE cc_start: 0.8299 (mp) cc_final: 0.7961 (mm) REVERT: F 402 GLU cc_start: 0.7408 (tp30) cc_final: 0.7169 (tp30) REVERT: F 408 SER cc_start: 0.7446 (m) cc_final: 0.7145 (p) REVERT: G 52 TYR cc_start: 0.7568 (m-80) cc_final: 0.7144 (m-80) REVERT: G 123 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.6683 (pm20) REVERT: G 130 GLU cc_start: 0.7871 (tp30) cc_final: 0.6891 (tm-30) REVERT: G 260 LYS cc_start: 0.8579 (tttt) cc_final: 0.8250 (tttp) REVERT: O 33 GLU cc_start: 0.7171 (pt0) cc_final: 0.6492 (pm20) REVERT: O 37 LYS cc_start: 0.7287 (tttt) cc_final: 0.6526 (tppt) REVERT: D 149 TYR cc_start: 0.6649 (m-10) cc_final: 0.6427 (m-10) REVERT: D 180 HIS cc_start: 0.7445 (t-90) cc_final: 0.7048 (t-90) REVERT: D 248 ASP cc_start: 0.7468 (m-30) cc_final: 0.7165 (m-30) REVERT: D 259 ASP cc_start: 0.8514 (t0) cc_final: 0.8313 (t0) REVERT: D 342 ILE cc_start: 0.8058 (mt) cc_final: 0.7779 (tt) REVERT: D 458 GLN cc_start: 0.5562 (OUTLIER) cc_final: 0.5161 (tp40) outliers start: 137 outliers final: 34 residues processed: 776 average time/residue: 1.3859 time to fit residues: 1316.8724 Evaluate side-chains 678 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 623 time to evaluate : 4.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain L residue 49 GLU Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 21 GLN Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 7 residue 65 LEU Chi-restraints excluded: chain 8 residue 66 MET Chi-restraints excluded: chain 1 residue 16 VAL Chi-restraints excluded: chain 2 residue 15 THR Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain 5 residue 62 LEU Chi-restraints excluded: chain 5 residue 67 VAL Chi-restraints excluded: chain 5 residue 75 MET Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain T residue 7 VAL Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 458 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 246 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 chunk 368 optimal weight: 0.6980 chunk 301 optimal weight: 8.9990 chunk 122 optimal weight: 0.5980 chunk 443 optimal weight: 6.9990 chunk 479 optimal weight: 0.0270 chunk 395 optimal weight: 1.9990 chunk 440 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 356 optimal weight: 6.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 172 HIS ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 45 GLN 2 39 ASN 2 45 GLN 4 45 GLN 5 39 ASN H 111 ASN ** N 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN R 44 GLN T 6 GLN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN B 70 ASN B 476 HIS D 174 ASN D 210 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38883 Z= 0.172 Angle : 0.577 10.106 52613 Z= 0.293 Chirality : 0.043 0.169 6140 Planarity : 0.004 0.045 6703 Dihedral : 6.824 122.313 5491 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 3.30 % Allowed : 17.57 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % 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: -0.39 (0.12), residues: 4931 helix: 0.64 (0.10), residues: 2662 sheet: -1.01 (0.21), residues: 574 loop : -1.33 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 176 HIS 0.009 0.001 HIS K 180 PHE 0.019 0.001 PHE C 464 TYR 0.028 0.001 TYR L 50 ARG 0.009 0.000 ARG H 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 693 time to evaluate : 4.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 134 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.8009 (ttt) REVERT: K 178 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8421 (mm-30) REVERT: L 49 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7827 (pm20) REVERT: L 87 MET cc_start: 0.7892 (mpp) cc_final: 0.7224 (mpp) REVERT: L 104 GLU cc_start: 0.7792 (pt0) cc_final: 0.7477 (pp20) REVERT: M 33 TRP cc_start: 0.8513 (m100) cc_final: 0.8277 (m-10) REVERT: 8 66 MET cc_start: 0.7709 (pp-130) cc_final: 0.7458 (pp-130) REVERT: 2 51 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7222 (mp) REVERT: 2 75 MET cc_start: 0.4771 (mmt) cc_final: 0.4173 (mpp) REVERT: 3 60 MET cc_start: 0.8000 (mmp) cc_final: 0.7751 (mmm) REVERT: 4 73 PHE cc_start: 0.5236 (m-80) cc_final: 0.4361 (t80) REVERT: 5 51 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7379 (mp) REVERT: 5 75 MET cc_start: 0.5367 (mpm) cc_final: 0.5150 (mpm) REVERT: H 15 GLN cc_start: 0.5158 (tp40) cc_final: 0.4198 (mt0) REVERT: H 59 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7409 (ptt180) REVERT: I 44 LYS cc_start: 0.8817 (mttt) cc_final: 0.8593 (mttm) REVERT: R 30 LEU cc_start: 0.9193 (mm) cc_final: 0.8992 (mm) REVERT: S 54 LYS cc_start: 0.8809 (tppt) cc_final: 0.8567 (tppt) REVERT: T 30 TYR cc_start: 0.6603 (t80) cc_final: 0.6222 (t80) REVERT: T 31 ASN cc_start: 0.8749 (m-40) cc_final: 0.8243 (p0) REVERT: T 40 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8031 (mm-30) REVERT: C 26 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7512 (mp0) REVERT: C 195 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7075 (tp30) REVERT: C 390 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.6806 (tpp) REVERT: C 484 ARG cc_start: 0.6445 (ttp80) cc_final: 0.5812 (ttm-80) REVERT: C 499 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7551 (tp30) REVERT: A 96 ASP cc_start: 0.8355 (p0) cc_final: 0.7979 (p0) REVERT: A 181 ASP cc_start: 0.7510 (m-30) cc_final: 0.7244 (t0) REVERT: A 218 LYS cc_start: 0.7780 (tttp) cc_final: 0.7562 (tttt) REVERT: A 226 MET cc_start: 0.9068 (tpt) cc_final: 0.8398 (tpt) REVERT: A 351 PHE cc_start: 0.7281 (m-80) cc_final: 0.6900 (t80) REVERT: A 362 ARG cc_start: 0.7479 (mtt180) cc_final: 0.6583 (mtt90) REVERT: B 477 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7846 (mm110) REVERT: B 496 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.6372 (tmtm) REVERT: B 500 ILE cc_start: 0.8004 (mt) cc_final: 0.7694 (mp) REVERT: E 195 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: E 205 GLU cc_start: 0.8194 (tt0) cc_final: 0.7760 (pt0) REVERT: E 234 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.6335 (mmt90) REVERT: E 390 ILE cc_start: 0.6167 (OUTLIER) cc_final: 0.5927 (mt) REVERT: E 476 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.7074 (mt) REVERT: F 171 GLU cc_start: 0.7465 (tp30) cc_final: 0.7241 (tp30) REVERT: F 217 LYS cc_start: 0.7826 (ptpp) cc_final: 0.7251 (mttp) REVERT: F 249 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7914 (mt0) REVERT: F 402 GLU cc_start: 0.7502 (tp30) cc_final: 0.7195 (tp30) REVERT: F 408 SER cc_start: 0.7455 (m) cc_final: 0.7163 (p) REVERT: G 123 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6779 (pm20) REVERT: G 130 GLU cc_start: 0.7955 (tp30) cc_final: 0.6911 (tm-30) REVERT: G 260 LYS cc_start: 0.8585 (tttt) cc_final: 0.8238 (tttp) REVERT: O 33 GLU cc_start: 0.7188 (pt0) cc_final: 0.6499 (pm20) REVERT: O 37 LYS cc_start: 0.7315 (tttt) cc_final: 0.6569 (tppt) REVERT: O 148 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.6916 (mp) REVERT: D 149 TYR cc_start: 0.6554 (m-10) cc_final: 0.6316 (m-10) REVERT: D 180 HIS cc_start: 0.7392 (t-90) cc_final: 0.7019 (t-90) REVERT: D 248 ASP cc_start: 0.7393 (m-30) cc_final: 0.7089 (m-30) REVERT: D 259 ASP cc_start: 0.8416 (t0) cc_final: 0.8074 (t0) REVERT: D 322 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7729 (t70) REVERT: D 342 ILE cc_start: 0.8147 (mt) cc_final: 0.7849 (tt) REVERT: D 458 GLN cc_start: 0.5632 (OUTLIER) cc_final: 0.5212 (tp40) outliers start: 133 outliers final: 40 residues processed: 760 average time/residue: 1.3976 time to fit residues: 1311.9059 Evaluate side-chains 689 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 631 time to evaluate : 4.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 134 MET Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 49 GLU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 1 residue 16 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 51 ILE Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 4 residue 45 GLN Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain T residue 25 TYR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 458 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 438 optimal weight: 10.0000 chunk 333 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 211 optimal weight: 0.0030 chunk 298 optimal weight: 7.9990 chunk 445 optimal weight: 5.9990 chunk 471 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 422 optimal weight: 8.9990 chunk 127 optimal weight: 0.7980 overall best weight: 2.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 92 GLN L 80 GLN ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 45 GLN 2 39 ASN 2 45 GLN 4 45 GLN H 32 ASN H 111 ASN ** N 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN A 396 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN G 120 HIS G 123 GLN O 112 HIS D 249 GLN D 364 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 38883 Z= 0.345 Angle : 0.637 10.077 52613 Z= 0.324 Chirality : 0.046 0.234 6140 Planarity : 0.004 0.044 6703 Dihedral : 6.912 120.982 5491 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.63 % Favored : 96.35 % Rotamer: Outliers : 4.24 % Allowed : 19.03 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % 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: -0.29 (0.12), residues: 4931 helix: 0.70 (0.10), residues: 2668 sheet: -0.96 (0.21), residues: 578 loop : -1.23 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 53 HIS 0.006 0.001 HIS N 127 PHE 0.039 0.002 PHE L 82 TYR 0.023 0.002 TYR G 44 ARG 0.009 0.000 ARG K 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 637 time to evaluate : 4.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 134 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8203 (ttt) REVERT: K 146 ARG cc_start: 0.8027 (ttm170) cc_final: 0.7538 (ttt-90) REVERT: K 150 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: L 49 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7800 (pm20) REVERT: L 54 ARG cc_start: 0.7461 (tmm160) cc_final: 0.7260 (tmm160) REVERT: L 87 MET cc_start: 0.7910 (mpp) cc_final: 0.7392 (mpp) REVERT: L 104 GLU cc_start: 0.7907 (pt0) cc_final: 0.7548 (pp20) REVERT: M 33 TRP cc_start: 0.8525 (m100) cc_final: 0.8268 (m-10) REVERT: M 69 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.6501 (t80) REVERT: 8 66 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7533 (pp-130) REVERT: 2 51 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7307 (mp) REVERT: 2 75 MET cc_start: 0.4656 (mmt) cc_final: 0.4034 (mpp) REVERT: 5 51 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7476 (mp) REVERT: H 15 GLN cc_start: 0.5167 (tp40) cc_final: 0.4184 (mt0) REVERT: H 59 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7337 (ptt180) REVERT: I 32 LYS cc_start: 0.7594 (tptp) cc_final: 0.7288 (tptp) REVERT: I 44 LYS cc_start: 0.8792 (mttt) cc_final: 0.8573 (mttm) REVERT: N 30 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8634 (mp) REVERT: N 163 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8194 (m-40) REVERT: P 6 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7771 (tt) REVERT: R 32 ARG cc_start: 0.6107 (OUTLIER) cc_final: 0.4950 (mmm-85) REVERT: R 69 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6813 (mp) REVERT: S 54 LYS cc_start: 0.8821 (tppt) cc_final: 0.8569 (tppt) REVERT: T 30 TYR cc_start: 0.6605 (t80) cc_final: 0.6402 (t80) REVERT: T 31 ASN cc_start: 0.8616 (m-40) cc_final: 0.8249 (p0) REVERT: T 40 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8176 (mm-30) REVERT: C 26 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7543 (mp0) REVERT: C 195 GLU cc_start: 0.7505 (tm-30) cc_final: 0.6983 (tp30) REVERT: C 390 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.6869 (tpp) REVERT: C 399 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6372 (pp20) REVERT: C 484 ARG cc_start: 0.6516 (ttp80) cc_final: 0.5881 (ttm170) REVERT: A 96 ASP cc_start: 0.8399 (p0) cc_final: 0.8000 (p0) REVERT: A 181 ASP cc_start: 0.7492 (m-30) cc_final: 0.7217 (t0) REVERT: A 218 LYS cc_start: 0.7879 (tttp) cc_final: 0.7509 (tttt) REVERT: A 226 MET cc_start: 0.9087 (tpt) cc_final: 0.8407 (tpt) REVERT: A 351 PHE cc_start: 0.7361 (m-80) cc_final: 0.6924 (t80) REVERT: A 362 ARG cc_start: 0.7582 (mtt180) cc_final: 0.6701 (mtt90) REVERT: A 475 GLN cc_start: 0.7849 (mp-120) cc_final: 0.7581 (pm20) REVERT: A 476 HIS cc_start: 0.6720 (m-70) cc_final: 0.6303 (m-70) REVERT: B 54 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: B 195 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: B 477 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7778 (mm110) REVERT: E 195 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7576 (mt-10) REVERT: E 205 GLU cc_start: 0.8213 (tt0) cc_final: 0.7768 (pt0) REVERT: E 227 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: E 234 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.5458 (mmp80) REVERT: F 30 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7368 (pt0) REVERT: F 171 GLU cc_start: 0.7478 (tp30) cc_final: 0.7272 (tp30) REVERT: F 202 GLU cc_start: 0.7479 (pt0) cc_final: 0.7269 (pt0) REVERT: F 217 LYS cc_start: 0.7951 (ptpp) cc_final: 0.7355 (mttp) REVERT: F 248 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8093 (m-30) REVERT: F 249 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7912 (mt0) REVERT: F 402 GLU cc_start: 0.7543 (tp30) cc_final: 0.7270 (tp30) REVERT: G 130 GLU cc_start: 0.7979 (tp30) cc_final: 0.6903 (tm-30) REVERT: G 260 LYS cc_start: 0.8606 (tttt) cc_final: 0.8249 (tttp) REVERT: O 33 GLU cc_start: 0.7258 (pt0) cc_final: 0.6539 (pm20) REVERT: O 37 LYS cc_start: 0.7316 (tttt) cc_final: 0.6575 (tppt) REVERT: D 149 TYR cc_start: 0.6596 (m-10) cc_final: 0.6184 (m-10) REVERT: D 180 HIS cc_start: 0.7513 (t-90) cc_final: 0.7097 (t-90) REVERT: D 248 ASP cc_start: 0.7357 (m-30) cc_final: 0.7062 (m-30) REVERT: D 322 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7804 (t70) REVERT: D 458 GLN cc_start: 0.5694 (OUTLIER) cc_final: 0.5428 (tp40) outliers start: 171 outliers final: 73 residues processed: 732 average time/residue: 1.4465 time to fit residues: 1294.0242 Evaluate side-chains 705 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 606 time to evaluate : 4.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain K residue 134 MET Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 49 GLU Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 65 LEU Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 65 LEU Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 66 MET Chi-restraints excluded: chain 1 residue 16 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 57 SER Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 51 ILE Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 2 residue 71 ILE Chi-restraints excluded: chain 3 residue 15 THR Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 32 ARG Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 25 TYR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 249 GLN Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 458 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 392 optimal weight: 4.9990 chunk 267 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 351 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 402 optimal weight: 5.9990 chunk 326 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 240 optimal weight: 1.9990 chunk 423 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 92 GLN ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 45 GLN 2 39 ASN 4 45 GLN H 32 ASN H 111 ASN ** N 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN R 44 GLN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN B 70 ASN E 378 GLN G 123 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38883 Z= 0.193 Angle : 0.593 11.216 52613 Z= 0.298 Chirality : 0.043 0.217 6140 Planarity : 0.004 0.048 6703 Dihedral : 6.695 121.117 5491 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.41 % Favored : 96.57 % Rotamer: Outliers : 3.95 % Allowed : 20.07 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.12), residues: 4931 helix: 0.99 (0.10), residues: 2661 sheet: -0.81 (0.21), residues: 581 loop : -1.02 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 53 HIS 0.006 0.001 HIS N 127 PHE 0.031 0.001 PHE L 82 TYR 0.022 0.001 TYR B 446 ARG 0.010 0.000 ARG M 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 670 time to evaluate : 4.532 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: K 146 ARG cc_start: 0.8018 (ttm170) cc_final: 0.7516 (ttt-90) REVERT: K 150 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: K 165 MET cc_start: 0.8170 (mtp) cc_final: 0.7880 (mmp) REVERT: K 174 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7958 (tt) REVERT: L 49 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7871 (pm20) REVERT: L 87 MET cc_start: 0.8007 (mpp) cc_final: 0.7296 (mpp) REVERT: L 104 GLU cc_start: 0.7891 (pt0) cc_final: 0.7547 (pp20) REVERT: M 33 TRP cc_start: 0.8517 (m100) cc_final: 0.8280 (m-10) REVERT: 8 66 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7419 (pp-130) REVERT: 2 51 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7258 (mp) REVERT: 2 75 MET cc_start: 0.4590 (mmt) cc_final: 0.3977 (mpp) REVERT: 3 60 MET cc_start: 0.7949 (mmp) cc_final: 0.7676 (mmm) REVERT: 5 51 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7452 (mp) REVERT: 5 75 MET cc_start: 0.5423 (mpm) cc_final: 0.3763 (mtm) REVERT: H 15 GLN cc_start: 0.5105 (tp40) cc_final: 0.4151 (mt0) REVERT: I 32 LYS cc_start: 0.7651 (tptp) cc_final: 0.7347 (tptp) REVERT: I 44 LYS cc_start: 0.8792 (mttt) cc_final: 0.8592 (mttm) REVERT: N 30 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8617 (mp) REVERT: N 163 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8121 (m110) REVERT: R 32 ARG cc_start: 0.6150 (OUTLIER) cc_final: 0.4998 (mmm-85) REVERT: S 54 LYS cc_start: 0.8835 (tppt) cc_final: 0.8559 (tppt) REVERT: S 90 GLU cc_start: 0.8239 (pp20) cc_final: 0.8003 (pp20) REVERT: T 30 TYR cc_start: 0.6657 (t80) cc_final: 0.6399 (t80) REVERT: T 31 ASN cc_start: 0.8484 (m-40) cc_final: 0.8140 (p0) REVERT: C 26 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7553 (mp0) REVERT: C 195 GLU cc_start: 0.7443 (tm-30) cc_final: 0.6934 (tp30) REVERT: C 390 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.6824 (tpp) REVERT: C 399 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6372 (pp20) REVERT: C 473 VAL cc_start: 0.7146 (OUTLIER) cc_final: 0.6943 (t) REVERT: C 475 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7284 (mt0) REVERT: C 484 ARG cc_start: 0.6479 (ttp80) cc_final: 0.5835 (ttm170) REVERT: A 96 ASP cc_start: 0.8343 (p0) cc_final: 0.7944 (p0) REVERT: A 154 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.7883 (m-30) REVERT: A 181 ASP cc_start: 0.7500 (m-30) cc_final: 0.7218 (t0) REVERT: A 218 LYS cc_start: 0.7804 (tttp) cc_final: 0.7578 (tttt) REVERT: A 226 MET cc_start: 0.9076 (tpt) cc_final: 0.8468 (tpt) REVERT: A 351 PHE cc_start: 0.7377 (m-80) cc_final: 0.6907 (t80) REVERT: A 362 ARG cc_start: 0.7551 (mtt180) cc_final: 0.6652 (mtt90) REVERT: A 475 GLN cc_start: 0.7843 (mp-120) cc_final: 0.7602 (pm20) REVERT: A 476 HIS cc_start: 0.6776 (m-70) cc_final: 0.6436 (m-70) REVERT: B 195 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7500 (mt-10) REVERT: B 477 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7781 (mm110) REVERT: E 195 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: E 205 GLU cc_start: 0.8178 (tt0) cc_final: 0.7747 (pt0) REVERT: E 227 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: E 234 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.5516 (mmp80) REVERT: F 30 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7313 (pt0) REVERT: F 217 LYS cc_start: 0.7879 (ptpp) cc_final: 0.7264 (mttp) REVERT: F 248 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8061 (m-30) REVERT: F 380 ILE cc_start: 0.8327 (mp) cc_final: 0.8017 (mm) REVERT: F 402 GLU cc_start: 0.7517 (tp30) cc_final: 0.7230 (tp30) REVERT: G 130 GLU cc_start: 0.7998 (tp30) cc_final: 0.6889 (tm-30) REVERT: G 260 LYS cc_start: 0.8573 (tttt) cc_final: 0.8217 (tttp) REVERT: O 33 GLU cc_start: 0.7295 (pt0) cc_final: 0.6578 (pm20) REVERT: O 37 LYS cc_start: 0.7289 (tttt) cc_final: 0.6587 (tppt) REVERT: D 59 SER cc_start: 0.8885 (m) cc_final: 0.8491 (p) REVERT: D 149 TYR cc_start: 0.6562 (m-10) cc_final: 0.6257 (m-10) REVERT: D 180 HIS cc_start: 0.7381 (t-90) cc_final: 0.6949 (t-90) REVERT: D 248 ASP cc_start: 0.7287 (m-30) cc_final: 0.6992 (m-30) REVERT: D 259 ASP cc_start: 0.8355 (t0) cc_final: 0.8106 (t0) REVERT: D 290 THR cc_start: 0.6391 (t) cc_final: 0.5943 (p) REVERT: D 322 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7767 (t70) REVERT: D 458 GLN cc_start: 0.5728 (OUTLIER) cc_final: 0.5476 (tp40) REVERT: D 462 MET cc_start: 0.6016 (mmt) cc_final: 0.5789 (mmt) outliers start: 159 outliers final: 66 residues processed: 761 average time/residue: 1.4034 time to fit residues: 1311.2484 Evaluate side-chains 706 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 617 time to evaluate : 4.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 49 GLU Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain 6 residue 9 ILE Chi-restraints excluded: chain 6 residue 41 SER Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 65 LEU Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 66 MET Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain 1 residue 16 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 51 ILE Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 15 THR Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 4 residue 45 GLN Chi-restraints excluded: chain 4 residue 71 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 51 ILE Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 32 ARG Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 25 TYR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 458 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 158 optimal weight: 0.7980 chunk 424 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 276 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 472 optimal weight: 6.9990 chunk 391 optimal weight: 0.9990 chunk 218 optimal weight: 7.9990 chunk 39 optimal weight: 0.3980 chunk 156 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 92 GLN ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 45 GLN 2 39 ASN 2 45 GLN 4 45 GLN H 111 ASN I 42 ASN ** N 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 GLN ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN G 123 GLN D 364 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 38883 Z= 0.198 Angle : 0.600 12.653 52613 Z= 0.300 Chirality : 0.043 0.294 6140 Planarity : 0.004 0.052 6703 Dihedral : 6.581 121.616 5489 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.35 % Favored : 96.63 % Rotamer: Outliers : 3.67 % Allowed : 21.84 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % 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: 0.29 (0.12), residues: 4931 helix: 1.13 (0.10), residues: 2653 sheet: -0.68 (0.21), residues: 582 loop : -0.90 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 53 HIS 0.006 0.001 HIS N 127 PHE 0.021 0.001 PHE L 82 TYR 0.030 0.001 TYR Q 47 ARG 0.010 0.000 ARG M 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 646 time to evaluate : 4.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 134 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8090 (ttt) REVERT: K 146 ARG cc_start: 0.8000 (ttm170) cc_final: 0.7504 (ttt-90) REVERT: K 150 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: K 164 MET cc_start: 0.8755 (tpp) cc_final: 0.8443 (tmm) REVERT: K 174 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7823 (tt) REVERT: L 49 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: L 50 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.6813 (t80) REVERT: L 87 MET cc_start: 0.7994 (mpp) cc_final: 0.7265 (mpp) REVERT: L 104 GLU cc_start: 0.7888 (pt0) cc_final: 0.7559 (pp20) REVERT: M 33 TRP cc_start: 0.8563 (m100) cc_final: 0.8291 (m-10) REVERT: M 69 PHE cc_start: 0.6588 (OUTLIER) cc_final: 0.5786 (t80) REVERT: 8 66 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7443 (pp-130) REVERT: 1 60 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.7123 (tpp) REVERT: 2 51 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7306 (mp) REVERT: 2 75 MET cc_start: 0.4605 (mmt) cc_final: 0.3982 (mpp) REVERT: 5 75 MET cc_start: 0.5551 (mpm) cc_final: 0.3850 (mtm) REVERT: H 15 GLN cc_start: 0.5217 (tp40) cc_final: 0.4168 (mt0) REVERT: N 30 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8625 (mp) REVERT: N 163 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.8122 (m110) REVERT: S 54 LYS cc_start: 0.8822 (tppt) cc_final: 0.8470 (tppt) REVERT: S 90 GLU cc_start: 0.8324 (pp20) cc_final: 0.7948 (pp20) REVERT: S 91 ILE cc_start: 0.8987 (mp) cc_final: 0.8773 (mm) REVERT: C 26 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7559 (mp0) REVERT: C 195 GLU cc_start: 0.7427 (tm-30) cc_final: 0.6905 (tp30) REVERT: C 390 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.6792 (tpp) REVERT: C 399 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6394 (pp20) REVERT: C 475 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7407 (mt0) REVERT: C 484 ARG cc_start: 0.6492 (ttp80) cc_final: 0.5836 (ttm-80) REVERT: A 89 LYS cc_start: 0.7874 (mptp) cc_final: 0.7664 (mmmt) REVERT: A 96 ASP cc_start: 0.8352 (p0) cc_final: 0.7947 (p0) REVERT: A 181 ASP cc_start: 0.7498 (m-30) cc_final: 0.7230 (t0) REVERT: A 218 LYS cc_start: 0.7842 (tttp) cc_final: 0.7591 (tttt) REVERT: A 226 MET cc_start: 0.9077 (tpt) cc_final: 0.8515 (tpt) REVERT: A 351 PHE cc_start: 0.7369 (m-80) cc_final: 0.6909 (t80) REVERT: A 362 ARG cc_start: 0.7535 (mtt180) cc_final: 0.6648 (mtt90) REVERT: A 475 GLN cc_start: 0.7865 (mp-120) cc_final: 0.7630 (pm20) REVERT: A 476 HIS cc_start: 0.6724 (m-70) cc_final: 0.6407 (m-70) REVERT: B 195 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: B 476 HIS cc_start: 0.7538 (m-70) cc_final: 0.7223 (m90) REVERT: E 195 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7524 (mt-10) REVERT: E 205 GLU cc_start: 0.8186 (tt0) cc_final: 0.7757 (pt0) REVERT: E 227 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7538 (mt-10) REVERT: E 234 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.5426 (mmp80) REVERT: F 30 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7327 (pt0) REVERT: F 171 GLU cc_start: 0.7485 (tp30) cc_final: 0.7129 (tp30) REVERT: F 217 LYS cc_start: 0.7872 (ptpp) cc_final: 0.7264 (mttp) REVERT: F 248 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8080 (m-30) REVERT: F 380 ILE cc_start: 0.8330 (mp) cc_final: 0.8027 (mm) REVERT: F 402 GLU cc_start: 0.7504 (tp30) cc_final: 0.7210 (tp30) REVERT: G 130 GLU cc_start: 0.8030 (tp30) cc_final: 0.6881 (tm-30) REVERT: G 260 LYS cc_start: 0.8572 (tttt) cc_final: 0.8215 (tttp) REVERT: O 33 GLU cc_start: 0.7228 (pt0) cc_final: 0.6470 (pm20) REVERT: O 37 LYS cc_start: 0.7327 (tttt) cc_final: 0.6571 (tppt) REVERT: D 59 SER cc_start: 0.8874 (m) cc_final: 0.8511 (p) REVERT: D 149 TYR cc_start: 0.6594 (m-10) cc_final: 0.6294 (m-10) REVERT: D 180 HIS cc_start: 0.7368 (t-90) cc_final: 0.6936 (t-90) REVERT: D 203 MET cc_start: 0.8602 (mtt) cc_final: 0.8305 (mtt) REVERT: D 248 ASP cc_start: 0.7215 (m-30) cc_final: 0.6905 (m-30) REVERT: D 259 ASP cc_start: 0.8341 (t0) cc_final: 0.8038 (t0) REVERT: D 290 THR cc_start: 0.6372 (t) cc_final: 0.5925 (p) REVERT: D 458 GLN cc_start: 0.5705 (OUTLIER) cc_final: 0.5469 (tp40) REVERT: D 462 MET cc_start: 0.6077 (mmt) cc_final: 0.5867 (mmt) outliers start: 148 outliers final: 75 residues processed: 726 average time/residue: 1.4057 time to fit residues: 1250.6612 Evaluate side-chains 708 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 612 time to evaluate : 4.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 134 MET Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 49 GLU Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 41 SER Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 66 MET Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain 1 residue 16 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 60 MET Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 51 ILE Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 15 THR Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain S residue 44 GLU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 25 TYR Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 458 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 455 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 344 optimal weight: 0.0870 chunk 267 optimal weight: 0.9980 chunk 397 optimal weight: 3.9990 chunk 263 optimal weight: 5.9990 chunk 470 optimal weight: 1.9990 chunk 294 optimal weight: 8.9990 chunk 286 optimal weight: 0.7980 chunk 217 optimal weight: 0.6980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 172 HIS L 80 GLN ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 45 GLN 2 39 ASN 2 45 GLN H 116 GLN ** N 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 GLN ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 38883 Z= 0.172 Angle : 0.592 13.492 52613 Z= 0.296 Chirality : 0.043 0.312 6140 Planarity : 0.004 0.052 6703 Dihedral : 6.359 121.855 5489 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.31 % Favored : 96.67 % Rotamer: Outliers : 3.42 % Allowed : 22.70 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.12), residues: 4931 helix: 1.25 (0.10), residues: 2657 sheet: -0.52 (0.21), residues: 581 loop : -0.79 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 53 HIS 0.005 0.001 HIS K 172 PHE 0.035 0.001 PHE 1 54 TYR 0.033 0.001 TYR A 397 ARG 0.009 0.000 ARG 5 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 659 time to evaluate : 4.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 134 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8053 (ttt) REVERT: K 146 ARG cc_start: 0.8021 (ttm170) cc_final: 0.7521 (ttt-90) REVERT: K 164 MET cc_start: 0.8776 (tpp) cc_final: 0.8493 (tmm) REVERT: K 174 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7826 (tt) REVERT: L 87 MET cc_start: 0.8005 (mpp) cc_final: 0.7230 (mpp) REVERT: L 104 GLU cc_start: 0.7872 (pt0) cc_final: 0.7552 (pp20) REVERT: M 33 TRP cc_start: 0.8551 (m100) cc_final: 0.8286 (m-10) REVERT: M 69 PHE cc_start: 0.6598 (OUTLIER) cc_final: 0.5677 (t80) REVERT: M 123 ASN cc_start: 0.8675 (m-40) cc_final: 0.8390 (p0) REVERT: 7 39 ASN cc_start: 0.7696 (t0) cc_final: 0.7433 (t0) REVERT: 8 66 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7437 (pp-130) REVERT: 2 75 MET cc_start: 0.4554 (mmt) cc_final: 0.3932 (mpp) REVERT: 5 75 MET cc_start: 0.5553 (mpm) cc_final: 0.3912 (mtm) REVERT: H 15 GLN cc_start: 0.5150 (tp40) cc_final: 0.4109 (mt0) REVERT: I 32 LYS cc_start: 0.7487 (tptt) cc_final: 0.7214 (tptp) REVERT: N 163 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.8119 (m110) REVERT: R 69 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6668 (mp) REVERT: S 54 LYS cc_start: 0.8770 (tppt) cc_final: 0.8480 (tppt) REVERT: S 90 GLU cc_start: 0.8323 (pp20) cc_final: 0.7978 (pp20) REVERT: S 91 ILE cc_start: 0.9012 (mp) cc_final: 0.8812 (mm) REVERT: C 26 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7564 (mp0) REVERT: C 195 GLU cc_start: 0.7394 (tm-30) cc_final: 0.6905 (tp30) REVERT: C 390 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.6766 (tpp) REVERT: C 477 GLN cc_start: 0.7855 (tp40) cc_final: 0.7142 (mm110) REVERT: C 484 ARG cc_start: 0.6493 (ttp80) cc_final: 0.5829 (ttm-80) REVERT: A 89 LYS cc_start: 0.7843 (mptp) cc_final: 0.7616 (mmmt) REVERT: A 96 ASP cc_start: 0.8358 (p0) cc_final: 0.7958 (p0) REVERT: A 181 ASP cc_start: 0.7511 (m-30) cc_final: 0.7241 (t0) REVERT: A 218 LYS cc_start: 0.7757 (tttp) cc_final: 0.7522 (tttt) REVERT: A 226 MET cc_start: 0.9076 (tpt) cc_final: 0.8526 (tpt) REVERT: A 351 PHE cc_start: 0.7309 (m-80) cc_final: 0.6790 (t80) REVERT: A 362 ARG cc_start: 0.7526 (mtt180) cc_final: 0.6505 (mtt180) REVERT: A 475 GLN cc_start: 0.7782 (mp-120) cc_final: 0.7509 (pm20) REVERT: A 476 HIS cc_start: 0.6663 (m-70) cc_final: 0.5992 (m-70) REVERT: B 476 HIS cc_start: 0.7508 (m-70) cc_final: 0.7216 (m90) REVERT: E 195 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7657 (mm-30) REVERT: E 205 GLU cc_start: 0.8193 (tt0) cc_final: 0.7790 (pt0) REVERT: E 227 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7532 (mt-10) REVERT: E 234 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.5410 (mmp80) REVERT: F 30 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7326 (pt0) REVERT: F 171 GLU cc_start: 0.7491 (tp30) cc_final: 0.7136 (tp30) REVERT: F 217 LYS cc_start: 0.7839 (ptpp) cc_final: 0.7236 (mttp) REVERT: F 248 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8086 (m-30) REVERT: F 402 GLU cc_start: 0.7485 (tp30) cc_final: 0.7189 (tp30) REVERT: G 130 GLU cc_start: 0.8050 (tp30) cc_final: 0.6850 (tm-30) REVERT: G 260 LYS cc_start: 0.8572 (tttt) cc_final: 0.8212 (tttp) REVERT: O 33 GLU cc_start: 0.7167 (pt0) cc_final: 0.6451 (pm20) REVERT: O 37 LYS cc_start: 0.7292 (tttt) cc_final: 0.6566 (tppt) REVERT: O 173 MET cc_start: 0.7698 (mtm) cc_final: 0.7036 (mtm) REVERT: D 59 SER cc_start: 0.8866 (m) cc_final: 0.8503 (p) REVERT: D 149 TYR cc_start: 0.6600 (m-10) cc_final: 0.6305 (m-10) REVERT: D 180 HIS cc_start: 0.7340 (t-90) cc_final: 0.6936 (t-90) REVERT: D 202 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7026 (tm-30) REVERT: D 248 ASP cc_start: 0.7087 (m-30) cc_final: 0.6764 (m-30) REVERT: D 259 ASP cc_start: 0.8318 (t0) cc_final: 0.7991 (t0) REVERT: D 458 GLN cc_start: 0.5675 (OUTLIER) cc_final: 0.5449 (tp40) outliers start: 138 outliers final: 68 residues processed: 734 average time/residue: 1.4346 time to fit residues: 1300.6756 Evaluate side-chains 706 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 625 time to evaluate : 4.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 134 MET Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 9 ILE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 66 MET Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain 1 residue 16 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 15 THR Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain S residue 44 GLU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 25 TYR Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 458 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 290 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 280 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 299 optimal weight: 1.9990 chunk 320 optimal weight: 7.9990 chunk 232 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 369 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 92 GLN ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN 8 45 GLN 2 39 ASN 2 45 GLN I 42 ASN ** N 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 GLN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN F 180 HIS ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 38883 Z= 0.310 Angle : 0.658 14.230 52613 Z= 0.330 Chirality : 0.045 0.327 6140 Planarity : 0.004 0.055 6703 Dihedral : 6.538 123.759 5486 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.61 % Favored : 96.37 % Rotamer: Outliers : 3.23 % Allowed : 23.57 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % 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: 0.29 (0.12), residues: 4931 helix: 1.07 (0.10), residues: 2662 sheet: -0.60 (0.21), residues: 583 loop : -0.83 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 53 HIS 0.008 0.001 HIS K 180 PHE 0.025 0.002 PHE L 82 TYR 0.041 0.002 TYR T 30 ARG 0.008 0.000 ARG 5 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 640 time to evaluate : 4.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 134 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8184 (ttt) REVERT: K 146 ARG cc_start: 0.8062 (ttm170) cc_final: 0.7564 (ttt-90) REVERT: K 164 MET cc_start: 0.8822 (tpp) cc_final: 0.8503 (tmm) REVERT: K 174 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7847 (tt) REVERT: L 87 MET cc_start: 0.7993 (mpp) cc_final: 0.7248 (mpp) REVERT: L 104 GLU cc_start: 0.7882 (pt0) cc_final: 0.7587 (pp20) REVERT: M 33 TRP cc_start: 0.8590 (m100) cc_final: 0.8284 (m-10) REVERT: M 69 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.5755 (t80) REVERT: 8 66 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7478 (pp-130) REVERT: 2 75 MET cc_start: 0.4537 (mmt) cc_final: 0.3918 (mpp) REVERT: 3 60 MET cc_start: 0.8043 (mmp) cc_final: 0.7728 (mmm) REVERT: 5 75 MET cc_start: 0.5615 (mpm) cc_final: 0.3900 (mtm) REVERT: H 15 GLN cc_start: 0.5201 (tp40) cc_final: 0.4163 (mt0) REVERT: I 32 LYS cc_start: 0.7563 (tptt) cc_final: 0.7192 (tptp) REVERT: N 163 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8230 (m110) REVERT: R 19 GLU cc_start: 0.2723 (OUTLIER) cc_final: 0.2064 (tt0) REVERT: R 32 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5088 (mmm160) REVERT: R 69 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6787 (mp) REVERT: S 54 LYS cc_start: 0.8797 (tppt) cc_final: 0.8517 (tppt) REVERT: S 85 TRP cc_start: 0.8403 (m100) cc_final: 0.7913 (t60) REVERT: S 90 GLU cc_start: 0.8374 (pp20) cc_final: 0.7995 (pp20) REVERT: C 25 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7553 (mp) REVERT: C 26 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7577 (mp0) REVERT: C 195 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6892 (tp30) REVERT: C 390 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.6887 (tpp) REVERT: C 399 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6412 (pp20) REVERT: C 477 GLN cc_start: 0.7817 (tp40) cc_final: 0.7074 (mm110) REVERT: C 484 ARG cc_start: 0.6516 (ttp80) cc_final: 0.5852 (ttm170) REVERT: A 96 ASP cc_start: 0.8381 (p0) cc_final: 0.7957 (p0) REVERT: A 181 ASP cc_start: 0.7483 (m-30) cc_final: 0.7227 (t0) REVERT: A 226 MET cc_start: 0.9069 (tpt) cc_final: 0.8432 (tpt) REVERT: A 351 PHE cc_start: 0.7405 (m-80) cc_final: 0.6894 (t80) REVERT: A 362 ARG cc_start: 0.7607 (mtt180) cc_final: 0.6702 (mtt90) REVERT: A 475 GLN cc_start: 0.7865 (mp-120) cc_final: 0.7532 (pm20) REVERT: A 476 HIS cc_start: 0.6755 (m-70) cc_final: 0.6077 (m-70) REVERT: B 195 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: B 460 LYS cc_start: 0.8539 (mmtp) cc_final: 0.8335 (mtpp) REVERT: B 476 HIS cc_start: 0.7694 (m-70) cc_final: 0.7390 (m90) REVERT: B 477 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7614 (mm110) REVERT: B 496 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7224 (mmtm) REVERT: E 195 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7645 (mm-30) REVERT: E 205 GLU cc_start: 0.8209 (tt0) cc_final: 0.7776 (pt0) REVERT: E 227 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7559 (mt-10) REVERT: E 234 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.5376 (mmp80) REVERT: F 30 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7368 (pt0) REVERT: F 171 GLU cc_start: 0.7490 (tp30) cc_final: 0.7120 (tp30) REVERT: F 217 LYS cc_start: 0.7941 (ptpp) cc_final: 0.7336 (mttp) REVERT: F 248 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8083 (m-30) REVERT: F 372 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7745 (m-30) REVERT: F 380 ILE cc_start: 0.8316 (mp) cc_final: 0.7997 (mm) REVERT: F 402 GLU cc_start: 0.7549 (tp30) cc_final: 0.7253 (tp30) REVERT: G 130 GLU cc_start: 0.8086 (tp30) cc_final: 0.6880 (tm-30) REVERT: G 260 LYS cc_start: 0.8592 (tttt) cc_final: 0.8226 (tttp) REVERT: O 33 GLU cc_start: 0.7189 (pt0) cc_final: 0.6460 (pm20) REVERT: O 37 LYS cc_start: 0.7329 (tttt) cc_final: 0.6604 (tppt) REVERT: O 173 MET cc_start: 0.7750 (mtm) cc_final: 0.7087 (mtm) REVERT: D 59 SER cc_start: 0.8900 (m) cc_final: 0.8537 (p) REVERT: D 149 TYR cc_start: 0.6618 (m-10) cc_final: 0.6277 (m-10) REVERT: D 180 HIS cc_start: 0.7450 (t-90) cc_final: 0.7009 (t-90) REVERT: D 202 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7080 (tm-30) REVERT: D 248 ASP cc_start: 0.7128 (m-30) cc_final: 0.6809 (m-30) REVERT: D 259 ASP cc_start: 0.8411 (t0) cc_final: 0.8046 (t0) REVERT: D 372 ASP cc_start: 0.8090 (m-30) cc_final: 0.7580 (m-30) outliers start: 130 outliers final: 62 residues processed: 707 average time/residue: 1.4405 time to fit residues: 1240.8052 Evaluate side-chains 694 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 612 time to evaluate : 4.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain K residue 134 MET Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 9 ILE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 66 MET Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain 1 residue 16 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 2 residue 71 ILE Chi-restraints excluded: chain 3 residue 15 THR Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 32 ARG Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain S residue 44 GLU Chi-restraints excluded: chain T residue 25 TYR Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 435 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 427 optimal weight: 10.0000 chunk 450 optimal weight: 5.9990 chunk 411 optimal weight: 0.9990 chunk 438 optimal weight: 3.9990 chunk 263 optimal weight: 0.9980 chunk 190 optimal weight: 0.8980 chunk 344 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 396 optimal weight: 3.9990 chunk 414 optimal weight: 7.9990 chunk 436 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 92 GLN ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN 8 45 GLN 2 39 ASN 2 45 GLN N 163 ASN P 8 ASN R 44 GLN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN G 123 GLN G 163 ASN D 458 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 38883 Z= 0.191 Angle : 0.636 13.260 52613 Z= 0.316 Chirality : 0.043 0.320 6140 Planarity : 0.004 0.051 6703 Dihedral : 6.365 124.066 5486 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.33 % Favored : 96.65 % Rotamer: Outliers : 2.63 % Allowed : 24.39 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.12), residues: 4931 helix: 1.20 (0.10), residues: 2658 sheet: -0.48 (0.21), residues: 570 loop : -0.75 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 51 HIS 0.005 0.001 HIS N 61 PHE 0.031 0.001 PHE S 29 TYR 0.043 0.001 TYR Q 47 ARG 0.010 0.000 ARG K 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 632 time to evaluate : 4.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 134 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8130 (ttt) REVERT: K 146 ARG cc_start: 0.8042 (ttm170) cc_final: 0.7532 (ttt-90) REVERT: K 164 MET cc_start: 0.8824 (tpp) cc_final: 0.8490 (tmm) REVERT: K 174 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7840 (tt) REVERT: L 87 MET cc_start: 0.7947 (mpp) cc_final: 0.7227 (mpp) REVERT: L 104 GLU cc_start: 0.7868 (pt0) cc_final: 0.7575 (pp20) REVERT: M 33 TRP cc_start: 0.8569 (m100) cc_final: 0.8066 (t60) REVERT: M 69 PHE cc_start: 0.6683 (OUTLIER) cc_final: 0.5782 (t80) REVERT: M 123 ASN cc_start: 0.8710 (m-40) cc_final: 0.8470 (p0) REVERT: 8 66 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7448 (pp-130) REVERT: 2 51 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7362 (mp) REVERT: 2 75 MET cc_start: 0.4441 (mmt) cc_final: 0.3836 (mpp) REVERT: 3 66 MET cc_start: 0.7566 (tpp) cc_final: 0.7365 (mmp) REVERT: 5 75 MET cc_start: 0.5713 (mpm) cc_final: 0.3989 (mtm) REVERT: H 15 GLN cc_start: 0.5172 (tp40) cc_final: 0.4121 (mt0) REVERT: I 32 LYS cc_start: 0.7545 (tptt) cc_final: 0.7187 (tptp) REVERT: N 30 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8548 (mp) REVERT: R 19 GLU cc_start: 0.2652 (OUTLIER) cc_final: 0.2356 (tt0) REVERT: R 69 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6672 (mp) REVERT: S 54 LYS cc_start: 0.8789 (tppt) cc_final: 0.8494 (tppt) REVERT: S 85 TRP cc_start: 0.8348 (m100) cc_final: 0.7894 (t60) REVERT: C 26 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7573 (mp0) REVERT: C 195 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6852 (tp30) REVERT: C 390 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.6858 (tpp) REVERT: C 477 GLN cc_start: 0.7828 (tp40) cc_final: 0.7087 (mm110) REVERT: C 484 ARG cc_start: 0.6501 (ttp80) cc_final: 0.5842 (ttm-80) REVERT: A 89 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7653 (mmmt) REVERT: A 96 ASP cc_start: 0.8358 (p0) cc_final: 0.7935 (p0) REVERT: A 181 ASP cc_start: 0.7480 (m-30) cc_final: 0.7228 (t0) REVERT: A 218 LYS cc_start: 0.7860 (tttp) cc_final: 0.7603 (tttt) REVERT: A 226 MET cc_start: 0.9065 (tpt) cc_final: 0.8542 (tpt) REVERT: A 351 PHE cc_start: 0.7355 (m-80) cc_final: 0.6842 (t80) REVERT: A 362 ARG cc_start: 0.7563 (mtt180) cc_final: 0.6660 (mtt90) REVERT: A 475 GLN cc_start: 0.7770 (mp-120) cc_final: 0.7489 (pm20) REVERT: A 476 HIS cc_start: 0.6702 (m-70) cc_final: 0.6090 (m-70) REVERT: A 498 LYS cc_start: 0.7455 (ptmt) cc_final: 0.6928 (pttm) REVERT: B 195 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7429 (mt-10) REVERT: B 476 HIS cc_start: 0.7555 (m-70) cc_final: 0.7280 (m90) REVERT: E 195 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7663 (mm-30) REVERT: E 205 GLU cc_start: 0.8186 (tt0) cc_final: 0.7749 (pt0) REVERT: E 227 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7538 (mt-10) REVERT: E 234 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.5475 (mmp80) REVERT: E 445 GLN cc_start: 0.7401 (mt0) cc_final: 0.7197 (mt0) REVERT: E 475 LYS cc_start: 0.7094 (mmmm) cc_final: 0.6855 (mmmm) REVERT: F 30 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7326 (pt0) REVERT: F 171 GLU cc_start: 0.7497 (tp30) cc_final: 0.7129 (tp30) REVERT: F 217 LYS cc_start: 0.7863 (ptpp) cc_final: 0.7250 (mttp) REVERT: F 248 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8104 (m-30) REVERT: F 372 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7738 (m-30) REVERT: F 380 ILE cc_start: 0.8312 (mp) cc_final: 0.7993 (mm) REVERT: F 402 GLU cc_start: 0.7522 (tp30) cc_final: 0.7226 (tp30) REVERT: G 4 LYS cc_start: 0.6972 (mptp) cc_final: 0.6650 (mppt) REVERT: G 130 GLU cc_start: 0.8041 (tp30) cc_final: 0.6818 (tm-30) REVERT: G 260 LYS cc_start: 0.8560 (tttt) cc_final: 0.8195 (tttp) REVERT: O 33 GLU cc_start: 0.7186 (pt0) cc_final: 0.6482 (pm20) REVERT: O 37 LYS cc_start: 0.7305 (tttt) cc_final: 0.6625 (tppt) REVERT: O 173 MET cc_start: 0.7779 (mtm) cc_final: 0.7144 (mtm) REVERT: D 59 SER cc_start: 0.8883 (m) cc_final: 0.8514 (p) REVERT: D 149 TYR cc_start: 0.6601 (m-10) cc_final: 0.6297 (m-10) REVERT: D 180 HIS cc_start: 0.7393 (t-90) cc_final: 0.7005 (t-90) REVERT: D 202 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7033 (tm-30) REVERT: D 248 ASP cc_start: 0.7070 (m-30) cc_final: 0.6742 (m-30) REVERT: D 259 ASP cc_start: 0.8386 (t0) cc_final: 0.8030 (t0) REVERT: D 372 ASP cc_start: 0.8110 (m-30) cc_final: 0.7612 (m-30) outliers start: 106 outliers final: 63 residues processed: 693 average time/residue: 1.4644 time to fit residues: 1237.7835 Evaluate side-chains 682 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 603 time to evaluate : 4.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 134 MET Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 9 ILE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 66 MET Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain 1 residue 16 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 51 ILE Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 15 THR Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 25 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 25 TYR Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 435 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 287 optimal weight: 2.9990 chunk 463 optimal weight: 0.0870 chunk 282 optimal weight: 0.7980 chunk 219 optimal weight: 0.0770 chunk 322 optimal weight: 6.9990 chunk 486 optimal weight: 5.9990 chunk 447 optimal weight: 0.1980 chunk 387 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 299 optimal weight: 0.0870 chunk 237 optimal weight: 0.7980 overall best weight: 0.2494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN L 80 GLN ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN 8 45 GLN 2 39 ASN 2 45 GLN H 116 GLN I 42 ASN ** N 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 GLN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN F 115 GLN F 224 GLN G 123 GLN D 458 GLN D 480 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 38883 Z= 0.166 Angle : 0.637 13.529 52613 Z= 0.314 Chirality : 0.043 0.311 6140 Planarity : 0.004 0.053 6703 Dihedral : 6.083 123.141 5486 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.10 % Favored : 96.88 % Rotamer: Outliers : 2.01 % Allowed : 25.21 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % 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: 0.63 (0.12), residues: 4931 helix: 1.31 (0.10), residues: 2657 sheet: -0.43 (0.22), residues: 572 loop : -0.59 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 28 HIS 0.005 0.001 HIS N 127 PHE 0.023 0.001 PHE R 79 TYR 0.032 0.001 TYR T 30 ARG 0.013 0.000 ARG K 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 648 time to evaluate : 4.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 134 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8113 (ttt) REVERT: K 146 ARG cc_start: 0.8050 (ttm170) cc_final: 0.7547 (ttt-90) REVERT: K 164 MET cc_start: 0.8811 (tpp) cc_final: 0.8507 (tmm) REVERT: K 174 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7808 (tt) REVERT: L 87 MET cc_start: 0.7994 (mpp) cc_final: 0.7314 (mpp) REVERT: L 104 GLU cc_start: 0.7842 (pt0) cc_final: 0.7564 (pp20) REVERT: M 33 TRP cc_start: 0.8543 (m100) cc_final: 0.8093 (t60) REVERT: M 69 PHE cc_start: 0.6721 (OUTLIER) cc_final: 0.5859 (t80) REVERT: 2 51 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7369 (mp) REVERT: 2 75 MET cc_start: 0.4359 (mmt) cc_final: 0.3736 (mpp) REVERT: 5 75 MET cc_start: 0.5714 (mpm) cc_final: 0.4009 (mtm) REVERT: H 15 GLN cc_start: 0.5132 (tp40) cc_final: 0.4029 (mt0) REVERT: I 32 LYS cc_start: 0.7539 (tptt) cc_final: 0.7173 (tptp) REVERT: N 209 ILE cc_start: 0.8844 (mt) cc_final: 0.8434 (mp) REVERT: R 19 GLU cc_start: 0.2535 (OUTLIER) cc_final: 0.2194 (tm-30) REVERT: S 54 LYS cc_start: 0.8748 (tppt) cc_final: 0.8454 (tppt) REVERT: S 85 TRP cc_start: 0.8319 (m100) cc_final: 0.7967 (t60) REVERT: C 26 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7495 (mp0) REVERT: C 195 GLU cc_start: 0.7358 (tm-30) cc_final: 0.6863 (tp30) REVERT: C 390 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.6781 (tpp) REVERT: C 477 GLN cc_start: 0.7822 (tp40) cc_final: 0.7095 (mm110) REVERT: C 484 ARG cc_start: 0.6488 (ttp80) cc_final: 0.5807 (ttm-80) REVERT: A 181 ASP cc_start: 0.7512 (m-30) cc_final: 0.7245 (t0) REVERT: A 218 LYS cc_start: 0.7724 (tttp) cc_final: 0.7514 (tttt) REVERT: A 226 MET cc_start: 0.9054 (tpt) cc_final: 0.8591 (tpt) REVERT: A 351 PHE cc_start: 0.7299 (m-80) cc_final: 0.6727 (t80) REVERT: A 362 ARG cc_start: 0.7503 (mtt180) cc_final: 0.6435 (mtt180) REVERT: A 475 GLN cc_start: 0.7790 (mp-120) cc_final: 0.7529 (pm20) REVERT: A 476 HIS cc_start: 0.6756 (m-70) cc_final: 0.6138 (m-70) REVERT: A 498 LYS cc_start: 0.7408 (ptmt) cc_final: 0.6894 (pttm) REVERT: B 89 LYS cc_start: 0.8621 (mtmm) cc_final: 0.8371 (mtmm) REVERT: B 195 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7378 (mt-10) REVERT: B 476 HIS cc_start: 0.7529 (m-70) cc_final: 0.7258 (m90) REVERT: E 195 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7591 (mm-30) REVERT: E 205 GLU cc_start: 0.8156 (tt0) cc_final: 0.7788 (pt0) REVERT: E 227 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7483 (mt-10) REVERT: E 234 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.5454 (mmp80) REVERT: E 375 ARG cc_start: 0.8133 (mmp-170) cc_final: 0.7852 (mmm160) REVERT: E 445 GLN cc_start: 0.7400 (mt0) cc_final: 0.7107 (mt0) REVERT: E 475 LYS cc_start: 0.7099 (mmmm) cc_final: 0.6866 (mmmm) REVERT: F 171 GLU cc_start: 0.7473 (tp30) cc_final: 0.7111 (tp30) REVERT: F 217 LYS cc_start: 0.7746 (ptpp) cc_final: 0.7047 (mmtp) REVERT: F 372 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7736 (m-30) REVERT: F 402 GLU cc_start: 0.7504 (tp30) cc_final: 0.7207 (tp30) REVERT: G 130 GLU cc_start: 0.8038 (tp30) cc_final: 0.6748 (tm-30) REVERT: G 260 LYS cc_start: 0.8552 (tttt) cc_final: 0.8193 (tttp) REVERT: O 33 GLU cc_start: 0.7133 (pt0) cc_final: 0.6408 (pm20) REVERT: O 37 LYS cc_start: 0.7330 (tttt) cc_final: 0.6610 (tppt) REVERT: O 173 MET cc_start: 0.7797 (mtm) cc_final: 0.7211 (mtm) REVERT: D 59 SER cc_start: 0.8820 (m) cc_final: 0.8471 (p) REVERT: D 149 TYR cc_start: 0.6573 (m-10) cc_final: 0.6333 (m-10) REVERT: D 180 HIS cc_start: 0.7322 (t-90) cc_final: 0.6928 (t-90) REVERT: D 202 GLU cc_start: 0.7512 (tm-30) cc_final: 0.6963 (tm-30) REVERT: D 248 ASP cc_start: 0.7019 (m-30) cc_final: 0.6686 (m-30) REVERT: D 259 ASP cc_start: 0.8284 (t0) cc_final: 0.7944 (t0) REVERT: D 372 ASP cc_start: 0.8088 (m-30) cc_final: 0.7599 (m-30) REVERT: D 480 HIS cc_start: 0.1870 (OUTLIER) cc_final: 0.1172 (m90) outliers start: 81 outliers final: 49 residues processed: 698 average time/residue: 1.4323 time to fit residues: 1222.4663 Evaluate side-chains 674 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 613 time to evaluate : 4.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 134 MET Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 88 GLN Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 9 ILE Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain 1 residue 16 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 51 ILE Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain T residue 25 TYR Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 195 GLU Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 480 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 307 optimal weight: 5.9990 chunk 412 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 356 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 387 optimal weight: 5.9990 chunk 162 optimal weight: 20.0000 chunk 398 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN 8 45 GLN 2 39 ASN 2 45 GLN 3 45 GLN H 116 GLN R 44 GLN ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN F 224 GLN G 123 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.151921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.115677 restraints weight = 58162.797| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.51 r_work: 0.3344 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 38883 Z= 0.419 Angle : 0.751 15.678 52613 Z= 0.374 Chirality : 0.048 0.300 6140 Planarity : 0.005 0.061 6703 Dihedral : 6.633 127.099 5486 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.59 % Favored : 96.37 % Rotamer: Outliers : 2.31 % Allowed : 25.58 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.12), residues: 4931 helix: 0.99 (0.10), residues: 2664 sheet: -0.61 (0.21), residues: 596 loop : -0.74 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 53 HIS 0.022 0.001 HIS D 480 PHE 0.034 0.002 PHE C 464 TYR 0.050 0.002 TYR Q 47 ARG 0.011 0.001 ARG H 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20575.25 seconds wall clock time: 364 minutes 14.01 seconds (21854.01 seconds total)