Starting phenix.real_space_refine on Mon Mar 18 04:06:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rda_4811/03_2024/6rda_4811.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rda_4811/03_2024/6rda_4811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rda_4811/03_2024/6rda_4811.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rda_4811/03_2024/6rda_4811.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rda_4811/03_2024/6rda_4811.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rda_4811/03_2024/6rda_4811.pdb" } resolution = 3.04 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= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 33 5.16 5 C 12734 2.51 5 N 3312 2.21 5 O 3776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 28": "NH1" <-> "NH2" Residue "1 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 69": "OD1" <-> "OD2" Residue "1 ASP 96": "OD1" <-> "OD2" Residue "1 ARG 150": "NH1" <-> "NH2" Residue "1 ASP 172": "OD1" <-> "OD2" Residue "1 ARG 182": "NH1" <-> "NH2" Residue "1 GLU 198": "OE1" <-> "OE2" Residue "1 ASP 199": "OD1" <-> "OD2" Residue "1 GLU 215": "OE1" <-> "OE2" Residue "1 GLU 229": "OE1" <-> "OE2" Residue "1 ARG 259": "NH1" <-> "NH2" Residue "1 ASP 283": "OD1" <-> "OD2" Residue "1 PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 329": "OE1" <-> "OE2" Residue "1 GLU 339": "OE1" <-> "OE2" Residue "1 GLU 341": "OE1" <-> "OE2" Residue "1 GLU 350": "OE1" <-> "OE2" Residue "1 GLU 355": "OE1" <-> "OE2" Residue "1 ARG 359": "NH1" <-> "NH2" Residue "1 GLU 385": "OE1" <-> "OE2" Residue "1 ARG 387": "NH1" <-> "NH2" Residue "1 TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 409": "OE1" <-> "OE2" Residue "1 TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 425": "OD1" <-> "OD2" Residue "1 ARG 434": "NH1" <-> "NH2" Residue "1 PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 457": "OE1" <-> "OE2" Residue "1 ASP 479": "OD1" <-> "OD2" Residue "1 GLU 496": "OE1" <-> "OE2" Residue "1 ASP 504": "OD1" <-> "OD2" Residue "1 ASP 508": "OD1" <-> "OD2" Residue "1 GLU 513": "OE1" <-> "OE2" Residue "1 ASP 539": "OD1" <-> "OD2" Residue "1 GLU 577": "OE1" <-> "OE2" Residue "1 ASP 601": "OD1" <-> "OD2" Residue "1 ARG 609": "NH1" <-> "NH2" Residue "2 ASP 7": "OD1" <-> "OD2" Residue "2 ASP 16": "OD1" <-> "OD2" Residue "2 GLU 22": "OE1" <-> "OE2" Residue "2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 ASP 60": "OD1" <-> "OD2" Residue "2 GLU 86": "OE1" <-> "OE2" Residue "2 GLU 139": "OE1" <-> "OE2" Residue "2 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 173": "NH1" <-> "NH2" Residue "2 ASP 189": "OD1" <-> "OD2" Residue "2 ASP 209": "OD1" <-> "OD2" Residue "2 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 230": "OD1" <-> "OD2" Residue "2 GLU 260": "OE1" <-> "OE2" Residue "2 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 326": "OE1" <-> "OE2" Residue "2 PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 346": "NH1" <-> "NH2" Residue "2 ASP 367": "OD1" <-> "OD2" Residue "2 TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 420": "OE1" <-> "OE2" Residue "2 GLU 422": "OE1" <-> "OE2" Residue "2 TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 102": "OD1" <-> "OD2" Residue "3 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 139": "OD1" <-> "OD2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 ASP 154": "OD1" <-> "OD2" Residue "3 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 175": "OE1" <-> "OE2" Residue "3 PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 213": "NH1" <-> "NH2" Residue "3 TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 233": "NH1" <-> "NH2" Residue "3 ARG 242": "NH1" <-> "NH2" Residue "3 ARG 257": "NH1" <-> "NH2" Residue "3 ASP 259": "OD1" <-> "OD2" Residue "3 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 299": "OE1" <-> "OE2" Residue "3 PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 84": "NH1" <-> "NH2" Residue "4 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 156": "OD1" <-> "OD2" Residue "4 ARG 176": "NH1" <-> "NH2" Residue "4 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 193": "OE1" <-> "OE2" Residue "4 PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 214": "OD1" <-> "OD2" Residue "4 GLU 218": "OE1" <-> "OE2" Residue "4 GLU 225": "OE1" <-> "OE2" Residue "4 ASP 231": "OD1" <-> "OD2" Residue "4 ARG 232": "NH1" <-> "NH2" Residue "4 ARG 255": "NH1" <-> "NH2" Residue "4 TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 6": "OE1" <-> "OE2" Residue "5 ARG 36": "NH1" <-> "NH2" Residue "5 ARG 50": "NH1" <-> "NH2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 109": "OD1" <-> "OD2" Residue "7 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 164": "NH1" <-> "NH2" Residue "7 ARG 165": "NH1" <-> "NH2" Residue "7 ARG 166": "NH1" <-> "NH2" Residue "7 PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 13": "NH1" <-> "NH2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "8 GLU 75": "OE1" <-> "OE2" Residue "8 TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 12": "OE1" <-> "OE2" Residue "9 PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 17": "OD1" <-> "OD2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 ARG 40": "NH1" <-> "NH2" Residue "9 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 74": "OE1" <-> "OE2" Residue "9 GLU 88": "OE1" <-> "OE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M ASP 132": "OD1" <-> "OD2" Residue "M ARG 145": "NH1" <-> "NH2" Residue "M PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 239": "NH1" <-> "NH2" Residue "M PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 206": "NH1" <-> "NH2" Residue "P GLU 216": "OE1" <-> "OE2" Residue "P PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 49": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19856 Number of models: 1 Model: "" Number of chains: 18 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 646 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "T" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 330 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "6" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Time building chain proxies: 10.90, per 1000 atoms: 0.55 Number of scatterers: 19856 At special positions: 0 Unit cell: (180.063, 116.883, 251.667, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 33 16.00 O 3776 8.00 N 3312 7.00 C 12734 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: 7.91 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4918 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 6 sheets defined 68.0% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain '0' and resid 3 through 8 removed outlier: 3.720A pdb=" N PHE 0 7 " --> pdb=" O TYR 0 3 " (cutoff:3.500A) Processing helix chain '0' and resid 17 through 31 removed outlier: 3.626A pdb=" N LEU 0 21 " --> pdb=" O GLY 0 17 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS 0 31 " --> pdb=" O ALA 0 27 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 50 removed outlier: 3.551A pdb=" N ALA 0 49 " --> pdb=" O ALA 0 45 " (cutoff:3.500A) Processing helix chain '0' and resid 51 through 56 removed outlier: 3.747A pdb=" N GLN 0 56 " --> pdb=" O ILE 0 52 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 73 removed outlier: 3.605A pdb=" N LYS 1 68 " --> pdb=" O LEU 1 64 " (cutoff:3.500A) Processing helix chain '1' and resid 96 through 100 removed outlier: 3.699A pdb=" N GLN 1 100 " --> pdb=" O PHE 1 97 " (cutoff:3.500A) Processing helix chain '1' and resid 103 through 105 No H-bonds generated for 'chain '1' and resid 103 through 105' Processing helix chain '1' and resid 106 through 139 removed outlier: 3.832A pdb=" N THR 1 135 " --> pdb=" O ALA 1 131 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 176 removed outlier: 4.112A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 204 removed outlier: 4.118A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL 1 204 " --> pdb=" O PHE 1 200 " (cutoff:3.500A) Processing helix chain '1' and resid 209 through 224 removed outlier: 3.642A pdb=" N SER 1 214 " --> pdb=" O ALA 1 210 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU 1 216 " --> pdb=" O GLU 1 212 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU 1 217 " --> pdb=" O VAL 1 213 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS 1 224 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 271 removed outlier: 3.534A pdb=" N LYS 1 247 " --> pdb=" O ALA 1 243 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG 1 259 " --> pdb=" O GLU 1 255 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 277 removed outlier: 3.532A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL 1 277 " --> pdb=" O LEU 1 274 " (cutoff:3.500A) Processing helix chain '1' and resid 282 through 286 Processing helix chain '1' and resid 289 through 293 Processing helix chain '1' and resid 297 through 305 removed outlier: 3.618A pdb=" N ALA 1 303 " --> pdb=" O GLU 1 299 " (cutoff:3.500A) Processing helix chain '1' and resid 310 through 316 Processing helix chain '1' and resid 323 through 327 removed outlier: 3.528A pdb=" N LYS 1 327 " --> pdb=" O PHE 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 330 through 334 Processing helix chain '1' and resid 338 through 351 removed outlier: 3.524A pdb=" N GLU 1 350 " --> pdb=" O GLN 1 346 " (cutoff:3.500A) Processing helix chain '1' and resid 353 through 362 Processing helix chain '1' and resid 363 through 367 removed outlier: 3.899A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) Processing helix chain '1' and resid 375 through 388 removed outlier: 3.599A pdb=" N ARG 1 381 " --> pdb=" O SER 1 377 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS 1 386 " --> pdb=" O VAL 1 382 " (cutoff:3.500A) Processing helix chain '1' and resid 392 through 415 removed outlier: 3.558A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU 1 401 " --> pdb=" O GLU 1 397 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU 1 415 " --> pdb=" O ALA 1 411 " (cutoff:3.500A) Processing helix chain '1' and resid 416 through 421 removed outlier: 3.552A pdb=" N GLY 1 421 " --> pdb=" O LYS 1 417 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.935A pdb=" N PHE 1 429 " --> pdb=" O ASP 1 425 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 444 Processing helix chain '1' and resid 446 through 460 removed outlier: 3.699A pdb=" N ALA 1 460 " --> pdb=" O LYS 1 456 " (cutoff:3.500A) Processing helix chain '1' and resid 463 through 478 removed outlier: 3.700A pdb=" N TYR 1 468 " --> pdb=" O PRO 1 464 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR 1 471 " --> pdb=" O ALA 1 467 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN 1 474 " --> pdb=" O VAL 1 470 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU 1 475 " --> pdb=" O THR 1 471 " (cutoff:3.500A) Processing helix chain '1' and resid 479 through 483 Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 515 removed outlier: 3.525A pdb=" N GLU 1 496 " --> pdb=" O GLN 1 492 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU 1 499 " --> pdb=" O GLU 1 495 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER 1 503 " --> pdb=" O GLU 1 499 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE 1 505 " --> pdb=" O GLU 1 501 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP 1 508 " --> pdb=" O ASP 1 504 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA 1 515 " --> pdb=" O ALA 1 511 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 Processing helix chain '1' and resid 541 through 549 removed outlier: 3.504A pdb=" N VAL 1 545 " --> pdb=" O PRO 1 541 " (cutoff:3.500A) Processing helix chain '1' and resid 549 through 562 removed outlier: 3.550A pdb=" N GLU 1 559 " --> pdb=" O LYS 1 555 " (cutoff:3.500A) Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 576 through 586 Processing helix chain '1' and resid 588 through 591 Processing helix chain '1' and resid 592 through 597 Processing helix chain '1' and resid 597 through 606 Processing helix chain '2' and resid 8 through 17 removed outlier: 3.643A pdb=" N GLU 2 14 " --> pdb=" O ALA 2 10 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 39 Processing helix chain '2' and resid 44 through 58 removed outlier: 3.719A pdb=" N TRP 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 77 removed outlier: 3.788A pdb=" N THR 2 67 " --> pdb=" O ALA 2 63 " (cutoff:3.500A) Processing helix chain '2' and resid 80 through 86 Processing helix chain '2' and resid 87 through 94 removed outlier: 3.509A pdb=" N ALA 2 91 " --> pdb=" O LEU 2 87 " (cutoff:3.500A) Processing helix chain '2' and resid 99 through 113 removed outlier: 3.692A pdb=" N ILE 2 105 " --> pdb=" O VAL 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 117 through 127 Processing helix chain '2' and resid 136 through 150 Processing helix chain '2' and resid 154 through 168 removed outlier: 3.567A pdb=" N ALA 2 160 " --> pdb=" O ALA 2 156 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER 2 167 " --> pdb=" O LYS 2 163 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 186 Processing helix chain '2' and resid 189 through 198 removed outlier: 4.302A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS 2 198 " --> pdb=" O ASP 2 194 " (cutoff:3.500A) Processing helix chain '2' and resid 209 through 221 removed outlier: 3.637A pdb=" N LEU 2 220 " --> pdb=" O ALA 2 216 " (cutoff:3.500A) Processing helix chain '2' and resid 228 through 233 Processing helix chain '2' and resid 240 through 253 removed outlier: 3.504A pdb=" N VAL 2 245 " --> pdb=" O PRO 2 241 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 276 removed outlier: 3.670A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL 2 269 " --> pdb=" O LEU 2 265 " (cutoff:3.500A) Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 277 through 280 removed outlier: 4.242A pdb=" N LEU 2 280 " --> pdb=" O PRO 2 277 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 277 through 280' Processing helix chain '2' and resid 281 through 295 removed outlier: 3.810A pdb=" N SER 2 295 " --> pdb=" O ALA 2 291 " (cutoff:3.500A) Processing helix chain '2' and resid 305 through 321 removed outlier: 3.641A pdb=" N LYS 2 309 " --> pdb=" O SER 2 305 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP 2 316 " --> pdb=" O GLY 2 312 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA 2 318 " --> pdb=" O ALA 2 314 " (cutoff:3.500A) Processing helix chain '2' and resid 326 through 341 removed outlier: 3.513A pdb=" N ASP 2 332 " --> pdb=" O ALA 2 328 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA 2 335 " --> pdb=" O ALA 2 331 " (cutoff:3.500A) Processing helix chain '2' and resid 345 through 353 removed outlier: 3.535A pdb=" N SER 2 351 " --> pdb=" O PRO 2 347 " (cutoff:3.500A) Processing helix chain '2' and resid 396 through 408 removed outlier: 4.305A pdb=" N ALA 2 400 " --> pdb=" O LEU 2 396 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 422 Processing helix chain '2' and resid 426 through 440 Processing helix chain '3' and resid 78 through 87 Processing helix chain '3' and resid 91 through 99 removed outlier: 3.620A pdb=" N ASN 3 97 " --> pdb=" O GLU 3 93 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA 3 99 " --> pdb=" O LEU 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 102 through 113 removed outlier: 3.807A pdb=" N TRP 3 106 " --> pdb=" O ASP 3 102 " (cutoff:3.500A) Processing helix chain '3' and resid 119 through 128 removed outlier: 3.752A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU 3 126 " --> pdb=" O VAL 3 122 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA 3 127 " --> pdb=" O LYS 3 123 " (cutoff:3.500A) Processing helix chain '3' and resid 131 through 135 Processing helix chain '3' and resid 136 through 150 Processing helix chain '3' and resid 154 through 166 removed outlier: 3.973A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 168 through 172 removed outlier: 3.609A pdb=" N PHE 3 172 " --> pdb=" O PHE 3 169 " (cutoff:3.500A) Processing helix chain '3' and resid 173 through 187 removed outlier: 4.076A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA 3 182 " --> pdb=" O LEU 3 178 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR 3 183 " --> pdb=" O GLN 3 179 " (cutoff:3.500A) Processing helix chain '3' and resid 191 through 204 removed outlier: 3.540A pdb=" N SER 3 201 " --> pdb=" O ASP 3 197 " (cutoff:3.500A) Processing helix chain '3' and resid 215 through 229 removed outlier: 3.546A pdb=" N LEU 3 219 " --> pdb=" O GLY 3 215 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN 3 229 " --> pdb=" O TYR 3 225 " (cutoff:3.500A) Processing helix chain '3' and resid 233 through 241 Processing helix chain '3' and resid 242 through 244 No H-bonds generated for 'chain '3' and resid 242 through 244' Processing helix chain '3' and resid 245 through 251 Processing helix chain '3' and resid 253 through 271 removed outlier: 3.882A pdb=" N SER 3 263 " --> pdb=" O ASP 3 259 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA 3 267 " --> pdb=" O SER 3 263 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR 3 270 " --> pdb=" O LYS 3 266 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 275 through 277 No H-bonds generated for 'chain '3' and resid 275 through 277' Processing helix chain '3' and resid 278 through 287 removed outlier: 3.827A pdb=" N ALA 3 285 " --> pdb=" O VAL 3 281 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL 3 287 " --> pdb=" O GLY 3 283 " (cutoff:3.500A) Processing helix chain '3' and resid 288 through 292 removed outlier: 4.109A pdb=" N GLU 3 291 " --> pdb=" O SER 3 288 " (cutoff:3.500A) Processing helix chain '3' and resid 293 through 309 removed outlier: 3.552A pdb=" N LEU 3 297 " --> pdb=" O SER 3 293 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL 3 303 " --> pdb=" O GLU 3 299 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN 3 309 " --> pdb=" O VAL 3 305 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 14 removed outlier: 3.563A pdb=" N TYR 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 35 removed outlier: 3.606A pdb=" N ALA 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA 4 35 " --> pdb=" O LYS 4 31 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 68 removed outlier: 3.505A pdb=" N GLN 4 52 " --> pdb=" O GLU 4 48 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA 4 60 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.719A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 96 Processing helix chain '4' and resid 100 through 113 removed outlier: 3.641A pdb=" N LYS 4 107 " --> pdb=" O ILE 4 103 " (cutoff:3.500A) Processing helix chain '4' and resid 118 through 126 Processing helix chain '4' and resid 131 through 150 removed outlier: 3.866A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER 4 144 " --> pdb=" O GLU 4 140 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 164 Processing helix chain '4' and resid 164 through 177 removed outlier: 3.515A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY 4 177 " --> pdb=" O ALA 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 179 through 189 removed outlier: 3.567A pdb=" N GLY 4 189 " --> pdb=" O ALA 4 185 " (cutoff:3.500A) Processing helix chain '4' and resid 194 through 234 removed outlier: 3.684A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP 4 206 " --> pdb=" O GLU 4 202 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA 4 213 " --> pdb=" O SER 4 209 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA 4 224 " --> pdb=" O LYS 4 220 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 259 removed outlier: 3.649A pdb=" N LYS 4 243 " --> pdb=" O ALA 4 239 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA 4 259 " --> pdb=" O ARG 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 285 removed outlier: 3.802A pdb=" N ALA 4 285 " --> pdb=" O SER 4 281 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 29 Processing helix chain '5' and resid 29 through 57 removed outlier: 3.946A pdb=" N THR 5 33 " --> pdb=" O GLN 5 29 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 67 Processing helix chain '5' and resid 72 through 81 Processing helix chain '5' and resid 89 through 107 removed outlier: 3.946A pdb=" N SER 5 97 " --> pdb=" O GLU 5 93 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL 5 102 " --> pdb=" O ALA 5 98 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN 5 107 " --> pdb=" O TYR 5 103 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 119 Processing helix chain '6' and resid 30 through 41 Processing helix chain '6' and resid 46 through 56 removed outlier: 5.402A pdb=" N LYS 6 52 " --> pdb=" O LEU 6 48 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N THR 6 53 " --> pdb=" O SER 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 72 through 94 removed outlier: 3.665A pdb=" N ILE 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 104 Processing helix chain '6' and resid 104 through 118 removed outlier: 3.513A pdb=" N LEU 6 108 " --> pdb=" O ASN 6 104 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU 6 113 " --> pdb=" O GLN 6 109 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER 6 117 " --> pdb=" O LEU 6 113 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER 6 118 " --> pdb=" O ILE 6 114 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 130 Processing helix chain '7' and resid 68 through 72 removed outlier: 4.096A pdb=" N SER 7 72 " --> pdb=" O LEU 7 69 " (cutoff:3.500A) Processing helix chain '7' and resid 83 through 105 removed outlier: 3.657A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU 7 103 " --> pdb=" O GLU 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 109 through 114 removed outlier: 3.682A pdb=" N TYR 7 114 " --> pdb=" O THR 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 120 Processing helix chain '7' and resid 125 through 145 removed outlier: 3.503A pdb=" N PHE 7 130 " --> pdb=" O ASP 7 126 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR 7 137 " --> pdb=" O ALA 7 133 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR 7 138 " --> pdb=" O ALA 7 134 " (cutoff:3.500A) Processing helix chain '7' and resid 146 through 148 No H-bonds generated for 'chain '7' and resid 146 through 148' Processing helix chain '7' and resid 149 through 155 removed outlier: 3.675A pdb=" N SER 7 155 " --> pdb=" O SER 7 151 " (cutoff:3.500A) Processing helix chain '7' and resid 157 through 166 Processing helix chain '7' and resid 174 through 181 Processing helix chain '7' and resid 182 through 187 Processing helix chain '8' and resid 26 through 31 Processing helix chain '8' and resid 31 through 39 Processing helix chain '8' and resid 39 through 78 removed outlier: 3.729A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA 8 76 " --> pdb=" O ALA 8 72 " (cutoff:3.500A) Processing helix chain '9' and resid 4 through 16 removed outlier: 3.824A pdb=" N GLY 9 8 " --> pdb=" O THR 9 4 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS 9 13 " --> pdb=" O LYS 9 9 " (cutoff:3.500A) Processing helix chain '9' and resid 36 through 55 removed outlier: 4.021A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 97 removed outlier: 3.669A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS 9 95 " --> pdb=" O LYS 9 91 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER 9 96 " --> pdb=" O GLU 9 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 119 Processing helix chain 'M' and resid 134 through 144 Processing helix chain 'M' and resid 147 through 164 removed outlier: 3.722A pdb=" N THR M 153 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER M 161 " --> pdb=" O CYS M 157 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS M 162 " --> pdb=" O THR M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 168 Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 177 through 199 removed outlier: 3.519A pdb=" N SER M 187 " --> pdb=" O GLY M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 265 removed outlier: 3.622A pdb=" N SER M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU M 261 " --> pdb=" O MET M 257 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 270 through 308 removed outlier: 4.040A pdb=" N THR M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY M 276 " --> pdb=" O PRO M 272 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER M 300 " --> pdb=" O SER M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 311 No H-bonds generated for 'chain 'M' and resid 309 through 311' Processing helix chain 'P' and resid 163 through 175 removed outlier: 3.956A pdb=" N VAL P 168 " --> pdb=" O LYS P 164 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU P 170 " --> pdb=" O GLU P 166 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS P 172 " --> pdb=" O VAL P 168 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS P 173 " --> pdb=" O GLU P 169 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 226 removed outlier: 3.793A pdb=" N GLU P 216 " --> pdb=" O ALA P 212 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS P 224 " --> pdb=" O ASN P 220 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 75 Proline residue: T 68 - end of helix removed outlier: 4.412A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 183 through 184 Processing sheet with id=AA2, first strand: chain '2' and resid 368 through 372 removed outlier: 4.464A pdb=" N ILE 2 368 " --> pdb=" O VAL 2 379 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ALA 2 414 " --> pdb=" O LYS 2 376 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU 2 378 " --> pdb=" O ALA 2 414 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL 2 416 " --> pdb=" O LEU 2 378 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN 2 380 " --> pdb=" O VAL 2 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 314 through 317 Processing sheet with id=AA4, first strand: chain '7' and resid 35 through 41 Processing sheet with id=AA5, first strand: chain '7' and resid 35 through 41 Processing sheet with id=AA6, first strand: chain 'P' and resid 188 through 190 removed outlier: 6.270A pdb=" N VAL P 156 " --> pdb=" O LYS P 189 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE P 198 " --> pdb=" O MET P 209 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 3171 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: 5.39 Time building geometry restraints manager: 8.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4741 1.33 - 1.45: 4139 1.45 - 1.57: 11305 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 20239 Sorted by residual: bond pdb=" CB THR 3 174 " pdb=" CG2 THR 3 174 " ideal model delta sigma weight residual 1.521 1.403 0.118 3.30e-02 9.18e+02 1.29e+01 bond pdb=" CB THR M 153 " pdb=" CG2 THR M 153 " ideal model delta sigma weight residual 1.521 1.405 0.116 3.30e-02 9.18e+02 1.23e+01 bond pdb=" C LEU M 167 " pdb=" N MET M 168 " ideal model delta sigma weight residual 1.331 1.239 0.092 2.83e-02 1.25e+03 1.05e+01 bond pdb=" N THR M 200 " pdb=" CA THR M 200 " ideal model delta sigma weight residual 1.460 1.486 -0.026 8.20e-03 1.49e+04 9.83e+00 bond pdb=" CB ARG 6 130 " pdb=" CG ARG 6 130 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 7.97e+00 ... (remaining 20234 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.58: 377 105.58 - 112.73: 10793 112.73 - 119.88: 7587 119.88 - 127.03: 8482 127.03 - 134.18: 230 Bond angle restraints: 27469 Sorted by residual: angle pdb=" N PRO 3 77 " pdb=" CA PRO 3 77 " pdb=" CB PRO 3 77 " ideal model delta sigma weight residual 103.00 110.34 -7.34 1.10e+00 8.26e-01 4.45e+01 angle pdb=" C THR M 200 " pdb=" CA THR M 200 " pdb=" CB THR M 200 " ideal model delta sigma weight residual 116.53 107.39 9.14 1.47e+00 4.63e-01 3.86e+01 angle pdb=" N VAL 1 204 " pdb=" CA VAL 1 204 " pdb=" C VAL 1 204 " ideal model delta sigma weight residual 111.77 105.34 6.43 1.04e+00 9.25e-01 3.82e+01 angle pdb=" N TYR 9 36 " pdb=" CA TYR 9 36 " pdb=" C TYR 9 36 " ideal model delta sigma weight residual 112.23 105.04 7.19 1.26e+00 6.30e-01 3.26e+01 angle pdb=" C VAL 7 157 " pdb=" N VAL 7 158 " pdb=" CA VAL 7 158 " ideal model delta sigma weight residual 120.33 124.86 -4.53 8.00e-01 1.56e+00 3.21e+01 ... (remaining 27464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 11094 17.51 - 35.03: 885 35.03 - 52.54: 157 52.54 - 70.05: 34 70.05 - 87.57: 12 Dihedral angle restraints: 12182 sinusoidal: 4595 harmonic: 7587 Sorted by residual: dihedral pdb=" CA VAL P 185 " pdb=" C VAL P 185 " pdb=" N MET P 186 " pdb=" CA MET P 186 " ideal model delta harmonic sigma weight residual 180.00 121.66 58.34 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA PHE 2 222 " pdb=" C PHE 2 222 " pdb=" N LYS 2 223 " pdb=" CA LYS 2 223 " ideal model delta harmonic sigma weight residual 180.00 148.42 31.58 0 5.00e+00 4.00e-02 3.99e+01 dihedral pdb=" CA LYS 5 119 " pdb=" C LYS 5 119 " pdb=" N PRO 5 120 " pdb=" CA PRO 5 120 " ideal model delta harmonic sigma weight residual -180.00 -151.43 -28.57 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 12179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2567 0.077 - 0.155: 537 0.155 - 0.232: 50 0.232 - 0.309: 7 0.309 - 0.386: 2 Chirality restraints: 3163 Sorted by residual: chirality pdb=" CB ILE 3 90 " pdb=" CA ILE 3 90 " pdb=" CG1 ILE 3 90 " pdb=" CG2 ILE 3 90 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CB VAL 5 113 " pdb=" CA VAL 5 113 " pdb=" CG1 VAL 5 113 " pdb=" CG2 VAL 5 113 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CG LEU 1 102 " pdb=" CB LEU 1 102 " pdb=" CD1 LEU 1 102 " pdb=" CD2 LEU 1 102 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 3160 not shown) Planarity restraints: 3505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU 5 31 " -0.056 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO 5 32 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO 5 32 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO 5 32 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR 1 92 " 0.051 5.00e-02 4.00e+02 7.69e-02 9.47e+00 pdb=" N PRO 1 93 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO 1 93 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO 1 93 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR 6 145 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.08e+00 pdb=" C THR 6 145 " 0.052 2.00e-02 2.50e+03 pdb=" O THR 6 145 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE 6 146 " -0.018 2.00e-02 2.50e+03 ... (remaining 3502 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 278 2.64 - 3.21: 17515 3.21 - 3.77: 30847 3.77 - 4.34: 45303 4.34 - 4.90: 72434 Nonbonded interactions: 166377 Sorted by model distance: nonbonded pdb="ZN ZN M 600 " pdb=" O HOH M 709 " model vdw 2.075 2.230 nonbonded pdb="ZN ZN M 600 " pdb=" O HOH 6 205 " model vdw 2.158 2.230 nonbonded pdb=" O THR 5 83 " pdb=" OH TYR 7 119 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR M 289 " pdb=" O HOH M 701 " model vdw 2.268 2.440 nonbonded pdb=" OH TYR 6 126 " pdb=" O HOH 6 201 " model vdw 2.268 2.440 ... (remaining 166372 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.680 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: 0.020 Extract box with map and model: 25.430 Check model and map are aligned: 0.290 Set scattering table: 0.200 Process input model: 54.200 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 : 0.013 0.118 20239 Z= 0.861 Angle : 1.039 10.350 27469 Z= 0.573 Chirality : 0.063 0.386 3163 Planarity : 0.008 0.083 3505 Dihedral : 13.768 87.569 7264 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.06 % Favored : 94.67 % Rotamer: Outliers : 0.58 % Allowed : 5.19 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -5.84 (0.11), residues: 2569 helix: -4.44 (0.05), residues: 1698 sheet: -1.21 (0.70), residues: 56 loop : -2.10 (0.18), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP 5 44 HIS 0.014 0.003 HIS 4 233 PHE 0.032 0.003 PHE 3 121 TYR 0.038 0.003 TYR 2 61 ARG 0.008 0.001 ARG 2 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 320 time to evaluate : 2.281 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7331 (pm20) REVERT: 1 34 GLU cc_start: 0.7613 (pm20) cc_final: 0.7134 (pm20) REVERT: 1 224 LYS cc_start: 0.7751 (pttt) cc_final: 0.7547 (pttt) REVERT: 1 437 VAL cc_start: 0.8703 (m) cc_final: 0.8380 (t) REVERT: 1 456 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8237 (ttmm) REVERT: 1 572 ASP cc_start: 0.8239 (m-30) cc_final: 0.7883 (m-30) REVERT: 2 21 ARG cc_start: 0.8140 (ptt180) cc_final: 0.7874 (mtm180) REVERT: 2 31 ASP cc_start: 0.7891 (m-30) cc_final: 0.7655 (m-30) REVERT: 2 197 LEU cc_start: 0.8569 (mt) cc_final: 0.8232 (mt) REVERT: 4 134 TYR cc_start: 0.8775 (t80) cc_final: 0.8415 (t80) REVERT: 4 214 ASP cc_start: 0.8008 (m-30) cc_final: 0.7802 (m-30) REVERT: 5 111 LYS cc_start: 0.8533 (mtpp) cc_final: 0.8166 (mmtm) REVERT: 7 135 ASP cc_start: 0.8347 (m-30) cc_final: 0.8068 (m-30) REVERT: M 199 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8137 (mmtp) REVERT: P 193 LYS cc_start: 0.7606 (mmtm) cc_final: 0.7267 (mmtt) REVERT: P 205 ARG cc_start: 0.7711 (ptt-90) cc_final: 0.3680 (mmm160) REVERT: P 213 LYS cc_start: 0.8508 (tmtt) cc_final: 0.8104 (tppt) REVERT: T 65 LYS cc_start: 0.8332 (mttp) cc_final: 0.8113 (mttm) outliers start: 12 outliers final: 8 residues processed: 329 average time/residue: 0.3947 time to fit residues: 186.1397 Evaluate side-chains 234 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 225 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 2 residue 204 THR Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain M residue 199 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 231 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 1 48 ASN 1 65 GLN 1 100 GLN 1 257 HIS 1 316 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 482 ASN 1 587 ASN 1 590 HIS 2 40 GLN 2 122 ASN 2 177 GLN 2 243 GLN 2 289 HIS 2 427 GLN 3 189 HIS 3 206 ASN 3 229 ASN 4 68 HIS 4 240 GLN 5 107 ASN 6 40 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 86 HIS ** 7 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 102 GLN 7 123 HIS 7 170 HIS 7 184 ASN 8 26 HIS 9 35 GLN M 108 ASN M 163 ASN P 220 ASN P 223 ASN T 64 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20239 Z= 0.196 Angle : 0.603 10.974 27469 Z= 0.320 Chirality : 0.039 0.162 3163 Planarity : 0.006 0.060 3505 Dihedral : 5.765 42.605 2760 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.62 % Favored : 96.19 % Rotamer: Outliers : 1.75 % Allowed : 7.66 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.18 (0.14), residues: 2569 helix: -2.23 (0.10), residues: 1708 sheet: -0.48 (0.74), residues: 56 loop : -1.45 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 4 206 HIS 0.007 0.001 HIS 4 233 PHE 0.013 0.001 PHE 2 149 TYR 0.022 0.001 TYR 4 211 ARG 0.006 0.000 ARG 1 359 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 257 time to evaluate : 2.050 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7293 (pm20) REVERT: 1 34 GLU cc_start: 0.7471 (pm20) cc_final: 0.7249 (pm20) REVERT: 1 359 ARG cc_start: 0.8419 (mtt-85) cc_final: 0.8201 (mmt90) REVERT: 1 572 ASP cc_start: 0.8150 (m-30) cc_final: 0.7784 (m-30) REVERT: 2 21 ARG cc_start: 0.8009 (ptt180) cc_final: 0.7740 (mtm180) REVERT: 2 31 ASP cc_start: 0.7716 (m-30) cc_final: 0.7490 (m-30) REVERT: 2 316 ASP cc_start: 0.7615 (m-30) cc_final: 0.7361 (m-30) REVERT: 4 111 GLN cc_start: 0.8083 (tt0) cc_final: 0.7810 (tt0) REVERT: 4 255 ARG cc_start: 0.8420 (ttp-110) cc_final: 0.8135 (ttp80) REVERT: 5 49 LYS cc_start: 0.8350 (ttpp) cc_final: 0.8121 (mtpp) REVERT: 5 111 LYS cc_start: 0.8626 (mtpp) cc_final: 0.8299 (mmtm) REVERT: P 205 ARG cc_start: 0.7744 (ptt-90) cc_final: 0.3619 (mmp-170) outliers start: 36 outliers final: 25 residues processed: 285 average time/residue: 0.3409 time to fit residues: 144.6970 Evaluate side-chains 251 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 226 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 2 residue 204 THR Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 6 residue 57 GLN Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 17 ASP Chi-restraints excluded: chain 9 residue 32 SER Chi-restraints excluded: chain 9 residue 39 LEU Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain P residue 195 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 231 optimal weight: 0.9980 chunk 250 optimal weight: 0.4980 chunk 206 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20239 Z= 0.216 Angle : 0.551 9.683 27469 Z= 0.288 Chirality : 0.040 0.167 3163 Planarity : 0.004 0.051 3505 Dihedral : 5.281 41.652 2756 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.74 % Favored : 96.15 % Rotamer: Outliers : 2.08 % Allowed : 8.97 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.52 (0.16), residues: 2569 helix: -0.84 (0.12), residues: 1719 sheet: -0.01 (0.78), residues: 56 loop : -1.07 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 9 73 HIS 0.008 0.001 HIS 8 78 PHE 0.014 0.001 PHE 1 529 TYR 0.024 0.001 TYR 4 211 ARG 0.004 0.000 ARG 1 359 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 238 time to evaluate : 2.144 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7256 (pm20) REVERT: 1 34 GLU cc_start: 0.7534 (pm20) cc_final: 0.7155 (pm20) REVERT: 1 209 ASN cc_start: 0.8170 (p0) cc_final: 0.7877 (p0) REVERT: 1 572 ASP cc_start: 0.8206 (m-30) cc_final: 0.7851 (m-30) REVERT: 2 316 ASP cc_start: 0.7650 (m-30) cc_final: 0.7389 (m-30) REVERT: 2 394 LYS cc_start: 0.8140 (pttt) cc_final: 0.7805 (ttpp) REVERT: 4 111 GLN cc_start: 0.8124 (tt0) cc_final: 0.7886 (tt0) REVERT: 5 111 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8330 (mmtm) REVERT: P 169 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7284 (mm-30) REVERT: P 205 ARG cc_start: 0.7710 (ptt-90) cc_final: 0.3743 (mmm160) outliers start: 43 outliers final: 31 residues processed: 267 average time/residue: 0.3376 time to fit residues: 135.9836 Evaluate side-chains 251 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 220 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 418 VAL Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 124 ASN Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 57 GLN Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 17 ASP Chi-restraints excluded: chain 9 residue 35 GLN Chi-restraints excluded: chain 9 residue 39 LEU Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain M residue 110 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 232 optimal weight: 0.0970 chunk 246 optimal weight: 10.0000 chunk 121 optimal weight: 0.6980 chunk 220 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 527 GLN 8 78 HIS ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20239 Z= 0.174 Angle : 0.514 8.210 27469 Z= 0.267 Chirality : 0.039 0.144 3163 Planarity : 0.004 0.047 3505 Dihedral : 5.040 44.617 2755 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.70 % Favored : 96.22 % Rotamer: Outliers : 1.84 % Allowed : 10.42 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.62 (0.16), residues: 2569 helix: -0.07 (0.13), residues: 1720 sheet: -0.00 (0.75), residues: 57 loop : -0.93 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 9 73 HIS 0.013 0.001 HIS 8 78 PHE 0.013 0.001 PHE 1 529 TYR 0.023 0.001 TYR 4 211 ARG 0.003 0.000 ARG 1 453 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 235 time to evaluate : 2.152 Fit side-chains REVERT: 0 41 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7114 (pm20) REVERT: 1 34 GLU cc_start: 0.7510 (pm20) cc_final: 0.7133 (pm20) REVERT: 1 219 LYS cc_start: 0.8231 (mttp) cc_final: 0.7882 (mtpt) REVERT: 1 572 ASP cc_start: 0.8207 (m-30) cc_final: 0.7865 (m-30) REVERT: 2 41 VAL cc_start: 0.7780 (OUTLIER) cc_final: 0.7481 (t) REVERT: 2 316 ASP cc_start: 0.7634 (m-30) cc_final: 0.7429 (m-30) REVERT: 2 394 LYS cc_start: 0.8083 (pttt) cc_final: 0.7791 (ttpp) REVERT: 4 111 GLN cc_start: 0.8145 (tt0) cc_final: 0.7912 (tt0) REVERT: 5 111 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8326 (mmtm) REVERT: 6 146 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8081 (t80) REVERT: 8 78 HIS cc_start: 0.7219 (t70) cc_final: 0.7017 (t-170) REVERT: 9 89 MET cc_start: 0.8436 (mtp) cc_final: 0.8220 (mtp) REVERT: P 169 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7288 (mm-30) REVERT: P 205 ARG cc_start: 0.7741 (ptt-90) cc_final: 0.3785 (mmp-170) outliers start: 38 outliers final: 30 residues processed: 260 average time/residue: 0.3396 time to fit residues: 134.1202 Evaluate side-chains 255 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 223 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 204 THR Chi-restraints excluded: chain 3 residue 90 ILE Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 54 GLU Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 17 ASP Chi-restraints excluded: chain 9 residue 39 LEU Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain T residue 50 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 0.0000 chunk 139 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 101 optimal weight: 0.0040 chunk 210 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 365 GLN 3 256 GLN 3 319 GLN 9 41 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20239 Z= 0.153 Angle : 0.495 7.860 27469 Z= 0.256 Chirality : 0.038 0.143 3163 Planarity : 0.004 0.046 3505 Dihedral : 4.829 47.267 2755 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.62 % Favored : 96.34 % Rotamer: Outliers : 2.04 % Allowed : 11.00 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2569 helix: 0.47 (0.13), residues: 1720 sheet: 0.16 (0.75), residues: 57 loop : -0.83 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 PHE 0.013 0.001 PHE 1 529 TYR 0.024 0.001 TYR 4 211 ARG 0.007 0.000 ARG 2 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 235 time to evaluate : 2.165 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7137 (pm20) REVERT: 1 34 GLU cc_start: 0.7490 (pm20) cc_final: 0.7125 (pm20) REVERT: 1 219 LYS cc_start: 0.8164 (mttp) cc_final: 0.7795 (mtpt) REVERT: 1 572 ASP cc_start: 0.8208 (m-30) cc_final: 0.7876 (m-30) REVERT: 2 41 VAL cc_start: 0.7734 (OUTLIER) cc_final: 0.7414 (t) REVERT: 2 316 ASP cc_start: 0.7642 (m-30) cc_final: 0.7422 (m-30) REVERT: 4 111 GLN cc_start: 0.8139 (tt0) cc_final: 0.7912 (tt0) REVERT: 5 111 LYS cc_start: 0.8560 (mtpp) cc_final: 0.8239 (mmtm) REVERT: 6 69 THR cc_start: 0.4969 (OUTLIER) cc_final: 0.4643 (p) REVERT: 6 146 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8063 (t80) REVERT: 9 13 LYS cc_start: 0.7606 (pttt) cc_final: 0.7135 (tttm) REVERT: P 169 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7380 (mm-30) REVERT: P 205 ARG cc_start: 0.7716 (ptt-90) cc_final: 0.3837 (mmm160) outliers start: 42 outliers final: 33 residues processed: 268 average time/residue: 0.3605 time to fit residues: 146.4396 Evaluate side-chains 249 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 213 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 418 VAL Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 204 THR Chi-restraints excluded: chain 3 residue 90 ILE Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 4 residue 6 VAL Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 124 ASN Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 17 ASP Chi-restraints excluded: chain 9 residue 39 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain T residue 50 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 2.9990 chunk 221 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 527 GLN 1 531 HIS 3 256 GLN 3 319 GLN 8 78 HIS 9 35 GLN 9 41 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 20239 Z= 0.387 Angle : 0.598 9.812 27469 Z= 0.305 Chirality : 0.044 0.156 3163 Planarity : 0.004 0.048 3505 Dihedral : 5.117 54.255 2755 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.24 % Favored : 95.64 % Rotamer: Outliers : 2.62 % Allowed : 11.44 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2569 helix: 0.37 (0.13), residues: 1723 sheet: 0.11 (0.74), residues: 57 loop : -1.01 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 3 109 HIS 0.011 0.001 HIS 8 78 PHE 0.014 0.002 PHE T 53 TYR 0.024 0.002 TYR 4 211 ARG 0.006 0.001 ARG 2 187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 220 time to evaluate : 2.211 Fit side-chains REVERT: 0 41 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7237 (pm20) REVERT: 1 34 GLU cc_start: 0.7617 (pm20) cc_final: 0.7236 (pm20) REVERT: 1 219 LYS cc_start: 0.8252 (mttp) cc_final: 0.7958 (mttt) REVERT: 1 572 ASP cc_start: 0.8185 (m-30) cc_final: 0.7837 (m-30) REVERT: 2 316 ASP cc_start: 0.7744 (m-30) cc_final: 0.7535 (m-30) REVERT: 4 13 TYR cc_start: 0.9152 (OUTLIER) cc_final: 0.8607 (m-80) REVERT: 4 111 GLN cc_start: 0.8162 (tt0) cc_final: 0.7954 (tt0) REVERT: 5 111 LYS cc_start: 0.8738 (mtpp) cc_final: 0.8383 (mmtm) REVERT: 6 69 THR cc_start: 0.5160 (OUTLIER) cc_final: 0.4760 (p) REVERT: 6 146 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8168 (t80) REVERT: M 270 MET cc_start: 0.6681 (tmm) cc_final: 0.6204 (mtp) REVERT: P 186 MET cc_start: 0.5206 (tpp) cc_final: 0.3853 (mmm) REVERT: P 205 ARG cc_start: 0.7615 (ptt-90) cc_final: 0.3703 (mmm160) outliers start: 54 outliers final: 42 residues processed: 260 average time/residue: 0.3297 time to fit residues: 129.5704 Evaluate side-chains 261 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 216 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 97 SER Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 3 residue 90 ILE Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 6 VAL Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 54 GLU Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 17 ASP Chi-restraints excluded: chain 9 residue 26 LEU Chi-restraints excluded: chain 9 residue 32 SER Chi-restraints excluded: chain 9 residue 35 GLN Chi-restraints excluded: chain 9 residue 39 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain T residue 50 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 4.9990 chunk 27 optimal weight: 0.0870 chunk 140 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 113 optimal weight: 0.3980 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 527 GLN 3 256 GLN 3 319 GLN 8 78 HIS 9 41 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20239 Z= 0.180 Angle : 0.513 10.279 27469 Z= 0.266 Chirality : 0.039 0.146 3163 Planarity : 0.004 0.048 3505 Dihedral : 4.933 56.006 2755 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.70 % Favored : 96.22 % Rotamer: Outliers : 2.04 % Allowed : 12.31 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2569 helix: 0.72 (0.13), residues: 1721 sheet: 0.21 (0.73), residues: 57 loop : -0.82 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.013 0.001 HIS 8 78 PHE 0.012 0.001 PHE 1 529 TYR 0.020 0.001 TYR 4 211 ARG 0.007 0.000 ARG 2 187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 225 time to evaluate : 2.068 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7227 (pm20) REVERT: 1 34 GLU cc_start: 0.7619 (pm20) cc_final: 0.7234 (pm20) REVERT: 1 219 LYS cc_start: 0.8124 (mttp) cc_final: 0.7805 (mtpt) REVERT: 1 572 ASP cc_start: 0.8171 (m-30) cc_final: 0.7842 (m-30) REVERT: 5 111 LYS cc_start: 0.8631 (mtpp) cc_final: 0.8296 (mmtm) REVERT: 6 69 THR cc_start: 0.5010 (OUTLIER) cc_final: 0.4627 (p) REVERT: 6 146 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8163 (t80) REVERT: 9 1 MET cc_start: 0.4860 (ptt) cc_final: 0.4411 (ttp) REVERT: 9 13 LYS cc_start: 0.7564 (pttt) cc_final: 0.7139 (tttm) REVERT: 9 89 MET cc_start: 0.8416 (mtp) cc_final: 0.8159 (mtp) REVERT: M 270 MET cc_start: 0.6643 (tmm) cc_final: 0.6236 (mtp) REVERT: P 186 MET cc_start: 0.4597 (tpp) cc_final: 0.3651 (mmm) REVERT: P 205 ARG cc_start: 0.7601 (ptt-90) cc_final: 0.3698 (mmm160) outliers start: 42 outliers final: 37 residues processed: 258 average time/residue: 0.3276 time to fit residues: 127.5807 Evaluate side-chains 255 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 216 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 90 ILE Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 4 residue 6 VAL Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 124 ASN Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 17 ASP Chi-restraints excluded: chain 9 residue 39 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain T residue 50 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 146 optimal weight: 0.0020 chunk 74 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 121 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 313 GLN 1 527 GLN 3 256 GLN 3 319 GLN 8 78 HIS 9 35 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20239 Z= 0.163 Angle : 0.501 11.519 27469 Z= 0.258 Chirality : 0.038 0.196 3163 Planarity : 0.004 0.046 3505 Dihedral : 4.755 59.320 2755 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 2.23 % Allowed : 12.22 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.17), residues: 2569 helix: 1.06 (0.13), residues: 1718 sheet: 0.30 (0.73), residues: 57 loop : -0.76 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.009 0.001 HIS 8 78 PHE 0.013 0.001 PHE 1 529 TYR 0.020 0.001 TYR 4 211 ARG 0.006 0.000 ARG 2 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 223 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7243 (pm20) REVERT: 0 47 TYR cc_start: 0.8401 (t80) cc_final: 0.8194 (t80) REVERT: 1 34 GLU cc_start: 0.7600 (pm20) cc_final: 0.7243 (pm20) REVERT: 1 219 LYS cc_start: 0.8063 (mttp) cc_final: 0.7732 (mtpt) REVERT: 1 572 ASP cc_start: 0.8188 (m-30) cc_final: 0.7859 (m-30) REVERT: 2 41 VAL cc_start: 0.7920 (OUTLIER) cc_final: 0.7617 (t) REVERT: 2 165 PHE cc_start: 0.8094 (m-10) cc_final: 0.7873 (m-80) REVERT: 4 13 TYR cc_start: 0.9109 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: 5 111 LYS cc_start: 0.8594 (mtpp) cc_final: 0.8259 (mmtm) REVERT: 6 146 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8188 (t80) REVERT: 9 13 LYS cc_start: 0.7674 (pttt) cc_final: 0.7168 (tttm) REVERT: 9 89 MET cc_start: 0.8443 (mtp) cc_final: 0.8221 (mtp) REVERT: M 270 MET cc_start: 0.6582 (tmm) cc_final: 0.6152 (mtp) REVERT: P 205 ARG cc_start: 0.7613 (ptt-90) cc_final: 0.3691 (mmm160) outliers start: 46 outliers final: 40 residues processed: 257 average time/residue: 0.3356 time to fit residues: 130.3775 Evaluate side-chains 258 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 215 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 416 LEU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 90 ILE Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 83 THR Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 17 ASP Chi-restraints excluded: chain 9 residue 35 GLN Chi-restraints excluded: chain 9 residue 39 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain T residue 50 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 0.5980 chunk 235 optimal weight: 0.9990 chunk 214 optimal weight: 4.9990 chunk 229 optimal weight: 0.0070 chunk 137 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 179 optimal weight: 0.1980 chunk 70 optimal weight: 0.6980 chunk 206 optimal weight: 0.7980 chunk 216 optimal weight: 0.7980 chunk 228 optimal weight: 0.6980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 256 GLN 3 319 GLN 8 78 HIS 9 35 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20239 Z= 0.149 Angle : 0.494 13.954 27469 Z= 0.254 Chirality : 0.038 0.173 3163 Planarity : 0.004 0.045 3505 Dihedral : 4.674 58.587 2755 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 2.13 % Allowed : 12.80 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.17), residues: 2569 helix: 1.26 (0.13), residues: 1717 sheet: 0.61 (0.75), residues: 57 loop : -0.65 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 PHE 0.025 0.001 PHE 3 121 TYR 0.022 0.001 TYR 4 211 ARG 0.006 0.000 ARG 2 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 219 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7111 (pm20) REVERT: 0 47 TYR cc_start: 0.8381 (t80) cc_final: 0.8180 (t80) REVERT: 1 34 GLU cc_start: 0.7625 (pm20) cc_final: 0.7269 (pm20) REVERT: 1 219 LYS cc_start: 0.8047 (mttp) cc_final: 0.7708 (mtpt) REVERT: 1 572 ASP cc_start: 0.8190 (m-30) cc_final: 0.7868 (m-30) REVERT: 2 41 VAL cc_start: 0.7865 (OUTLIER) cc_final: 0.7566 (t) REVERT: 2 165 PHE cc_start: 0.8077 (m-10) cc_final: 0.7864 (m-80) REVERT: 4 13 TYR cc_start: 0.9094 (OUTLIER) cc_final: 0.8294 (m-80) REVERT: 5 111 LYS cc_start: 0.8553 (mtpp) cc_final: 0.8218 (mmtm) REVERT: 6 146 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8144 (t80) REVERT: 9 13 LYS cc_start: 0.7591 (pttt) cc_final: 0.7108 (tttm) REVERT: M 270 MET cc_start: 0.6475 (tmm) cc_final: 0.6035 (mtp) REVERT: P 205 ARG cc_start: 0.7622 (ptt-90) cc_final: 0.3691 (mmm160) outliers start: 44 outliers final: 36 residues processed: 256 average time/residue: 0.3390 time to fit residues: 133.2986 Evaluate side-chains 255 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 216 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 97 SER Chi-restraints excluded: chain 2 residue 154 ASP Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 90 ILE Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 83 THR Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 17 ASP Chi-restraints excluded: chain 9 residue 35 GLN Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain T residue 50 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 1.9990 chunk 242 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 254 optimal weight: 2.9990 chunk 233 optimal weight: 0.0000 chunk 202 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 319 GLN 8 78 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20239 Z= 0.169 Angle : 0.500 14.090 27469 Z= 0.256 Chirality : 0.039 0.167 3163 Planarity : 0.004 0.044 3505 Dihedral : 4.630 56.933 2754 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 2.04 % Allowed : 12.55 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.17), residues: 2569 helix: 1.35 (0.13), residues: 1713 sheet: 0.57 (0.74), residues: 57 loop : -0.64 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 PHE 0.022 0.001 PHE 3 121 TYR 0.022 0.001 TYR 4 211 ARG 0.006 0.000 ARG 7 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 218 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7113 (pm20) REVERT: 0 47 TYR cc_start: 0.8406 (t80) cc_final: 0.8199 (t80) REVERT: 1 34 GLU cc_start: 0.7651 (pm20) cc_final: 0.7300 (pm20) REVERT: 1 219 LYS cc_start: 0.8042 (mttp) cc_final: 0.7699 (mtpt) REVERT: 1 572 ASP cc_start: 0.8204 (m-30) cc_final: 0.7881 (m-30) REVERT: 2 41 VAL cc_start: 0.7894 (OUTLIER) cc_final: 0.7596 (t) REVERT: 2 165 PHE cc_start: 0.8088 (m-10) cc_final: 0.7872 (m-80) REVERT: 4 13 TYR cc_start: 0.9096 (OUTLIER) cc_final: 0.8304 (m-80) REVERT: 5 111 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8227 (mmtm) REVERT: 6 146 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8150 (t80) REVERT: 9 13 LYS cc_start: 0.7720 (pttt) cc_final: 0.7174 (tttm) REVERT: M 270 MET cc_start: 0.6479 (tmm) cc_final: 0.6025 (mtp) REVERT: P 205 ARG cc_start: 0.7627 (ptt-90) cc_final: 0.3690 (mmm160) outliers start: 42 outliers final: 39 residues processed: 253 average time/residue: 0.3241 time to fit residues: 125.1793 Evaluate side-chains 256 residues out of total 2067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 214 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 399 MET Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 97 SER Chi-restraints excluded: chain 2 residue 154 ASP Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 90 ILE Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 4 residue 13 TYR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 83 THR Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 17 ASP Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain T residue 50 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 186 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 202 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 78 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.103080 restraints weight = 26550.323| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.34 r_work: 0.2892 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20239 Z= 0.198 Angle : 0.516 14.056 27469 Z= 0.263 Chirality : 0.039 0.162 3163 Planarity : 0.004 0.044 3505 Dihedral : 4.660 54.894 2754 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.70 % Favored : 96.19 % Rotamer: Outliers : 2.13 % Allowed : 12.51 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.17), residues: 2569 helix: 1.37 (0.13), residues: 1713 sheet: 0.57 (0.74), residues: 57 loop : -0.59 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 4 206 HIS 0.007 0.001 HIS 4 233 PHE 0.020 0.001 PHE 3 121 TYR 0.021 0.001 TYR 4 211 ARG 0.002 0.000 ARG 7 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4891.68 seconds wall clock time: 88 minutes 56.84 seconds (5336.84 seconds total)