Starting phenix.real_space_refine on Fri Mar 6 11:37:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qo5_53257/03_2026/9qo5_53257.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qo5_53257/03_2026/9qo5_53257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qo5_53257/03_2026/9qo5_53257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qo5_53257/03_2026/9qo5_53257.map" model { file = "/net/cci-nas-00/data/ceres_data/9qo5_53257/03_2026/9qo5_53257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qo5_53257/03_2026/9qo5_53257.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 6 5.49 5 S 166 5.16 5 C 18943 2.51 5 N 5068 2.21 5 O 5634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29818 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3308 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3267 Classifications: {'peptide': 398} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 3 Chain: "C" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3191 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 13, 'TRANS': 386} Chain breaks: 1 Chain: "D" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2833 Classifications: {'peptide': 351} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 341} Chain breaks: 2 Chain: "F" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2244 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 271} Chain breaks: 1 Chain: "G" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 4, 'TRANS': 211} Chain: "H" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1374 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain breaks: 1 Chain: "I" Number of atoms: 5042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5042 Classifications: {'peptide': 618} Link IDs: {'PTRANS': 10, 'TRANS': 607} Chain breaks: 6 Chain: "J" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 65 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "L" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1021 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2565 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 13, 'TRANS': 310} Chain: "N" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 614 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 6, 'TRANS': 64} Chain: "E" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2381 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 10, 'TRANS': 289} Chain breaks: 1 Chain: "P" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 170 Classifications: {'peptide': 20} Modifications used: {'COO': 1} Link IDs: {'TRANS': 19} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 5.93, per 1000 atoms: 0.20 Number of scatterers: 29818 At special positions: 0 Unit cell: (135, 204.12, 186.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 166 16.00 P 6 15.00 O 5634 8.00 N 5068 7.00 C 18943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS G 178 " - pdb=" SG CYS G 181 " distance=2.11 Simple disulfide: pdb=" SG CYS M 240 " - pdb=" SG CYS M 266 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.69 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" NE2 HIS E 140 " pdb="ZN ZN E 401 " - pdb=" NE2 HIS E 138 " 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7104 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 11 sheets defined 67.2% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.521A pdb=" N ILE A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 Processing helix chain 'A' and resid 87 through 105 removed outlier: 3.572A pdb=" N TYR A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 148 removed outlier: 3.560A pdb=" N GLU A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.748A pdb=" N TYR A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 177 through 187 Processing helix chain 'A' and resid 194 through 213 removed outlier: 3.758A pdb=" N VAL A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 228 Processing helix chain 'A' and resid 240 through 260 removed outlier: 4.800A pdb=" N LEU A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 271 removed outlier: 3.731A pdb=" N ALA A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 298 removed outlier: 3.800A pdb=" N VAL A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 316 through 322 removed outlier: 3.790A pdb=" N LEU A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 334 removed outlier: 4.018A pdb=" N ARG A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 353 removed outlier: 4.016A pdb=" N ASN A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 379 removed outlier: 3.523A pdb=" N GLN A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 393 Processing helix chain 'A' and resid 396 through 411 Processing helix chain 'A' and resid 430 through 463 removed outlier: 3.584A pdb=" N THR A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 41 removed outlier: 3.631A pdb=" N SER B 39 " --> pdb=" O GLN B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 60 Processing helix chain 'B' and resid 67 through 81 removed outlier: 4.326A pdb=" N LYS B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 104 through 121 Processing helix chain 'B' and resid 126 through 142 removed outlier: 3.811A pdb=" N GLU B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 162 removed outlier: 3.537A pdb=" N TRP B 148 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.534A pdb=" N ILE B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 208 removed outlier: 4.065A pdb=" N ALA B 207 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 removed outlier: 4.002A pdb=" N TYR B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 248 removed outlier: 3.615A pdb=" N MET B 234 " --> pdb=" O HIS B 230 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 248 " --> pdb=" O MET B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 269 removed outlier: 3.938A pdb=" N THR B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 288 removed outlier: 3.796A pdb=" N CYS B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 305 through 320 removed outlier: 3.612A pdb=" N ALA B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 340 through 364 removed outlier: 3.689A pdb=" N GLU B 345 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 350 " --> pdb=" O HIS B 346 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS B 364 " --> pdb=" O ILE B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 419 through 441 removed outlier: 3.578A pdb=" N LYS B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TRP B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN B 436 " --> pdb=" O ASN B 432 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 16 Processing helix chain 'C' and resid 20 through 31 removed outlier: 4.236A pdb=" N LEU C 24 " --> pdb=" O GLN C 20 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C 26 " --> pdb=" O THR C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 38 removed outlier: 4.000A pdb=" N LYS C 37 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN C 38 " --> pdb=" O LEU C 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 34 through 38' Processing helix chain 'C' and resid 56 through 66 Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.740A pdb=" N ILE C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 114 Processing helix chain 'C' and resid 116 through 119 removed outlier: 3.546A pdb=" N ARG C 119 " --> pdb=" O GLN C 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 116 through 119' Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'C' and resid 141 through 152 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 177 through 195 removed outlier: 3.861A pdb=" N PHE C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY C 189 " --> pdb=" O TYR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 removed outlier: 3.514A pdb=" N ALA C 201 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR C 211 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 235 removed outlier: 3.556A pdb=" N LEU C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 253 removed outlier: 3.567A pdb=" N ARG C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 257 through 269 removed outlier: 3.594A pdb=" N THR C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 293 through 310 removed outlier: 3.588A pdb=" N GLN C 297 " --> pdb=" O GLY C 293 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER C 300 " --> pdb=" O LYS C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 Processing helix chain 'C' and resid 330 through 344 removed outlier: 3.726A pdb=" N ALA C 334 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 399 removed outlier: 3.748A pdb=" N VAL C 399 " --> pdb=" O GLN C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 408 Processing helix chain 'D' and resid 41 through 53 removed outlier: 3.545A pdb=" N LEU D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ALA D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL D 53 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 72 removed outlier: 3.628A pdb=" N THR D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 90 through 91 No H-bonds generated for 'chain 'D' and resid 90 through 91' Processing helix chain 'D' and resid 92 through 96 Processing helix chain 'D' and resid 101 through 118 removed outlier: 3.914A pdb=" N ARG D 107 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLN D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.562A pdb=" N VAL D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 124 through 129' Processing helix chain 'D' and resid 141 through 158 Processing helix chain 'D' and resid 160 through 171 removed outlier: 3.645A pdb=" N ALA D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA D 166 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR D 167 " --> pdb=" O GLN D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 198 Processing helix chain 'D' and resid 202 through 212 Processing helix chain 'D' and resid 218 through 236 Processing helix chain 'D' and resid 239 through 252 removed outlier: 3.643A pdb=" N ASP D 252 " --> pdb=" O THR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.569A pdb=" N GLN D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.806A pdb=" N GLU D 280 " --> pdb=" O ASN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 285 No H-bonds generated for 'chain 'D' and resid 284 through 285' Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 298 through 315 removed outlier: 3.946A pdb=" N LYS D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU D 315 " --> pdb=" O SER D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 329 Processing helix chain 'D' and resid 331 through 345 removed outlier: 3.527A pdb=" N GLU D 345 " --> pdb=" O GLN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 392 removed outlier: 3.650A pdb=" N THR D 369 " --> pdb=" O GLU D 365 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN D 390 " --> pdb=" O GLU D 386 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR D 391 " --> pdb=" O LYS D 387 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA D 392 " --> pdb=" O ILE D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 406 removed outlier: 3.798A pdb=" N ALA D 405 " --> pdb=" O GLU D 401 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 62 removed outlier: 4.063A pdb=" N ILE F 48 " --> pdb=" O HIS F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 113 removed outlier: 3.564A pdb=" N LYS F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 144 removed outlier: 3.976A pdb=" N ILE F 136 " --> pdb=" O ASP F 132 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS F 137 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 215 through 248 removed outlier: 3.739A pdb=" N GLU F 219 " --> pdb=" O SER F 215 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLN F 224 " --> pdb=" O HIS F 220 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA F 227 " --> pdb=" O ALA F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 267 removed outlier: 3.684A pdb=" N LEU F 257 " --> pdb=" O ASN F 253 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU F 267 " --> pdb=" O LEU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 313 removed outlier: 3.845A pdb=" N VAL F 311 " --> pdb=" O ASN F 307 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU F 312 " --> pdb=" O LYS F 308 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 19 removed outlier: 3.779A pdb=" N PHE G 15 " --> pdb=" O LEU G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 37 Processing helix chain 'G' and resid 43 through 49 removed outlier: 3.823A pdb=" N LEU G 49 " --> pdb=" O GLU G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 54 Processing helix chain 'G' and resid 60 through 73 removed outlier: 3.745A pdb=" N LEU G 64 " --> pdb=" O ASN G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 81 Processing helix chain 'G' and resid 82 through 85 removed outlier: 3.766A pdb=" N LEU G 85 " --> pdb=" O LYS G 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 82 through 85' Processing helix chain 'G' and resid 89 through 106 Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 124 through 138 removed outlier: 3.678A pdb=" N LEU G 128 " --> pdb=" O ASN G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 225 removed outlier: 3.758A pdb=" N ILE G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN G 206 " --> pdb=" O HIS G 202 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN G 207 " --> pdb=" O ASN G 203 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN G 208 " --> pdb=" O ARG G 204 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL G 209 " --> pdb=" O THR G 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 26 Processing helix chain 'H' and resid 33 through 48 Processing helix chain 'H' and resid 49 through 60 removed outlier: 3.512A pdb=" N ALA H 53 " --> pdb=" O ASP H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 66 Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.501A pdb=" N VAL H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN H 83 " --> pdb=" O GLN H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 94 removed outlier: 3.663A pdb=" N TYR H 90 " --> pdb=" O PHE H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 101 No H-bonds generated for 'chain 'H' and resid 99 through 101' Processing helix chain 'H' and resid 102 through 124 Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'H' and resid 140 through 151 removed outlier: 3.646A pdb=" N ALA H 144 " --> pdb=" O PRO H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 208 Processing helix chain 'I' and resid 17 through 29 removed outlier: 4.080A pdb=" N ASP I 22 " --> pdb=" O ASP I 18 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASP I 23 " --> pdb=" O GLN I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 55 removed outlier: 4.063A pdb=" N MET I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR I 46 " --> pdb=" O TYR I 42 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS I 48 " --> pdb=" O GLU I 44 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL I 49 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER I 55 " --> pdb=" O ASN I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 108 removed outlier: 3.922A pdb=" N ASP I 106 " --> pdb=" O ASN I 102 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU I 108 " --> pdb=" O LEU I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 137 removed outlier: 4.011A pdb=" N LYS I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS I 137 " --> pdb=" O LEU I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 151 Processing helix chain 'I' and resid 158 through 172 Processing helix chain 'I' and resid 173 through 188 removed outlier: 3.800A pdb=" N LYS I 177 " --> pdb=" O ARG I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 192 Processing helix chain 'I' and resid 197 through 211 removed outlier: 3.971A pdb=" N ILE I 201 " --> pdb=" O ASN I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 255 removed outlier: 3.692A pdb=" N GLU I 230 " --> pdb=" O THR I 226 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE I 232 " --> pdb=" O TYR I 228 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER I 234 " --> pdb=" O GLU I 230 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLN I 235 " --> pdb=" O SER I 231 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR I 245 " --> pdb=" O GLU I 241 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR I 249 " --> pdb=" O THR I 245 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU I 250 " --> pdb=" O ARG I 246 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN I 254 " --> pdb=" O GLU I 250 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN I 255 " --> pdb=" O PHE I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 279 removed outlier: 4.131A pdb=" N GLN I 272 " --> pdb=" O LEU I 268 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG I 273 " --> pdb=" O LEU I 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 297 removed outlier: 4.821A pdb=" N LYS I 290 " --> pdb=" O GLU I 286 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE I 296 " --> pdb=" O GLU I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 313 removed outlier: 3.863A pdb=" N PHE I 303 " --> pdb=" O HIS I 299 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN I 308 " --> pdb=" O HIS I 304 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN I 309 " --> pdb=" O THR I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 removed outlier: 4.161A pdb=" N MET I 322 " --> pdb=" O ASP I 318 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR I 323 " --> pdb=" O LEU I 319 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 334 Processing helix chain 'I' and resid 335 through 354 removed outlier: 4.166A pdb=" N LEU I 339 " --> pdb=" O GLU I 335 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU I 340 " --> pdb=" O LEU I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 355 through 361 removed outlier: 5.503A pdb=" N ALA I 358 " --> pdb=" O CYS I 355 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA I 359 " --> pdb=" O GLY I 356 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU I 360 " --> pdb=" O GLU I 357 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 384 removed outlier: 3.505A pdb=" N TYR I 366 " --> pdb=" O ASP I 362 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS I 374 " --> pdb=" O VAL I 370 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA I 379 " --> pdb=" O LYS I 375 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU I 380 " --> pdb=" O LYS I 376 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL I 381 " --> pdb=" O TYR I 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 404 removed outlier: 3.644A pdb=" N ASN I 404 " --> pdb=" O GLY I 400 " (cutoff:3.500A) Processing helix chain 'I' and resid 406 through 410 Processing helix chain 'I' and resid 417 through 430 removed outlier: 3.763A pdb=" N LEU I 422 " --> pdb=" O SER I 418 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 454 Processing helix chain 'I' and resid 458 through 476 removed outlier: 4.327A pdb=" N PHE I 462 " --> pdb=" O ASP I 458 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS I 476 " --> pdb=" O LYS I 472 " (cutoff:3.500A) Processing helix chain 'I' and resid 481 through 496 removed outlier: 3.684A pdb=" N GLU I 485 " --> pdb=" O SER I 481 " (cutoff:3.500A) Processing helix chain 'I' and resid 497 through 500 Processing helix chain 'I' and resid 501 through 527 removed outlier: 3.737A pdb=" N ILE I 511 " --> pdb=" O MET I 507 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS I 515 " --> pdb=" O ILE I 511 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP I 516 " --> pdb=" O GLY I 512 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN I 527 " --> pdb=" O LYS I 523 " (cutoff:3.500A) Processing helix chain 'I' and resid 556 through 558 No H-bonds generated for 'chain 'I' and resid 556 through 558' Processing helix chain 'I' and resid 559 through 566 Processing helix chain 'I' and resid 569 through 574 Processing helix chain 'I' and resid 604 through 613 removed outlier: 4.092A pdb=" N GLN I 613 " --> pdb=" O ALA I 609 " (cutoff:3.500A) Processing helix chain 'I' and resid 614 through 616 No H-bonds generated for 'chain 'I' and resid 614 through 616' Processing helix chain 'I' and resid 621 through 630 Processing helix chain 'I' and resid 632 through 644 Processing helix chain 'L' and resid 17 through 24 removed outlier: 3.989A pdb=" N ALA L 21 " --> pdb=" O ASP L 17 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS L 22 " --> pdb=" O VAL L 18 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN L 23 " --> pdb=" O GLU L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 33 removed outlier: 3.739A pdb=" N ASP L 33 " --> pdb=" O THR L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 65 removed outlier: 3.794A pdb=" N LYS L 57 " --> pdb=" O ALA L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 93 Processing helix chain 'L' and resid 99 through 111 removed outlier: 3.519A pdb=" N LEU L 103 " --> pdb=" O THR L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 128 Processing helix chain 'L' and resid 134 through 139 Processing helix chain 'L' and resid 149 through 157 Processing helix chain 'M' and resid 101 through 111 removed outlier: 4.179A pdb=" N CYS M 111 " --> pdb=" O GLY M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 121 Processing helix chain 'M' and resid 124 through 132 removed outlier: 3.630A pdb=" N SER M 132 " --> pdb=" O TYR M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 148 through 158 removed outlier: 3.514A pdb=" N THR M 152 " --> pdb=" O HIS M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 203 Processing helix chain 'M' and resid 219 through 227 Processing helix chain 'M' and resid 244 through 255 removed outlier: 3.788A pdb=" N LEU M 248 " --> pdb=" O SER M 244 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER M 253 " --> pdb=" O GLN M 249 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS M 255 " --> pdb=" O LEU M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 281 Processing helix chain 'M' and resid 298 through 309 removed outlier: 3.641A pdb=" N LEU M 302 " --> pdb=" O GLN M 298 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG M 308 " --> pdb=" O THR M 304 " (cutoff:3.500A) Processing helix chain 'M' and resid 324 through 328 Processing helix chain 'M' and resid 330 through 334 removed outlier: 3.661A pdb=" N GLN M 333 " --> pdb=" O GLU M 330 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 359 removed outlier: 4.078A pdb=" N ILE M 359 " --> pdb=" O LEU M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 383 removed outlier: 4.087A pdb=" N LEU M 378 " --> pdb=" O GLY M 374 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 30 removed outlier: 3.645A pdb=" N LYS N 30 " --> pdb=" O LYS N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 47 Processing helix chain 'E' and resid 26 through 30 Processing helix chain 'E' and resid 32 through 42 Processing helix chain 'E' and resid 44 through 49 removed outlier: 3.987A pdb=" N ASP E 48 " --> pdb=" O PRO E 44 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N HIS E 49 " --> pdb=" O TRP E 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 44 through 49' Processing helix chain 'E' and resid 59 through 72 removed outlier: 3.791A pdb=" N GLY E 72 " --> pdb=" O HIS E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 125 removed outlier: 3.899A pdb=" N ALA E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS E 125 " --> pdb=" O ILE E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 160 removed outlier: 3.755A pdb=" N GLN E 160 " --> pdb=" O MET E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 210 through 217 removed outlier: 3.612A pdb=" N VAL E 216 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 241 through 244 Processing helix chain 'E' and resid 245 through 251 removed outlier: 3.709A pdb=" N THR E 249 " --> pdb=" O TYR E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 281 removed outlier: 3.645A pdb=" N ALA E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN E 279 " --> pdb=" O GLN E 275 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU E 280 " --> pdb=" O SER E 276 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY E 281 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 329 removed outlier: 3.604A pdb=" N LYS E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU E 313 " --> pdb=" O LYS E 309 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA E 314 " --> pdb=" O THR E 310 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 383 through 385 removed outlier: 7.470A pdb=" N LEU C 315 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL A 417 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU C 317 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU C 315 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR H 126 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE C 351 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE H 128 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN H 154 " --> pdb=" O LEU H 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 400 through 403 removed outlier: 6.218A pdb=" N THR B 367 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE D 351 " --> pdb=" O HIS D 360 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 319 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN D 317 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN G 142 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 178 through 186 removed outlier: 4.363A pdb=" N VAL F 167 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N LEU F 150 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU F 122 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N LEU F 152 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP F 124 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N LEU F 154 " --> pdb=" O TRP F 124 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR F 126 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N PHE F 121 " --> pdb=" O GLY F 74 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY F 74 " --> pdb=" O PHE F 121 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY F 123 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR F 125 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN F 85 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS F 75 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL F 83 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N SER F 40 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL F 83 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA F 42 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ASN F 85 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 92 through 93 Processing sheet with id=AA5, first strand: chain 'I' and resid 590 through 591 Processing sheet with id=AA6, first strand: chain 'M' and resid 185 through 187 Processing sheet with id=AA7, first strand: chain 'M' and resid 210 through 212 removed outlier: 3.791A pdb=" N SER M 264 " --> pdb=" O LEU M 237 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU M 261 " --> pdb=" O GLN M 287 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 339 through 341 Processing sheet with id=AA9, first strand: chain 'N' and resid 7 through 8 Processing sheet with id=AB1, first strand: chain 'N' and resid 7 through 8 Processing sheet with id=AB2, first strand: chain 'E' and resid 54 through 58 removed outlier: 6.816A pdb=" N TYR E 54 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ILE E 92 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS E 56 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASP E 94 " --> pdb=" O LYS E 56 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N SER E 58 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 11.538A pdb=" N PHE E 96 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N MET E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ASP E 86 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ILE E 92 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS E 84 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP E 94 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY E 135 " --> pdb=" O MET E 81 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP E 136 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ILE E 170 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N HIS E 138 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N LEU E 183 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL E 226 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA E 185 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE E 229 " --> pdb=" O ILE E 57 " (cutoff:3.500A) 1659 hydrogen bonds defined for protein. 4854 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: 5.57 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8516 1.33 - 1.46: 5502 1.46 - 1.58: 16071 1.58 - 1.70: 6 1.70 - 1.83: 261 Bond restraints: 30356 Sorted by residual: bond pdb=" C GLU G 176 " pdb=" O GLU G 176 " ideal model delta sigma weight residual 1.237 1.279 -0.042 1.16e-02 7.43e+03 1.33e+01 bond pdb=" O14 IHP B 501 " pdb=" P4 IHP B 501 " ideal model delta sigma weight residual 1.671 1.600 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O12 IHP B 501 " pdb=" P2 IHP B 501 " ideal model delta sigma weight residual 1.675 1.605 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" O15 IHP B 501 " pdb=" P5 IHP B 501 " ideal model delta sigma weight residual 1.675 1.609 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" N VAL G 184 " pdb=" CA VAL G 184 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.23e-02 6.61e+03 1.00e+01 ... (remaining 30351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 40256 2.40 - 4.81: 660 4.81 - 7.21: 68 7.21 - 9.61: 7 9.61 - 12.02: 6 Bond angle restraints: 40997 Sorted by residual: angle pdb=" N ASP G 179 " pdb=" CA ASP G 179 " pdb=" C ASP G 179 " ideal model delta sigma weight residual 111.36 101.22 10.14 1.09e+00 8.42e-01 8.66e+01 angle pdb=" C CYS G 178 " pdb=" CA CYS G 178 " pdb=" CB CYS G 178 " ideal model delta sigma weight residual 109.72 121.74 -12.02 1.92e+00 2.71e-01 3.92e+01 angle pdb=" C ASP B 340 " pdb=" CA ASP B 340 " pdb=" CB ASP B 340 " ideal model delta sigma weight residual 109.82 120.15 -10.33 1.65e+00 3.67e-01 3.92e+01 angle pdb=" N LEU L 116 " pdb=" CA LEU L 116 " pdb=" C LEU L 116 " ideal model delta sigma weight residual 111.28 104.65 6.63 1.09e+00 8.42e-01 3.70e+01 angle pdb=" N CYS G 181 " pdb=" CA CYS G 181 " pdb=" C CYS G 181 " ideal model delta sigma weight residual 111.11 103.90 7.21 1.20e+00 6.94e-01 3.61e+01 ... (remaining 40992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.19: 16967 26.19 - 52.38: 1384 52.38 - 78.57: 160 78.57 - 104.76: 24 104.76 - 130.95: 7 Dihedral angle restraints: 18542 sinusoidal: 7620 harmonic: 10922 Sorted by residual: dihedral pdb=" C CYS G 178 " pdb=" N CYS G 178 " pdb=" CA CYS G 178 " pdb=" CB CYS G 178 " ideal model delta harmonic sigma weight residual -122.60 -138.80 16.20 0 2.50e+00 1.60e-01 4.20e+01 dihedral pdb=" CA GLY E 87 " pdb=" C GLY E 87 " pdb=" N GLU E 88 " pdb=" CA GLU E 88 " ideal model delta harmonic sigma weight residual 180.00 155.47 24.53 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" N CYS G 178 " pdb=" C CYS G 178 " pdb=" CA CYS G 178 " pdb=" CB CYS G 178 " ideal model delta harmonic sigma weight residual 122.80 133.40 -10.60 0 2.50e+00 1.60e-01 1.80e+01 ... (remaining 18539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.020: 4626 1.020 - 2.040: 0 2.040 - 3.059: 0 3.059 - 4.079: 0 4.079 - 5.099: 4 Chirality restraints: 4630 Sorted by residual: chirality pdb=" C2 IHP B 501 " pdb=" C1 IHP B 501 " pdb=" C3 IHP B 501 " pdb=" O12 IHP B 501 " both_signs ideal model delta sigma weight residual False -2.52 2.58 -5.10 2.00e-01 2.50e+01 6.50e+02 chirality pdb=" C3 IHP B 501 " pdb=" C2 IHP B 501 " pdb=" C4 IHP B 501 " pdb=" O13 IHP B 501 " both_signs ideal model delta sigma weight residual False -2.34 2.54 -4.88 2.00e-01 2.50e+01 5.95e+02 chirality pdb=" C5 IHP B 501 " pdb=" C4 IHP B 501 " pdb=" C6 IHP B 501 " pdb=" O15 IHP B 501 " both_signs ideal model delta sigma weight residual False -2.42 2.46 -4.88 2.00e-01 2.50e+01 5.95e+02 ... (remaining 4627 not shown) Planarity restraints: 5228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 303 " -0.441 9.50e-02 1.11e+02 1.98e-01 2.41e+01 pdb=" NE ARG A 303 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 303 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 303 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 303 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 67 " 0.046 5.00e-02 4.00e+02 7.12e-02 8.10e+00 pdb=" N PRO A 68 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU L 115 " 0.013 2.00e-02 2.50e+03 2.75e-02 7.54e+00 pdb=" C LEU L 115 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU L 115 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU L 116 " 0.016 2.00e-02 2.50e+03 ... (remaining 5225 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 19 2.27 - 2.92: 12779 2.92 - 3.58: 44128 3.58 - 4.24: 62735 4.24 - 4.90: 107386 Nonbonded interactions: 227047 Sorted by model distance: nonbonded pdb="ZN ZN E 401 " pdb=" O HOH E 501 " model vdw 1.608 2.230 nonbonded pdb=" OD2 ASP E 151 " pdb="ZN ZN E 401 " model vdw 1.929 2.230 nonbonded pdb=" O ILE P 56 " pdb=" OXT GLN P 57 " model vdw 2.094 3.040 nonbonded pdb=" N GLU I 558 " pdb=" OE1 GLU I 558 " model vdw 2.186 3.120 nonbonded pdb=" OE1 GLU D 345 " pdb=" NH2 ARG D 347 " model vdw 2.196 3.120 ... (remaining 227042 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.400 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: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.980 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 30360 Z= 0.187 Angle : 0.714 12.017 41001 Z= 0.386 Chirality : 0.149 5.099 4630 Planarity : 0.005 0.198 5228 Dihedral : 18.023 130.947 11432 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.16 % Favored : 95.82 % Rotamer: Outliers : 2.25 % Allowed : 26.02 % Favored : 71.73 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3634 helix: 1.38 (0.11), residues: 2207 sheet: -1.15 (0.33), residues: 216 loop : -1.71 (0.18), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 401 TYR 0.020 0.001 TYR C 203 PHE 0.017 0.001 PHE I 402 TRP 0.016 0.001 TRP N 43 HIS 0.017 0.001 HIS I 304 Details of bonding type rmsd covalent geometry : bond 0.00382 (30356) covalent geometry : angle 0.71176 (40997) SS BOND : bond 0.05864 ( 2) SS BOND : angle 5.17663 ( 4) hydrogen bonds : bond 0.15392 ( 1657) hydrogen bonds : angle 5.34855 ( 4854) metal coordination : bond 0.00409 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 1016 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 146 ASP cc_start: 0.7746 (t0) cc_final: 0.7444 (t0) REVERT: A 159 GLU cc_start: 0.8116 (mp0) cc_final: 0.7104 (tm-30) REVERT: A 170 ASP cc_start: 0.8484 (t0) cc_final: 0.8262 (t0) REVERT: A 172 TYR cc_start: 0.7094 (m-10) cc_final: 0.6693 (m-80) REVERT: A 174 ASP cc_start: 0.8082 (t0) cc_final: 0.7619 (t0) REVERT: A 180 ASN cc_start: 0.7747 (m-40) cc_final: 0.7516 (p0) REVERT: A 207 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8072 (ttmt) REVERT: A 211 TYR cc_start: 0.7643 (m-80) cc_final: 0.7420 (m-80) REVERT: A 224 LYS cc_start: 0.8398 (ttmt) cc_final: 0.8135 (mmtm) REVERT: A 226 GLU cc_start: 0.5916 (OUTLIER) cc_final: 0.5604 (mp0) REVERT: A 296 CYS cc_start: 0.8227 (m) cc_final: 0.7531 (m) REVERT: A 305 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7386 (mm-30) REVERT: A 307 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7713 (tm-30) REVERT: A 343 LYS cc_start: 0.7322 (mmmm) cc_final: 0.7121 (mmmm) REVERT: A 349 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6706 (ptmm) REVERT: A 365 LEU cc_start: 0.7181 (mt) cc_final: 0.6849 (mt) REVERT: A 416 ARG cc_start: 0.8201 (mmt-90) cc_final: 0.7629 (mmt-90) REVERT: A 437 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6835 (mm-30) REVERT: A 446 PHE cc_start: 0.8126 (t80) cc_final: 0.7815 (t80) REVERT: A 447 GLN cc_start: 0.7565 (mt0) cc_final: 0.7298 (mt0) REVERT: A 451 LYS cc_start: 0.7945 (mtmt) cc_final: 0.7642 (mtmt) REVERT: A 453 MET cc_start: 0.7905 (tmm) cc_final: 0.7654 (tmm) REVERT: A 467 LYS cc_start: 0.8075 (tptt) cc_final: 0.7636 (tptt) REVERT: B 74 GLN cc_start: 0.7332 (tp-100) cc_final: 0.7027 (tm-30) REVERT: B 95 LEU cc_start: 0.8121 (mt) cc_final: 0.7845 (pp) REVERT: B 110 LYS cc_start: 0.8472 (mtmm) cc_final: 0.8046 (mtmm) REVERT: B 196 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7254 (mt-10) REVERT: B 234 MET cc_start: 0.6885 (mmm) cc_final: 0.6370 (mmm) REVERT: B 244 MET cc_start: 0.7104 (tmm) cc_final: 0.6611 (tmm) REVERT: B 338 MET cc_start: 0.7095 (mmt) cc_final: 0.6655 (mmm) REVERT: B 390 VAL cc_start: 0.7659 (t) cc_final: 0.7397 (p) REVERT: B 395 ASP cc_start: 0.7274 (m-30) cc_final: 0.6856 (m-30) REVERT: B 404 GLN cc_start: 0.7966 (tt0) cc_final: 0.7615 (tt0) REVERT: B 425 ASP cc_start: 0.6760 (t0) cc_final: 0.6463 (t0) REVERT: B 426 LYS cc_start: 0.7750 (mttp) cc_final: 0.7492 (mttp) REVERT: B 430 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7516 (mm-40) REVERT: B 436 GLN cc_start: 0.8462 (tp40) cc_final: 0.8014 (tp-100) REVERT: C 13 ARG cc_start: 0.8189 (mtp180) cc_final: 0.7756 (mtt180) REVERT: C 58 VAL cc_start: 0.8332 (m) cc_final: 0.8129 (p) REVERT: C 81 VAL cc_start: 0.8469 (m) cc_final: 0.8208 (p) REVERT: C 166 MET cc_start: 0.6838 (mmt) cc_final: 0.5925 (mmp) REVERT: C 214 MET cc_start: 0.7494 (mpp) cc_final: 0.6659 (mpp) REVERT: C 218 HIS cc_start: 0.7452 (m170) cc_final: 0.6342 (m-70) REVERT: C 222 GLU cc_start: 0.7582 (mp0) cc_final: 0.7100 (mp0) REVERT: C 224 TYR cc_start: 0.7335 (t80) cc_final: 0.7063 (t80) REVERT: C 247 GLN cc_start: 0.7540 (pp30) cc_final: 0.7089 (pp30) REVERT: C 271 ASN cc_start: 0.7862 (t0) cc_final: 0.7625 (t0) REVERT: C 312 LYS cc_start: 0.7868 (mmmm) cc_final: 0.7395 (mmmm) REVERT: C 316 THR cc_start: 0.7968 (OUTLIER) cc_final: 0.7607 (p) REVERT: C 325 ARG cc_start: 0.7243 (mtt-85) cc_final: 0.6881 (ttm-80) REVERT: C 327 GLN cc_start: 0.7767 (mp10) cc_final: 0.7219 (mp10) REVERT: C 357 MET cc_start: 0.7575 (mmm) cc_final: 0.7241 (mmm) REVERT: C 380 MET cc_start: 0.7260 (mtp) cc_final: 0.6795 (mtt) REVERT: C 386 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7741 (tp) REVERT: C 405 GLN cc_start: 0.8182 (tp40) cc_final: 0.7902 (tp40) REVERT: D 82 LYS cc_start: 0.7456 (ptmt) cc_final: 0.6862 (ptpp) REVERT: D 157 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7999 (tp30) REVERT: D 245 MET cc_start: 0.5878 (mmm) cc_final: 0.5477 (tpp) REVERT: D 256 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6787 (mm110) REVERT: D 265 GLU cc_start: 0.8160 (tt0) cc_final: 0.7526 (tm-30) REVERT: D 266 LYS cc_start: 0.8532 (mmmm) cc_final: 0.8124 (mmmm) REVERT: D 323 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6796 (mm-30) REVERT: D 341 GLN cc_start: 0.7320 (pt0) cc_final: 0.6925 (tt0) REVERT: D 355 ILE cc_start: 0.8516 (tt) cc_final: 0.8295 (tt) REVERT: F 30 VAL cc_start: 0.8093 (m) cc_final: 0.7827 (t) REVERT: F 82 GLU cc_start: 0.7618 (tt0) cc_final: 0.7031 (mt-10) REVERT: F 97 LYS cc_start: 0.8101 (ptpp) cc_final: 0.7653 (mppt) REVERT: F 153 LYS cc_start: 0.8253 (tttp) cc_final: 0.7727 (ttmt) REVERT: F 206 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6519 (mtt) REVERT: F 249 GLU cc_start: 0.7921 (mp0) cc_final: 0.7470 (mp0) REVERT: F 264 CYS cc_start: 0.8160 (m) cc_final: 0.7548 (m) REVERT: G 33 GLN cc_start: 0.8707 (mt0) cc_final: 0.8304 (mt0) REVERT: G 74 THR cc_start: 0.6493 (OUTLIER) cc_final: 0.6201 (p) REVERT: G 103 SER cc_start: 0.8609 (t) cc_final: 0.8152 (p) REVERT: G 107 ARG cc_start: 0.7355 (ptp90) cc_final: 0.6962 (ptp90) REVERT: G 212 GLU cc_start: 0.8183 (tp30) cc_final: 0.7907 (tp30) REVERT: G 214 THR cc_start: 0.7616 (OUTLIER) cc_final: 0.7284 (p) REVERT: G 217 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7501 (tppt) REVERT: H 21 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7804 (mt-10) REVERT: H 35 PRO cc_start: 0.8419 (Cg_exo) cc_final: 0.8120 (Cg_endo) REVERT: H 39 GLN cc_start: 0.7271 (mt0) cc_final: 0.6994 (mt0) REVERT: H 58 LYS cc_start: 0.8280 (mttt) cc_final: 0.7887 (mttt) REVERT: I 92 LEU cc_start: 0.8321 (mt) cc_final: 0.7992 (mp) REVERT: I 93 LYS cc_start: 0.8339 (tttt) cc_final: 0.7978 (ptpt) REVERT: I 128 PHE cc_start: 0.7618 (t80) cc_final: 0.7128 (t80) REVERT: I 148 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7154 (mm-30) REVERT: I 167 TRP cc_start: 0.7376 (t-100) cc_final: 0.6725 (t-100) REVERT: I 229 LYS cc_start: 0.8980 (mmmt) cc_final: 0.7931 (mmmm) REVERT: I 267 ARG cc_start: 0.8078 (mmm160) cc_final: 0.7835 (mmm-85) REVERT: I 268 LEU cc_start: 0.8687 (mm) cc_final: 0.8483 (mm) REVERT: I 272 GLN cc_start: 0.8296 (pp30) cc_final: 0.7668 (pp30) REVERT: I 297 GLU cc_start: 0.6887 (tm-30) cc_final: 0.6604 (tm-30) REVERT: I 321 ARG cc_start: 0.8101 (mpp80) cc_final: 0.7891 (mpp80) REVERT: I 325 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7562 (mp) REVERT: I 365 MET cc_start: 0.7803 (mmm) cc_final: 0.7224 (mmm) REVERT: I 376 LYS cc_start: 0.8674 (tttt) cc_final: 0.8372 (tttt) REVERT: I 402 PHE cc_start: 0.8010 (p90) cc_final: 0.7775 (p90) REVERT: I 472 LYS cc_start: 0.8446 (tptt) cc_final: 0.8038 (tptp) REVERT: I 493 LYS cc_start: 0.8157 (ttpt) cc_final: 0.7214 (tmtt) REVERT: L 14 PHE cc_start: 0.8340 (m-80) cc_final: 0.8025 (m-80) REVERT: L 30 MET cc_start: 0.8495 (mtp) cc_final: 0.8256 (tmm) REVERT: L 62 CYS cc_start: 0.8830 (m) cc_final: 0.8546 (p) REVERT: L 109 TYR cc_start: 0.7265 (t80) cc_final: 0.6940 (t80) REVERT: M 137 TRP cc_start: 0.7041 (m100) cc_final: 0.6726 (m100) REVERT: M 278 VAL cc_start: 0.7786 (p) cc_final: 0.7445 (p) REVERT: M 291 SER cc_start: 0.5510 (p) cc_final: 0.4544 (t) REVERT: M 298 GLN cc_start: 0.6486 (mp10) cc_final: 0.6092 (mp10) REVERT: M 320 SER cc_start: 0.7813 (m) cc_final: 0.7097 (p) REVERT: M 368 PHE cc_start: 0.7668 (m-80) cc_final: 0.7431 (m-10) REVERT: M 370 ILE cc_start: 0.8788 (pt) cc_final: 0.8448 (tt) REVERT: E 134 ILE cc_start: 0.7412 (tt) cc_final: 0.7173 (tt) REVERT: E 171 ASP cc_start: 0.7499 (t0) cc_final: 0.7250 (t0) REVERT: E 230 LYS cc_start: 0.8603 (pttt) cc_final: 0.8252 (pttm) REVERT: E 261 TYR cc_start: 0.7872 (t80) cc_final: 0.7552 (t80) REVERT: E 270 SER cc_start: 0.7729 (m) cc_final: 0.7518 (p) REVERT: E 305 ARG cc_start: 0.7690 (ttp-170) cc_final: 0.7451 (mtp-110) outliers start: 74 outliers final: 38 residues processed: 1054 average time/residue: 0.1959 time to fit residues: 316.2109 Evaluate side-chains 1008 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 962 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 344 ILE Chi-restraints excluded: chain I residue 371 LEU Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain M residue 182 ARG Chi-restraints excluded: chain M residue 193 ILE Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain P residue 54 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 197 optimal weight: 0.0970 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS D 241 GLN F 303 ASN ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 299 HIS L 158 GLN ** M 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 389 ASN E 110 GLN E 258 ASN E 265 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.154364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127133 restraints weight = 58431.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.130976 restraints weight = 30627.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.133491 restraints weight = 18967.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.135172 restraints weight = 13390.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.136305 restraints weight = 10457.515| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30360 Z= 0.136 Angle : 0.635 14.015 41001 Z= 0.325 Chirality : 0.041 0.326 4630 Planarity : 0.005 0.081 5228 Dihedral : 6.168 66.581 4114 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.68 % Rotamer: Outliers : 3.92 % Allowed : 23.50 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3634 helix: 1.38 (0.11), residues: 2246 sheet: -0.64 (0.35), residues: 202 loop : -1.68 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 193 TYR 0.025 0.001 TYR N 12 PHE 0.024 0.001 PHE I 251 TRP 0.021 0.002 TRP N 43 HIS 0.011 0.001 HIS I 304 Details of bonding type rmsd covalent geometry : bond 0.00294 (30356) covalent geometry : angle 0.63346 (40997) SS BOND : bond 0.00348 ( 2) SS BOND : angle 4.26727 ( 4) hydrogen bonds : bond 0.04859 ( 1657) hydrogen bonds : angle 4.38864 ( 4854) metal coordination : bond 0.00348 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 990 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASP cc_start: 0.7514 (t0) cc_final: 0.7197 (t0) REVERT: A 159 GLU cc_start: 0.8196 (mp0) cc_final: 0.6953 (tm-30) REVERT: A 170 ASP cc_start: 0.8514 (t0) cc_final: 0.8294 (t0) REVERT: A 172 TYR cc_start: 0.7142 (m-10) cc_final: 0.6734 (m-10) REVERT: A 174 ASP cc_start: 0.8109 (t0) cc_final: 0.7779 (t0) REVERT: A 180 ASN cc_start: 0.7724 (m-40) cc_final: 0.7272 (p0) REVERT: A 207 LYS cc_start: 0.8485 (ttmt) cc_final: 0.8129 (ttmt) REVERT: A 211 TYR cc_start: 0.7516 (m-80) cc_final: 0.7105 (m-80) REVERT: A 226 GLU cc_start: 0.5888 (OUTLIER) cc_final: 0.5571 (mp0) REVERT: A 248 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7023 (ttpt) REVERT: A 284 LEU cc_start: 0.8205 (mm) cc_final: 0.7927 (mt) REVERT: A 296 CYS cc_start: 0.8303 (m) cc_final: 0.7722 (m) REVERT: A 307 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7852 (tm-30) REVERT: A 365 LEU cc_start: 0.7081 (mt) cc_final: 0.6725 (mt) REVERT: A 402 ASP cc_start: 0.7385 (m-30) cc_final: 0.6777 (m-30) REVERT: A 416 ARG cc_start: 0.8230 (mmt-90) cc_final: 0.7731 (mmt-90) REVERT: A 446 PHE cc_start: 0.7975 (t80) cc_final: 0.7706 (t80) REVERT: A 467 LYS cc_start: 0.8109 (tptt) cc_final: 0.7725 (tptt) REVERT: B 55 GLN cc_start: 0.6439 (OUTLIER) cc_final: 0.6068 (pp30) REVERT: B 110 LYS cc_start: 0.8401 (mtmm) cc_final: 0.8010 (mtmm) REVERT: B 196 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7358 (mt-10) REVERT: B 220 GLN cc_start: 0.7758 (tt0) cc_final: 0.7221 (tp40) REVERT: B 234 MET cc_start: 0.6901 (mmm) cc_final: 0.6351 (mmm) REVERT: B 244 MET cc_start: 0.7117 (tmm) cc_final: 0.6711 (tmm) REVERT: B 318 TYR cc_start: 0.7064 (t80) cc_final: 0.6817 (t80) REVERT: B 330 LEU cc_start: 0.6362 (tp) cc_final: 0.6053 (tt) REVERT: B 338 MET cc_start: 0.7180 (mmt) cc_final: 0.6328 (mmt) REVERT: B 364 LYS cc_start: 0.7694 (ttpp) cc_final: 0.7331 (pttm) REVERT: B 395 ASP cc_start: 0.6921 (m-30) cc_final: 0.6434 (m-30) REVERT: B 404 GLN cc_start: 0.7939 (tt0) cc_final: 0.7606 (tt0) REVERT: B 406 ASN cc_start: 0.8849 (m-40) cc_final: 0.8641 (m110) REVERT: B 430 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7487 (mm-40) REVERT: B 436 GLN cc_start: 0.8483 (tp40) cc_final: 0.7573 (tp-100) REVERT: C 13 ARG cc_start: 0.8313 (mtp180) cc_final: 0.7836 (mtt180) REVERT: C 81 VAL cc_start: 0.8500 (m) cc_final: 0.8220 (p) REVERT: C 82 GLN cc_start: 0.8491 (tt0) cc_final: 0.8100 (pt0) REVERT: C 166 MET cc_start: 0.6754 (mmt) cc_final: 0.5805 (mmp) REVERT: C 167 MET cc_start: 0.7326 (ptp) cc_final: 0.7085 (ptp) REVERT: C 214 MET cc_start: 0.7633 (mpp) cc_final: 0.6965 (mpp) REVERT: C 218 HIS cc_start: 0.7514 (m170) cc_final: 0.6727 (m170) REVERT: C 222 GLU cc_start: 0.7455 (mp0) cc_final: 0.7206 (mp0) REVERT: C 224 TYR cc_start: 0.7333 (t80) cc_final: 0.7067 (t80) REVERT: C 247 GLN cc_start: 0.7644 (pp30) cc_final: 0.7224 (pp30) REVERT: C 316 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7782 (p) REVERT: C 325 ARG cc_start: 0.7395 (mtt-85) cc_final: 0.7138 (ttm-80) REVERT: C 327 GLN cc_start: 0.7908 (mp10) cc_final: 0.7378 (mp10) REVERT: C 357 MET cc_start: 0.7573 (mmm) cc_final: 0.7280 (mmt) REVERT: C 380 MET cc_start: 0.7284 (mtp) cc_final: 0.6833 (mtt) REVERT: C 405 GLN cc_start: 0.8089 (tp40) cc_final: 0.7671 (tp40) REVERT: D 157 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7528 (mm-30) REVERT: D 221 GLU cc_start: 0.5451 (OUTLIER) cc_final: 0.5154 (pp20) REVERT: D 245 MET cc_start: 0.6102 (mmm) cc_final: 0.5606 (tpp) REVERT: D 265 GLU cc_start: 0.8163 (tt0) cc_final: 0.7420 (tm-30) REVERT: D 277 GLN cc_start: 0.7793 (pm20) cc_final: 0.7497 (pm20) REVERT: D 323 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6801 (mm-30) REVERT: D 341 GLN cc_start: 0.7429 (pt0) cc_final: 0.7068 (tt0) REVERT: F 97 LYS cc_start: 0.7996 (ptpp) cc_final: 0.7503 (mppt) REVERT: F 111 GLN cc_start: 0.8513 (tt0) cc_final: 0.8307 (tt0) REVERT: F 153 LYS cc_start: 0.8179 (tttp) cc_final: 0.7583 (ttmt) REVERT: F 166 SER cc_start: 0.8205 (m) cc_final: 0.7331 (p) REVERT: F 185 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7667 (tm-30) REVERT: F 186 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7555 (tt) REVERT: F 230 MET cc_start: 0.6768 (tpp) cc_final: 0.6476 (tpp) REVERT: F 249 GLU cc_start: 0.7880 (mp0) cc_final: 0.7549 (mp0) REVERT: F 264 CYS cc_start: 0.8160 (m) cc_final: 0.7604 (m) REVERT: G 33 GLN cc_start: 0.8612 (mt0) cc_final: 0.8272 (mt0) REVERT: G 103 SER cc_start: 0.8577 (t) cc_final: 0.8189 (p) REVERT: G 107 ARG cc_start: 0.7292 (ptp90) cc_final: 0.6897 (ptp90) REVERT: G 151 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6748 (mp) REVERT: G 212 GLU cc_start: 0.8138 (tp30) cc_final: 0.7841 (tp30) REVERT: G 214 THR cc_start: 0.7661 (t) cc_final: 0.7321 (p) REVERT: G 217 LYS cc_start: 0.7901 (ttpt) cc_final: 0.7509 (tppt) REVERT: H 21 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7713 (mt-10) REVERT: H 35 PRO cc_start: 0.8528 (Cg_exo) cc_final: 0.8188 (Cg_endo) REVERT: H 58 LYS cc_start: 0.8166 (mttt) cc_final: 0.7827 (mttt) REVERT: I 43 MET cc_start: 0.6516 (tmm) cc_final: 0.6263 (tmm) REVERT: I 128 PHE cc_start: 0.7466 (t80) cc_final: 0.6971 (t80) REVERT: I 148 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7164 (mm-30) REVERT: I 151 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7331 (tm-30) REVERT: I 167 TRP cc_start: 0.7214 (t-100) cc_final: 0.6509 (t-100) REVERT: I 168 ARG cc_start: 0.8095 (mtp-110) cc_final: 0.7603 (ttm-80) REVERT: I 233 GLU cc_start: 0.7335 (pt0) cc_final: 0.6968 (pm20) REVERT: I 235 GLN cc_start: 0.7811 (mp10) cc_final: 0.7576 (mp10) REVERT: I 237 LEU cc_start: 0.8742 (tt) cc_final: 0.8477 (pp) REVERT: I 267 ARG cc_start: 0.7792 (mmm160) cc_final: 0.7415 (mmm-85) REVERT: I 268 LEU cc_start: 0.8722 (mm) cc_final: 0.8510 (mm) REVERT: I 271 GLU cc_start: 0.7796 (pm20) cc_final: 0.7279 (pp20) REVERT: I 272 GLN cc_start: 0.7972 (pp30) cc_final: 0.6955 (pp30) REVERT: I 297 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6258 (tm-30) REVERT: I 319 LEU cc_start: 0.8754 (mt) cc_final: 0.8516 (mt) REVERT: I 321 ARG cc_start: 0.8041 (mpp80) cc_final: 0.7828 (mtm-85) REVERT: I 325 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7398 (mp) REVERT: I 365 MET cc_start: 0.7434 (mmm) cc_final: 0.6933 (mmm) REVERT: I 368 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7777 (mm-40) REVERT: I 376 LYS cc_start: 0.8491 (tttt) cc_final: 0.8123 (tptp) REVERT: I 417 LYS cc_start: 0.7266 (ttmm) cc_final: 0.7043 (ttmm) REVERT: I 452 VAL cc_start: 0.8668 (m) cc_final: 0.8358 (p) REVERT: I 466 TYR cc_start: 0.7041 (t80) cc_final: 0.6678 (t80) REVERT: I 472 LYS cc_start: 0.8352 (tptt) cc_final: 0.7867 (tptp) REVERT: I 491 LYS cc_start: 0.8369 (mmtt) cc_final: 0.8161 (mmtt) REVERT: I 507 MET cc_start: 0.7352 (mtm) cc_final: 0.6157 (mtm) REVERT: I 545 TRP cc_start: 0.6949 (m100) cc_final: 0.6647 (m100) REVERT: L 14 PHE cc_start: 0.8407 (m-80) cc_final: 0.8138 (m-80) REVERT: L 19 GLU cc_start: 0.7011 (tm-30) cc_final: 0.6766 (tm-30) REVERT: M 165 CYS cc_start: 0.7577 (OUTLIER) cc_final: 0.6793 (m) REVERT: M 204 GLN cc_start: 0.7340 (mm-40) cc_final: 0.6842 (mm-40) REVERT: M 291 SER cc_start: 0.5911 (p) cc_final: 0.4881 (t) REVERT: M 298 GLN cc_start: 0.6680 (mp10) cc_final: 0.6128 (mp10) REVERT: M 320 SER cc_start: 0.7860 (m) cc_final: 0.7223 (p) REVERT: M 368 PHE cc_start: 0.7606 (m-80) cc_final: 0.7316 (m-10) REVERT: M 370 ILE cc_start: 0.8785 (pt) cc_final: 0.8489 (tt) REVERT: M 416 LEU cc_start: 0.7181 (mm) cc_final: 0.6961 (mm) REVERT: N 38 MET cc_start: 0.7843 (mtm) cc_final: 0.7626 (ttm) REVERT: N 43 TRP cc_start: 0.7454 (p-90) cc_final: 0.6743 (p-90) REVERT: E 35 GLN cc_start: 0.7394 (tm-30) cc_final: 0.7097 (tm-30) REVERT: E 75 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7245 (pp) REVERT: E 171 ASP cc_start: 0.7134 (t0) cc_final: 0.6899 (t0) REVERT: E 258 ASN cc_start: 0.7366 (OUTLIER) cc_final: 0.6775 (p0) REVERT: E 261 TYR cc_start: 0.7651 (t80) cc_final: 0.7352 (t80) REVERT: E 270 SER cc_start: 0.7686 (m) cc_final: 0.7354 (p) REVERT: E 277 GLU cc_start: 0.7571 (tt0) cc_final: 0.7328 (tt0) REVERT: E 305 ARG cc_start: 0.7471 (ttp-170) cc_final: 0.7220 (mtp180) outliers start: 129 outliers final: 72 residues processed: 1058 average time/residue: 0.1975 time to fit residues: 320.3142 Evaluate side-chains 1035 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 950 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 431 GLN Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 243 LYS Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 47 HIS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 226 THR Chi-restraints excluded: chain I residue 297 GLU Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 436 ASN Chi-restraints excluded: chain I residue 502 SER Chi-restraints excluded: chain I residue 524 HIS Chi-restraints excluded: chain I residue 640 LEU Chi-restraints excluded: chain I residue 684 ILE Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 165 CYS Chi-restraints excluded: chain M residue 182 ARG Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 325 ASN Chi-restraints excluded: chain M residue 361 THR Chi-restraints excluded: chain M residue 409 ILE Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 323 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 211 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 213 optimal weight: 5.9990 chunk 95 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 218 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN A 376 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN C 132 GLN D 182 GLN D 241 GLN F 67 GLN ** F 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** I 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 299 HIS I 463 GLN M 229 ASN M 236 ASN ** M 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 392 HIS E 258 ASN E 265 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.153842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.126433 restraints weight = 59020.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.130311 restraints weight = 31087.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.132829 restraints weight = 19357.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.134520 restraints weight = 13689.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.135641 restraints weight = 10711.065| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30360 Z= 0.137 Angle : 0.618 17.187 41001 Z= 0.317 Chirality : 0.040 0.202 4630 Planarity : 0.004 0.064 5228 Dihedral : 5.335 57.829 4054 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.05 % Favored : 95.93 % Rotamer: Outliers : 4.29 % Allowed : 24.13 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3634 helix: 1.35 (0.11), residues: 2249 sheet: -0.62 (0.34), residues: 214 loop : -1.65 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 193 TYR 0.024 0.001 TYR D 148 PHE 0.025 0.001 PHE B 54 TRP 0.029 0.002 TRP I 581 HIS 0.011 0.001 HIS I 280 Details of bonding type rmsd covalent geometry : bond 0.00303 (30356) covalent geometry : angle 0.61576 (40997) SS BOND : bond 0.01957 ( 2) SS BOND : angle 5.76794 ( 4) hydrogen bonds : bond 0.04652 ( 1657) hydrogen bonds : angle 4.26805 ( 4854) metal coordination : bond 0.00349 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 968 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASP cc_start: 0.7586 (t0) cc_final: 0.7257 (t0) REVERT: A 149 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8076 (tt) REVERT: A 159 GLU cc_start: 0.8101 (mp0) cc_final: 0.7225 (tm-30) REVERT: A 172 TYR cc_start: 0.7184 (m-10) cc_final: 0.6761 (m-10) REVERT: A 174 ASP cc_start: 0.8135 (t0) cc_final: 0.7810 (t0) REVERT: A 180 ASN cc_start: 0.7708 (m-40) cc_final: 0.7314 (p0) REVERT: A 211 TYR cc_start: 0.7305 (m-80) cc_final: 0.6569 (m-80) REVERT: A 224 LYS cc_start: 0.8351 (ttmt) cc_final: 0.8114 (mmtm) REVERT: A 226 GLU cc_start: 0.5971 (OUTLIER) cc_final: 0.5671 (mp0) REVERT: A 296 CYS cc_start: 0.8378 (m) cc_final: 0.7697 (m) REVERT: A 307 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7879 (tm-30) REVERT: A 317 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8115 (mtmm) REVERT: A 365 LEU cc_start: 0.7090 (mt) cc_final: 0.6726 (mt) REVERT: A 416 ARG cc_start: 0.8260 (mmt-90) cc_final: 0.7727 (mmt-90) REVERT: A 454 MET cc_start: 0.7422 (mtt) cc_final: 0.7218 (mtt) REVERT: A 462 ASN cc_start: 0.7966 (m-40) cc_final: 0.7765 (t0) REVERT: A 467 LYS cc_start: 0.8130 (tptt) cc_final: 0.7753 (tptt) REVERT: B 37 TYR cc_start: 0.7256 (t80) cc_final: 0.6767 (t80) REVERT: B 55 GLN cc_start: 0.6379 (OUTLIER) cc_final: 0.6007 (pp30) REVERT: B 66 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6918 (tm-30) REVERT: B 88 MET cc_start: 0.5162 (mmt) cc_final: 0.4586 (mmt) REVERT: B 110 LYS cc_start: 0.8447 (mtmm) cc_final: 0.8189 (mttt) REVERT: B 117 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7860 (p0) REVERT: B 196 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7384 (mt-10) REVERT: B 220 GLN cc_start: 0.7886 (tt0) cc_final: 0.7315 (tp40) REVERT: B 234 MET cc_start: 0.6919 (mmm) cc_final: 0.6303 (mmm) REVERT: B 244 MET cc_start: 0.7189 (tmm) cc_final: 0.6928 (tmm) REVERT: B 318 TYR cc_start: 0.7040 (t80) cc_final: 0.6756 (t80) REVERT: B 322 ASP cc_start: 0.5792 (t70) cc_final: 0.5514 (t70) REVERT: B 330 LEU cc_start: 0.6214 (tp) cc_final: 0.6011 (tt) REVERT: B 338 MET cc_start: 0.7088 (mmt) cc_final: 0.6536 (mmm) REVERT: B 364 LYS cc_start: 0.7708 (ttpp) cc_final: 0.7265 (pttp) REVERT: B 395 ASP cc_start: 0.6952 (m-30) cc_final: 0.6392 (m-30) REVERT: B 404 GLN cc_start: 0.8069 (tt0) cc_final: 0.7713 (tt0) REVERT: B 430 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7522 (mm-40) REVERT: B 436 GLN cc_start: 0.8512 (tp40) cc_final: 0.7857 (tp40) REVERT: C 13 ARG cc_start: 0.8321 (mtp180) cc_final: 0.7808 (mtt180) REVERT: C 81 VAL cc_start: 0.8549 (m) cc_final: 0.8259 (p) REVERT: C 82 GLN cc_start: 0.8543 (tt0) cc_final: 0.8120 (pt0) REVERT: C 100 PHE cc_start: 0.7227 (t80) cc_final: 0.6991 (t80) REVERT: C 166 MET cc_start: 0.6722 (mmt) cc_final: 0.5897 (mmp) REVERT: C 167 MET cc_start: 0.7389 (ptp) cc_final: 0.6996 (ptp) REVERT: C 214 MET cc_start: 0.7682 (mpp) cc_final: 0.6988 (mpp) REVERT: C 218 HIS cc_start: 0.7613 (m170) cc_final: 0.6885 (m170) REVERT: C 222 GLU cc_start: 0.7408 (mp0) cc_final: 0.7169 (mp0) REVERT: C 224 TYR cc_start: 0.7374 (t80) cc_final: 0.7140 (t80) REVERT: C 245 THR cc_start: 0.8762 (m) cc_final: 0.8477 (t) REVERT: C 247 GLN cc_start: 0.7639 (pp30) cc_final: 0.7261 (pp30) REVERT: C 285 THR cc_start: 0.8051 (m) cc_final: 0.7792 (t) REVERT: C 327 GLN cc_start: 0.7956 (mp10) cc_final: 0.7438 (mp10) REVERT: C 380 MET cc_start: 0.7258 (mtp) cc_final: 0.6850 (mtt) REVERT: C 405 GLN cc_start: 0.8055 (tp40) cc_final: 0.7770 (tp40) REVERT: D 221 GLU cc_start: 0.5494 (OUTLIER) cc_final: 0.5169 (pp20) REVERT: D 241 GLN cc_start: 0.5832 (tp-100) cc_final: 0.5577 (tp40) REVERT: D 256 GLN cc_start: 0.7123 (mm-40) cc_final: 0.6905 (tp-100) REVERT: D 264 LEU cc_start: 0.8697 (tp) cc_final: 0.8349 (tt) REVERT: D 265 GLU cc_start: 0.8111 (tt0) cc_final: 0.7357 (tm-30) REVERT: D 266 LYS cc_start: 0.8651 (mmmm) cc_final: 0.8291 (mmtp) REVERT: D 323 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6807 (mm-30) REVERT: D 341 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.7062 (tt0) REVERT: F 153 LYS cc_start: 0.8215 (tttp) cc_final: 0.7482 (ttmt) REVERT: F 166 SER cc_start: 0.8176 (m) cc_final: 0.7082 (p) REVERT: F 185 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7670 (tm-30) REVERT: F 186 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7529 (tt) REVERT: F 206 MET cc_start: 0.6869 (tpp) cc_final: 0.6544 (mtt) REVERT: F 230 MET cc_start: 0.6848 (tpp) cc_final: 0.6557 (tpp) REVERT: F 249 GLU cc_start: 0.7928 (mp0) cc_final: 0.7617 (mp0) REVERT: F 264 CYS cc_start: 0.8189 (m) cc_final: 0.7669 (m) REVERT: F 308 LYS cc_start: 0.8385 (mttp) cc_final: 0.8076 (ttmm) REVERT: G 33 GLN cc_start: 0.8621 (mt0) cc_final: 0.8260 (mt0) REVERT: G 54 GLU cc_start: 0.7339 (tp30) cc_final: 0.6843 (tp30) REVERT: G 103 SER cc_start: 0.8563 (t) cc_final: 0.8175 (p) REVERT: G 107 ARG cc_start: 0.7347 (ptp90) cc_final: 0.6961 (ptp90) REVERT: G 151 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6719 (mp) REVERT: G 212 GLU cc_start: 0.8137 (tp30) cc_final: 0.7817 (tp30) REVERT: G 214 THR cc_start: 0.7624 (t) cc_final: 0.7213 (p) REVERT: G 217 LYS cc_start: 0.7884 (ttpt) cc_final: 0.7498 (tppt) REVERT: H 21 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7747 (mt-10) REVERT: H 39 GLN cc_start: 0.7329 (mt0) cc_final: 0.7112 (mt0) REVERT: H 58 LYS cc_start: 0.8165 (mttt) cc_final: 0.7823 (mttt) REVERT: I 31 VAL cc_start: 0.7062 (OUTLIER) cc_final: 0.6398 (t) REVERT: I 43 MET cc_start: 0.6580 (tmm) cc_final: 0.6217 (tmm) REVERT: I 93 LYS cc_start: 0.7976 (pttm) cc_final: 0.7676 (ptpt) REVERT: I 124 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7450 (mm-30) REVERT: I 128 PHE cc_start: 0.7537 (t80) cc_final: 0.7067 (t80) REVERT: I 148 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7133 (tp30) REVERT: I 168 ARG cc_start: 0.8134 (mtp-110) cc_final: 0.7620 (ttm-80) REVERT: I 211 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.6438 (mt) REVERT: I 233 GLU cc_start: 0.7324 (pt0) cc_final: 0.6976 (pm20) REVERT: I 235 GLN cc_start: 0.7615 (mp10) cc_final: 0.7404 (mp10) REVERT: I 259 GLU cc_start: 0.6696 (pm20) cc_final: 0.6325 (pm20) REVERT: I 261 MET cc_start: 0.6276 (mpp) cc_final: 0.6030 (mpp) REVERT: I 268 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8405 (mm) REVERT: I 272 GLN cc_start: 0.7977 (pp30) cc_final: 0.7491 (pp30) REVERT: I 274 ARG cc_start: 0.7607 (ttp-170) cc_final: 0.7243 (mtp180) REVERT: I 284 GLN cc_start: 0.7317 (pm20) cc_final: 0.6934 (pm20) REVERT: I 297 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6362 (tm-30) REVERT: I 319 LEU cc_start: 0.8736 (mt) cc_final: 0.8518 (mt) REVERT: I 325 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7456 (mp) REVERT: I 365 MET cc_start: 0.7462 (mmm) cc_final: 0.6951 (mmm) REVERT: I 368 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7794 (mm-40) REVERT: I 376 LYS cc_start: 0.8583 (tttt) cc_final: 0.8113 (tptp) REVERT: I 397 LYS cc_start: 0.8272 (tptt) cc_final: 0.7921 (tptt) REVERT: I 401 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6542 (ttp-110) REVERT: I 424 ARG cc_start: 0.7540 (mtp85) cc_final: 0.7251 (mtp85) REVERT: I 452 VAL cc_start: 0.8657 (m) cc_final: 0.8372 (p) REVERT: I 472 LYS cc_start: 0.8337 (tptt) cc_final: 0.7849 (tptp) REVERT: I 477 GLN cc_start: 0.8102 (mp10) cc_final: 0.7847 (pp30) REVERT: I 507 MET cc_start: 0.7425 (mtm) cc_final: 0.6026 (mtm) REVERT: I 545 TRP cc_start: 0.6953 (m100) cc_final: 0.6651 (m100) REVERT: I 638 GLN cc_start: 0.8266 (mp10) cc_final: 0.8066 (mt0) REVERT: L 14 PHE cc_start: 0.8431 (m-80) cc_final: 0.8005 (m-80) REVERT: L 55 LEU cc_start: 0.8881 (mt) cc_final: 0.8677 (mt) REVERT: L 102 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7759 (mm-30) REVERT: L 158 GLN cc_start: 0.8070 (tp-100) cc_final: 0.7752 (tp-100) REVERT: M 119 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7357 (ptmt) REVERT: M 154 ARG cc_start: 0.7583 (mtm110) cc_final: 0.6883 (mtp-110) REVERT: M 165 CYS cc_start: 0.7587 (t) cc_final: 0.6765 (m) REVERT: M 291 SER cc_start: 0.6029 (p) cc_final: 0.4892 (t) REVERT: M 298 GLN cc_start: 0.6741 (mp10) cc_final: 0.6232 (mp10) REVERT: M 320 SER cc_start: 0.7827 (m) cc_final: 0.7178 (p) REVERT: M 322 MET cc_start: 0.7041 (mmm) cc_final: 0.6657 (mpp) REVERT: M 368 PHE cc_start: 0.7735 (m-80) cc_final: 0.7364 (m-10) REVERT: M 370 ILE cc_start: 0.8797 (pt) cc_final: 0.8498 (tt) REVERT: M 416 LEU cc_start: 0.7253 (mm) cc_final: 0.7022 (mm) REVERT: N 43 TRP cc_start: 0.7446 (p-90) cc_final: 0.7142 (p-90) REVERT: E 38 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7258 (mt-10) REVERT: E 43 LYS cc_start: 0.8111 (mttm) cc_final: 0.7896 (mptt) REVERT: E 258 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.6879 (p0) REVERT: E 270 SER cc_start: 0.7674 (m) cc_final: 0.7300 (p) REVERT: E 277 GLU cc_start: 0.7597 (tt0) cc_final: 0.7379 (tt0) REVERT: E 305 ARG cc_start: 0.7531 (ttp-170) cc_final: 0.7201 (mtp180) outliers start: 141 outliers final: 74 residues processed: 1034 average time/residue: 0.1921 time to fit residues: 305.4950 Evaluate side-chains 1029 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 938 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 431 GLN Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 243 LYS Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 47 HIS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 297 GLU Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 401 ARG Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 502 SER Chi-restraints excluded: chain I residue 612 LEU Chi-restraints excluded: chain I residue 684 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 193 ILE Chi-restraints excluded: chain M residue 241 SER Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 325 ASN Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 409 ILE Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 323 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 53 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 330 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 326 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 359 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 376 GLN B 152 ASN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN D 206 GLN D 209 ASN D 241 GLN D 390 GLN ** F 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** I 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 463 GLN ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 108 ASN M 229 ASN M 236 ASN M 249 GLN ** M 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN E 258 ASN E 265 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.152626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.125456 restraints weight = 58018.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.129279 restraints weight = 30787.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.131755 restraints weight = 19112.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.133393 restraints weight = 13525.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.134502 restraints weight = 10580.051| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 30360 Z= 0.150 Angle : 0.627 18.756 41001 Z= 0.322 Chirality : 0.041 0.310 4630 Planarity : 0.004 0.063 5228 Dihedral : 5.259 56.814 4045 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.05 % Allowed : 24.13 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3634 helix: 1.33 (0.11), residues: 2255 sheet: -0.68 (0.34), residues: 219 loop : -1.61 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 193 TYR 0.038 0.002 TYR D 148 PHE 0.023 0.001 PHE I 569 TRP 0.027 0.002 TRP I 581 HIS 0.006 0.001 HIS I 304 Details of bonding type rmsd covalent geometry : bond 0.00331 (30356) covalent geometry : angle 0.62247 (40997) SS BOND : bond 0.01322 ( 2) SS BOND : angle 7.54502 ( 4) hydrogen bonds : bond 0.04728 ( 1657) hydrogen bonds : angle 4.26750 ( 4854) metal coordination : bond 0.00372 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 970 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.6856 (tpp) cc_final: 0.6632 (tpp) REVERT: A 146 ASP cc_start: 0.7523 (t0) cc_final: 0.7204 (t0) REVERT: A 149 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8101 (tt) REVERT: A 172 TYR cc_start: 0.7148 (m-10) cc_final: 0.6712 (m-10) REVERT: A 174 ASP cc_start: 0.8113 (t0) cc_final: 0.7661 (t0) REVERT: A 180 ASN cc_start: 0.7694 (m-40) cc_final: 0.7200 (p0) REVERT: A 207 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8336 (ttmt) REVERT: A 224 LYS cc_start: 0.8355 (ttmt) cc_final: 0.8123 (mmtm) REVERT: A 226 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5623 (mp0) REVERT: A 296 CYS cc_start: 0.8332 (m) cc_final: 0.7716 (m) REVERT: A 304 GLN cc_start: 0.7636 (mt0) cc_final: 0.7171 (mp10) REVERT: A 343 LYS cc_start: 0.7340 (mmmm) cc_final: 0.6992 (mmmm) REVERT: A 365 LEU cc_start: 0.7127 (mt) cc_final: 0.6800 (mt) REVERT: A 416 ARG cc_start: 0.8296 (mmt-90) cc_final: 0.7753 (mmt-90) REVERT: A 467 LYS cc_start: 0.8135 (tptt) cc_final: 0.7756 (tptt) REVERT: B 37 TYR cc_start: 0.7235 (t80) cc_final: 0.6767 (t80) REVERT: B 55 GLN cc_start: 0.6301 (OUTLIER) cc_final: 0.5948 (pp30) REVERT: B 106 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7649 (p0) REVERT: B 110 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8116 (mttt) REVERT: B 111 SER cc_start: 0.8754 (m) cc_final: 0.8282 (p) REVERT: B 117 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7892 (p0) REVERT: B 196 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7423 (mt-10) REVERT: B 220 GLN cc_start: 0.7934 (tt0) cc_final: 0.7368 (tp40) REVERT: B 234 MET cc_start: 0.6799 (mmm) cc_final: 0.6359 (mmm) REVERT: B 264 ASN cc_start: 0.8420 (m110) cc_final: 0.8210 (m-40) REVERT: B 318 TYR cc_start: 0.7065 (t80) cc_final: 0.6698 (t80) REVERT: B 322 ASP cc_start: 0.5946 (t70) cc_final: 0.5720 (t70) REVERT: B 338 MET cc_start: 0.7012 (mmt) cc_final: 0.6424 (mmm) REVERT: B 364 LYS cc_start: 0.7718 (ttpp) cc_final: 0.7184 (pttp) REVERT: B 395 ASP cc_start: 0.6930 (m-30) cc_final: 0.6458 (m-30) REVERT: B 404 GLN cc_start: 0.8125 (tt0) cc_final: 0.7676 (tt0) REVERT: B 426 LYS cc_start: 0.7863 (mttp) cc_final: 0.7526 (mttp) REVERT: C 13 ARG cc_start: 0.8289 (mtp180) cc_final: 0.7736 (mtt180) REVERT: C 81 VAL cc_start: 0.8498 (m) cc_final: 0.8224 (p) REVERT: C 82 GLN cc_start: 0.8483 (tt0) cc_final: 0.8098 (pt0) REVERT: C 166 MET cc_start: 0.6659 (mmt) cc_final: 0.6108 (mmt) REVERT: C 167 MET cc_start: 0.7366 (ptp) cc_final: 0.7056 (ptp) REVERT: C 214 MET cc_start: 0.7685 (mpp) cc_final: 0.6978 (mpp) REVERT: C 222 GLU cc_start: 0.7420 (mp0) cc_final: 0.7161 (mp0) REVERT: C 224 TYR cc_start: 0.7417 (t80) cc_final: 0.7155 (t80) REVERT: C 245 THR cc_start: 0.8732 (m) cc_final: 0.8468 (t) REVERT: C 247 GLN cc_start: 0.7737 (pp30) cc_final: 0.7386 (pp30) REVERT: C 285 THR cc_start: 0.8101 (m) cc_final: 0.7861 (t) REVERT: C 316 THR cc_start: 0.8051 (m) cc_final: 0.7849 (p) REVERT: C 327 GLN cc_start: 0.7989 (mp10) cc_final: 0.7465 (mp10) REVERT: C 380 MET cc_start: 0.7272 (mtp) cc_final: 0.6923 (mtt) REVERT: C 405 GLN cc_start: 0.8061 (tp40) cc_final: 0.7722 (tp40) REVERT: D 218 HIS cc_start: 0.5521 (OUTLIER) cc_final: 0.5090 (t-90) REVERT: D 264 LEU cc_start: 0.8655 (tp) cc_final: 0.8391 (tt) REVERT: D 323 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6802 (mm-30) REVERT: D 341 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6535 (tt0) REVERT: D 349 ASN cc_start: 0.8319 (t0) cc_final: 0.7752 (m-40) REVERT: D 364 ARG cc_start: 0.6917 (mtm180) cc_final: 0.6548 (mtm-85) REVERT: F 153 LYS cc_start: 0.8233 (tttp) cc_final: 0.7631 (ttmt) REVERT: F 185 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7690 (tm-30) REVERT: F 186 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7595 (tt) REVERT: F 206 MET cc_start: 0.6867 (tpp) cc_final: 0.6620 (mtt) REVERT: F 249 GLU cc_start: 0.7926 (mp0) cc_final: 0.7679 (mp0) REVERT: F 264 CYS cc_start: 0.8229 (m) cc_final: 0.7711 (m) REVERT: F 299 CYS cc_start: 0.8065 (t) cc_final: 0.7742 (t) REVERT: F 308 LYS cc_start: 0.8389 (mttp) cc_final: 0.8113 (ttmm) REVERT: G 33 GLN cc_start: 0.8619 (mt0) cc_final: 0.8253 (mt0) REVERT: G 54 GLU cc_start: 0.7359 (tp30) cc_final: 0.6850 (tp30) REVERT: G 72 TYR cc_start: 0.7359 (m-10) cc_final: 0.7151 (m-10) REVERT: G 93 GLN cc_start: 0.8488 (mt0) cc_final: 0.8119 (mm-40) REVERT: G 103 SER cc_start: 0.8548 (t) cc_final: 0.8172 (p) REVERT: G 107 ARG cc_start: 0.7357 (ptp90) cc_final: 0.6967 (ptp90) REVERT: G 199 LYS cc_start: 0.7860 (tttt) cc_final: 0.7591 (ttmt) REVERT: G 212 GLU cc_start: 0.8135 (tp30) cc_final: 0.7857 (tp30) REVERT: G 214 THR cc_start: 0.7634 (t) cc_final: 0.7220 (p) REVERT: G 217 LYS cc_start: 0.7851 (ttpt) cc_final: 0.7484 (tppt) REVERT: H 21 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7728 (mt-10) REVERT: H 58 LYS cc_start: 0.8158 (mttt) cc_final: 0.7792 (mttt) REVERT: I 31 VAL cc_start: 0.7329 (OUTLIER) cc_final: 0.6737 (t) REVERT: I 43 MET cc_start: 0.6564 (tmm) cc_final: 0.6152 (tmm) REVERT: I 93 LYS cc_start: 0.7907 (pttm) cc_final: 0.7690 (pttt) REVERT: I 124 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7439 (mm-30) REVERT: I 128 PHE cc_start: 0.7528 (t80) cc_final: 0.7048 (t80) REVERT: I 147 ARG cc_start: 0.7569 (tpt90) cc_final: 0.7025 (mmm160) REVERT: I 148 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7112 (tp30) REVERT: I 228 TYR cc_start: 0.7460 (t80) cc_final: 0.7037 (t80) REVERT: I 233 GLU cc_start: 0.7458 (pt0) cc_final: 0.6950 (pm20) REVERT: I 261 MET cc_start: 0.6340 (mpp) cc_final: 0.5940 (mpp) REVERT: I 272 GLN cc_start: 0.8120 (pp30) cc_final: 0.7351 (pp30) REVERT: I 274 ARG cc_start: 0.7546 (ttp-170) cc_final: 0.7121 (ttp-170) REVERT: I 297 GLU cc_start: 0.6907 (tm-30) cc_final: 0.6537 (tm-30) REVERT: I 325 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7417 (mp) REVERT: I 365 MET cc_start: 0.7344 (mmm) cc_final: 0.6880 (mmm) REVERT: I 368 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7622 (mm-40) REVERT: I 376 LYS cc_start: 0.8602 (tttt) cc_final: 0.8036 (tptp) REVERT: I 424 ARG cc_start: 0.7543 (mtp85) cc_final: 0.7236 (mtp85) REVERT: I 452 VAL cc_start: 0.8674 (m) cc_final: 0.8382 (p) REVERT: I 460 ASP cc_start: 0.7881 (p0) cc_final: 0.7612 (p0) REVERT: I 472 LYS cc_start: 0.8339 (tptt) cc_final: 0.7903 (tptp) REVERT: I 491 LYS cc_start: 0.8240 (mmtt) cc_final: 0.8020 (mmtt) REVERT: I 573 ARG cc_start: 0.7028 (mmm-85) cc_final: 0.6479 (mtp85) REVERT: I 638 GLN cc_start: 0.8406 (mp10) cc_final: 0.8161 (mt0) REVERT: I 680 LEU cc_start: 0.8512 (mt) cc_final: 0.7997 (pp) REVERT: L 14 PHE cc_start: 0.8436 (m-80) cc_final: 0.8075 (m-80) REVERT: L 57 LYS cc_start: 0.8361 (mmtt) cc_final: 0.8104 (tptp) REVERT: L 158 GLN cc_start: 0.7969 (tp-100) cc_final: 0.7640 (tp-100) REVERT: M 169 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.6724 (m-80) REVERT: M 204 GLN cc_start: 0.7304 (mm-40) cc_final: 0.6856 (mm-40) REVERT: M 291 SER cc_start: 0.5974 (p) cc_final: 0.4938 (t) REVERT: M 298 GLN cc_start: 0.6962 (mp10) cc_final: 0.6251 (mp10) REVERT: M 320 SER cc_start: 0.7862 (m) cc_final: 0.7225 (p) REVERT: M 322 MET cc_start: 0.7043 (mmm) cc_final: 0.6718 (mpp) REVERT: M 368 PHE cc_start: 0.7692 (m-80) cc_final: 0.7434 (m-10) REVERT: M 370 ILE cc_start: 0.8826 (pt) cc_final: 0.8570 (tt) REVERT: N 38 MET cc_start: 0.7707 (ttm) cc_final: 0.7387 (ttm) REVERT: N 43 TRP cc_start: 0.7452 (p-90) cc_final: 0.7065 (p-90) REVERT: E 43 LYS cc_start: 0.8279 (mttm) cc_final: 0.8057 (mptt) REVERT: E 171 ASP cc_start: 0.7258 (t0) cc_final: 0.6998 (t0) REVERT: E 240 LEU cc_start: 0.7919 (tp) cc_final: 0.7670 (tt) REVERT: E 258 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.6983 (p0) REVERT: E 270 SER cc_start: 0.7645 (m) cc_final: 0.7279 (p) REVERT: E 277 GLU cc_start: 0.7689 (tt0) cc_final: 0.7402 (tt0) REVERT: E 305 ARG cc_start: 0.7478 (ttp-170) cc_final: 0.7192 (mtp180) outliers start: 166 outliers final: 101 residues processed: 1051 average time/residue: 0.1916 time to fit residues: 308.4453 Evaluate side-chains 1064 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 951 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 431 GLN Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 243 LYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 165 LYS Chi-restraints excluded: chain G residue 190 GLN Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 47 HIS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 416 SER Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 502 SER Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 684 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 193 ILE Chi-restraints excluded: chain M residue 249 GLN Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 325 ASN Chi-restraints excluded: chain M residue 361 THR Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 409 ILE Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 52 GLN Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 323 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 221 optimal weight: 6.9990 chunk 242 optimal weight: 5.9990 chunk 125 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 343 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 271 optimal weight: 0.3980 chunk 231 optimal weight: 0.6980 chunk 314 optimal weight: 0.0020 chunk 330 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN A 376 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN C 378 GLN D 206 GLN D 390 GLN F 54 HIS ** F 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** I 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 HIS ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 ASN M 236 ASN ** M 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN E 265 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.153954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.126511 restraints weight = 58743.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.130411 restraints weight = 30948.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.132930 restraints weight = 19211.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.134622 restraints weight = 13600.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.135758 restraints weight = 10644.255| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 30360 Z= 0.124 Angle : 0.635 21.316 41001 Z= 0.321 Chirality : 0.041 0.525 4630 Planarity : 0.004 0.065 5228 Dihedral : 5.271 59.671 4045 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.59 % Allowed : 25.23 % Favored : 70.18 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3634 helix: 1.41 (0.11), residues: 2247 sheet: -0.43 (0.36), residues: 205 loop : -1.63 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 193 TYR 0.043 0.001 TYR D 148 PHE 0.011 0.001 PHE I 251 TRP 0.031 0.002 TRP I 545 HIS 0.015 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00273 (30356) covalent geometry : angle 0.62729 (40997) SS BOND : bond 0.00220 ( 2) SS BOND : angle 9.92640 ( 4) hydrogen bonds : bond 0.04294 ( 1657) hydrogen bonds : angle 4.17102 ( 4854) metal coordination : bond 0.00225 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 970 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8182 (tt) REVERT: A 77 MET cc_start: 0.6750 (tpp) cc_final: 0.6519 (tpp) REVERT: A 149 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8054 (tt) REVERT: A 172 TYR cc_start: 0.7136 (m-10) cc_final: 0.6681 (m-10) REVERT: A 174 ASP cc_start: 0.8105 (t0) cc_final: 0.7793 (t0) REVERT: A 180 ASN cc_start: 0.7634 (m-40) cc_final: 0.7189 (p0) REVERT: A 219 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7811 (mm) REVERT: A 224 LYS cc_start: 0.8349 (ttmt) cc_final: 0.8084 (mmtm) REVERT: A 226 GLU cc_start: 0.5867 (OUTLIER) cc_final: 0.5584 (mp0) REVERT: A 296 CYS cc_start: 0.8284 (m) cc_final: 0.7730 (m) REVERT: A 304 GLN cc_start: 0.7678 (mt0) cc_final: 0.7411 (mp10) REVERT: A 317 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8078 (mtmm) REVERT: A 365 LEU cc_start: 0.7107 (mt) cc_final: 0.6742 (mt) REVERT: A 416 ARG cc_start: 0.8273 (mmt-90) cc_final: 0.7732 (mmt-90) REVERT: A 467 LYS cc_start: 0.8150 (tptt) cc_final: 0.7754 (tptt) REVERT: B 37 TYR cc_start: 0.7170 (t80) cc_final: 0.6729 (t80) REVERT: B 40 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.6168 (tptm) REVERT: B 55 GLN cc_start: 0.6268 (OUTLIER) cc_final: 0.5898 (pp30) REVERT: B 88 MET cc_start: 0.5051 (mmt) cc_final: 0.4228 (mmm) REVERT: B 110 LYS cc_start: 0.8453 (mtmm) cc_final: 0.8119 (mttt) REVERT: B 111 SER cc_start: 0.8710 (m) cc_final: 0.8250 (p) REVERT: B 117 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7837 (p0) REVERT: B 196 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7359 (mt-10) REVERT: B 220 GLN cc_start: 0.7914 (tt0) cc_final: 0.7088 (tp40) REVERT: B 234 MET cc_start: 0.6887 (mmm) cc_final: 0.6380 (mmm) REVERT: B 244 MET cc_start: 0.6753 (tmm) cc_final: 0.6310 (mmm) REVERT: B 264 ASN cc_start: 0.8483 (m110) cc_final: 0.8198 (m110) REVERT: B 318 TYR cc_start: 0.7081 (t80) cc_final: 0.6743 (t80) REVERT: B 338 MET cc_start: 0.7023 (mmt) cc_final: 0.6516 (mmm) REVERT: B 361 LYS cc_start: 0.7717 (ttpt) cc_final: 0.7423 (tttp) REVERT: B 396 ASN cc_start: 0.7993 (t0) cc_final: 0.7793 (t0) REVERT: B 404 GLN cc_start: 0.8069 (tt0) cc_final: 0.7771 (tt0) REVERT: B 425 ASP cc_start: 0.6759 (t0) cc_final: 0.6454 (t0) REVERT: B 426 LYS cc_start: 0.7827 (mttp) cc_final: 0.7336 (mtpp) REVERT: B 436 GLN cc_start: 0.8423 (tp40) cc_final: 0.7644 (tp40) REVERT: C 13 ARG cc_start: 0.8277 (mtp180) cc_final: 0.7776 (mtt180) REVERT: C 68 MET cc_start: 0.7190 (tmm) cc_final: 0.6728 (tmm) REVERT: C 81 VAL cc_start: 0.8437 (m) cc_final: 0.8162 (p) REVERT: C 82 GLN cc_start: 0.8438 (tt0) cc_final: 0.8079 (pt0) REVERT: C 166 MET cc_start: 0.6594 (mmt) cc_final: 0.6121 (mmt) REVERT: C 167 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.7017 (ptp) REVERT: C 214 MET cc_start: 0.7710 (mpp) cc_final: 0.7001 (mpp) REVERT: C 224 TYR cc_start: 0.7367 (t80) cc_final: 0.7009 (t80) REVERT: C 245 THR cc_start: 0.8720 (m) cc_final: 0.8462 (t) REVERT: C 247 GLN cc_start: 0.7731 (pp30) cc_final: 0.7351 (pp30) REVERT: C 316 THR cc_start: 0.8042 (m) cc_final: 0.7796 (p) REVERT: C 327 GLN cc_start: 0.8019 (mp10) cc_final: 0.7510 (mp10) REVERT: C 380 MET cc_start: 0.7189 (mtp) cc_final: 0.6825 (mtt) REVERT: C 405 GLN cc_start: 0.8039 (tp40) cc_final: 0.7741 (tp40) REVERT: D 206 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8159 (mm-40) REVERT: D 256 GLN cc_start: 0.7322 (tp-100) cc_final: 0.6979 (mm-40) REVERT: D 264 LEU cc_start: 0.8625 (tp) cc_final: 0.8377 (tt) REVERT: D 323 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6761 (mm-30) REVERT: D 341 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.7015 (tt0) REVERT: D 349 ASN cc_start: 0.8284 (t0) cc_final: 0.7846 (m-40) REVERT: D 364 ARG cc_start: 0.6890 (mtm180) cc_final: 0.6552 (mtm-85) REVERT: D 373 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7405 (mm-40) REVERT: F 153 LYS cc_start: 0.8174 (tttp) cc_final: 0.7710 (tttp) REVERT: F 185 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7677 (tm-30) REVERT: F 186 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7520 (tt) REVERT: F 196 GLU cc_start: 0.8277 (tt0) cc_final: 0.7986 (tt0) REVERT: F 230 MET cc_start: 0.6798 (tpp) cc_final: 0.6347 (tpp) REVERT: F 249 GLU cc_start: 0.7908 (mp0) cc_final: 0.7696 (mp0) REVERT: F 264 CYS cc_start: 0.8123 (m) cc_final: 0.7678 (m) REVERT: F 299 CYS cc_start: 0.8020 (t) cc_final: 0.7695 (t) REVERT: F 308 LYS cc_start: 0.8307 (mttp) cc_final: 0.8086 (ttmm) REVERT: G 33 GLN cc_start: 0.8596 (mt0) cc_final: 0.8221 (mt0) REVERT: G 54 GLU cc_start: 0.7317 (tp30) cc_final: 0.6799 (tp30) REVERT: G 93 GLN cc_start: 0.8481 (mt0) cc_final: 0.8092 (mm-40) REVERT: G 103 SER cc_start: 0.8538 (t) cc_final: 0.8168 (p) REVERT: G 107 ARG cc_start: 0.7306 (ptp90) cc_final: 0.6947 (ptp90) REVERT: G 212 GLU cc_start: 0.8110 (tp30) cc_final: 0.7890 (tp30) REVERT: G 214 THR cc_start: 0.7588 (t) cc_final: 0.7154 (p) REVERT: G 217 LYS cc_start: 0.7852 (ttpt) cc_final: 0.7482 (tppt) REVERT: H 21 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7696 (mt-10) REVERT: H 58 LYS cc_start: 0.8115 (mttt) cc_final: 0.7761 (mttt) REVERT: H 90 TYR cc_start: 0.6721 (m-10) cc_final: 0.6503 (m-10) REVERT: I 31 VAL cc_start: 0.7208 (OUTLIER) cc_final: 0.6572 (t) REVERT: I 43 MET cc_start: 0.6524 (tmm) cc_final: 0.6164 (tmm) REVERT: I 99 TYR cc_start: 0.7895 (t80) cc_final: 0.7379 (t80) REVERT: I 128 PHE cc_start: 0.7512 (t80) cc_final: 0.7046 (t80) REVERT: I 210 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7908 (tm-30) REVERT: I 228 TYR cc_start: 0.7483 (t80) cc_final: 0.7093 (t80) REVERT: I 233 GLU cc_start: 0.7373 (pt0) cc_final: 0.6752 (pm20) REVERT: I 261 MET cc_start: 0.6191 (mpp) cc_final: 0.5523 (mpp) REVERT: I 265 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7194 (mt-10) REVERT: I 272 GLN cc_start: 0.8068 (pp30) cc_final: 0.7468 (pp30) REVERT: I 274 ARG cc_start: 0.7484 (ttp-170) cc_final: 0.7091 (ttp-170) REVERT: I 297 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6521 (tm-30) REVERT: I 300 LEU cc_start: 0.8446 (pt) cc_final: 0.8214 (pt) REVERT: I 306 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7214 (mm-30) REVERT: I 325 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7277 (mp) REVERT: I 365 MET cc_start: 0.7280 (mmm) cc_final: 0.6945 (mmm) REVERT: I 368 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7780 (mm-40) REVERT: I 376 LYS cc_start: 0.8537 (tttt) cc_final: 0.7977 (tptp) REVERT: I 401 ARG cc_start: 0.7605 (ttt180) cc_final: 0.7325 (ttt-90) REVERT: I 420 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6411 (tm-30) REVERT: I 424 ARG cc_start: 0.7547 (mtp85) cc_final: 0.7155 (mtp85) REVERT: I 425 TYR cc_start: 0.7229 (t80) cc_final: 0.6862 (t80) REVERT: I 472 LYS cc_start: 0.8266 (tptt) cc_final: 0.7832 (tptp) REVERT: I 474 LEU cc_start: 0.7956 (tt) cc_final: 0.7715 (tp) REVERT: I 638 GLN cc_start: 0.8421 (mp10) cc_final: 0.8179 (mt0) REVERT: I 680 LEU cc_start: 0.8581 (mt) cc_final: 0.8054 (pp) REVERT: L 14 PHE cc_start: 0.8414 (m-80) cc_final: 0.8129 (m-80) REVERT: L 158 GLN cc_start: 0.7953 (tp-100) cc_final: 0.7627 (tp-100) REVERT: M 105 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7928 (mt) REVERT: M 129 ARG cc_start: 0.8053 (ptm-80) cc_final: 0.7844 (ptm-80) REVERT: M 169 PHE cc_start: 0.6910 (OUTLIER) cc_final: 0.6690 (m-80) REVERT: M 204 GLN cc_start: 0.7263 (mm-40) cc_final: 0.6792 (mm-40) REVERT: M 291 SER cc_start: 0.5707 (p) cc_final: 0.4672 (t) REVERT: M 298 GLN cc_start: 0.6906 (mp10) cc_final: 0.6201 (mp10) REVERT: M 312 LEU cc_start: 0.7345 (mt) cc_final: 0.7077 (mm) REVERT: M 320 SER cc_start: 0.7839 (m) cc_final: 0.7283 (p) REVERT: M 368 PHE cc_start: 0.7631 (m-80) cc_final: 0.7372 (m-10) REVERT: M 370 ILE cc_start: 0.8802 (pt) cc_final: 0.8559 (tt) REVERT: N 23 MET cc_start: 0.6732 (ttm) cc_final: 0.6520 (mtm) REVERT: N 38 MET cc_start: 0.7680 (ttm) cc_final: 0.7342 (ttm) REVERT: N 43 TRP cc_start: 0.7396 (p-90) cc_final: 0.6987 (p-90) REVERT: E 270 SER cc_start: 0.7573 (m) cc_final: 0.7228 (p) REVERT: E 277 GLU cc_start: 0.7653 (tt0) cc_final: 0.7403 (tt0) REVERT: E 305 ARG cc_start: 0.7465 (ttp-170) cc_final: 0.7162 (mtp180) outliers start: 151 outliers final: 94 residues processed: 1037 average time/residue: 0.1924 time to fit residues: 307.5441 Evaluate side-chains 1063 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 952 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 431 GLN Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 372 LYS Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 243 LYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 165 LYS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 47 HIS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 297 GLU Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 416 SER Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 581 TRP Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain I residue 684 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 193 ILE Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 325 ASN Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 409 ILE Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 52 GLN Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 323 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 68 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 360 optimal weight: 0.8980 chunk 352 optimal weight: 0.6980 chunk 222 optimal weight: 0.9990 chunk 232 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 286 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 349 optimal weight: 0.8980 chunk 361 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 197 HIS A 376 GLN C 126 GLN D 241 GLN ** F 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN G 94 ASN ** I 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 181 ASN ** I 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 ASN M 236 ASN ** M 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 HIS E 265 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.153121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.125833 restraints weight = 58090.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.129644 restraints weight = 30813.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.132106 restraints weight = 19245.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133756 restraints weight = 13695.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.134864 restraints weight = 10767.602| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 30360 Z= 0.141 Angle : 0.640 20.726 41001 Z= 0.326 Chirality : 0.041 0.452 4630 Planarity : 0.004 0.064 5228 Dihedral : 5.259 56.463 4045 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.62 % Rotamer: Outliers : 4.98 % Allowed : 25.23 % Favored : 69.79 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3634 helix: 1.36 (0.11), residues: 2250 sheet: -0.42 (0.36), residues: 205 loop : -1.65 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 193 TYR 0.043 0.001 TYR D 148 PHE 0.015 0.001 PHE I 251 TRP 0.024 0.002 TRP I 545 HIS 0.012 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00315 (30356) covalent geometry : angle 0.63288 (40997) SS BOND : bond 0.00400 ( 2) SS BOND : angle 9.47560 ( 4) hydrogen bonds : bond 0.04476 ( 1657) hydrogen bonds : angle 4.20822 ( 4854) metal coordination : bond 0.00273 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 973 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8228 (tt) REVERT: A 149 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8047 (tt) REVERT: A 172 TYR cc_start: 0.7157 (m-10) cc_final: 0.6707 (m-10) REVERT: A 174 ASP cc_start: 0.8108 (t0) cc_final: 0.7791 (t0) REVERT: A 180 ASN cc_start: 0.7657 (m-40) cc_final: 0.7214 (p0) REVERT: A 219 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7772 (mm) REVERT: A 224 LYS cc_start: 0.8333 (ttmt) cc_final: 0.8066 (mmtm) REVERT: A 226 GLU cc_start: 0.5870 (OUTLIER) cc_final: 0.5655 (mp0) REVERT: A 296 CYS cc_start: 0.8296 (m) cc_final: 0.7745 (m) REVERT: A 317 LYS cc_start: 0.8319 (mtmm) cc_final: 0.8096 (mtmm) REVERT: A 365 LEU cc_start: 0.7137 (mt) cc_final: 0.6779 (mt) REVERT: A 416 ARG cc_start: 0.8279 (mmt-90) cc_final: 0.7779 (mmt-90) REVERT: A 467 LYS cc_start: 0.8143 (tptt) cc_final: 0.7776 (tptt) REVERT: B 37 TYR cc_start: 0.7164 (t80) cc_final: 0.6768 (t80) REVERT: B 40 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.6293 (tttt) REVERT: B 55 GLN cc_start: 0.6199 (OUTLIER) cc_final: 0.5841 (pp30) REVERT: B 88 MET cc_start: 0.5027 (mmt) cc_final: 0.4250 (mmm) REVERT: B 100 ARG cc_start: 0.7849 (tpt170) cc_final: 0.7505 (tpt170) REVERT: B 106 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7529 (p0) REVERT: B 110 LYS cc_start: 0.8404 (mtmm) cc_final: 0.8044 (mttt) REVERT: B 111 SER cc_start: 0.8737 (m) cc_final: 0.8278 (p) REVERT: B 196 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7425 (mt-10) REVERT: B 234 MET cc_start: 0.6812 (mmm) cc_final: 0.6278 (mmm) REVERT: B 244 MET cc_start: 0.6805 (tmm) cc_final: 0.6334 (mmm) REVERT: B 264 ASN cc_start: 0.8498 (m110) cc_final: 0.8234 (m110) REVERT: B 318 TYR cc_start: 0.7099 (t80) cc_final: 0.6642 (t80) REVERT: B 361 LYS cc_start: 0.7679 (ttpt) cc_final: 0.7412 (tttp) REVERT: B 395 ASP cc_start: 0.7107 (m-30) cc_final: 0.6822 (t0) REVERT: B 404 GLN cc_start: 0.8122 (tt0) cc_final: 0.7696 (tt0) REVERT: B 425 ASP cc_start: 0.6766 (t0) cc_final: 0.6452 (t0) REVERT: B 426 LYS cc_start: 0.7908 (mttp) cc_final: 0.7537 (mtpp) REVERT: C 21 MET cc_start: 0.6811 (ttp) cc_final: 0.6190 (tpt) REVERT: C 68 MET cc_start: 0.7158 (tmm) cc_final: 0.6755 (tmm) REVERT: C 81 VAL cc_start: 0.8429 (m) cc_final: 0.8150 (p) REVERT: C 82 GLN cc_start: 0.8423 (tt0) cc_final: 0.8076 (pt0) REVERT: C 166 MET cc_start: 0.6637 (mmt) cc_final: 0.6155 (mmt) REVERT: C 167 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.7022 (ptp) REVERT: C 186 TYR cc_start: 0.8024 (t80) cc_final: 0.7792 (t80) REVERT: C 192 TYR cc_start: 0.7240 (m-80) cc_final: 0.7037 (m-80) REVERT: C 214 MET cc_start: 0.7708 (mpp) cc_final: 0.6976 (mpp) REVERT: C 224 TYR cc_start: 0.7423 (t80) cc_final: 0.7076 (t80) REVERT: C 245 THR cc_start: 0.8723 (m) cc_final: 0.8468 (t) REVERT: C 247 GLN cc_start: 0.7808 (pp30) cc_final: 0.7455 (pp30) REVERT: C 285 THR cc_start: 0.8174 (m) cc_final: 0.7930 (t) REVERT: C 304 LYS cc_start: 0.8660 (mtmm) cc_final: 0.8454 (mtmm) REVERT: C 316 THR cc_start: 0.8119 (m) cc_final: 0.7849 (p) REVERT: C 327 GLN cc_start: 0.8045 (mp10) cc_final: 0.7525 (mp10) REVERT: C 380 MET cc_start: 0.7258 (mtp) cc_final: 0.6982 (mtt) REVERT: C 405 GLN cc_start: 0.8034 (tp40) cc_final: 0.7777 (tp40) REVERT: D 245 MET cc_start: 0.6214 (mmm) cc_final: 0.5482 (tpp) REVERT: D 264 LEU cc_start: 0.8624 (tp) cc_final: 0.8398 (tt) REVERT: D 323 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6766 (mm-30) REVERT: D 341 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7036 (tt0) REVERT: D 349 ASN cc_start: 0.8261 (t0) cc_final: 0.7758 (m-40) REVERT: D 364 ARG cc_start: 0.6886 (mtm180) cc_final: 0.6562 (mtm-85) REVERT: D 400 MET cc_start: 0.7597 (mtm) cc_final: 0.6831 (mtm) REVERT: F 153 LYS cc_start: 0.8182 (tttp) cc_final: 0.7711 (tttp) REVERT: F 185 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7689 (tm-30) REVERT: F 186 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7522 (tt) REVERT: F 196 GLU cc_start: 0.8234 (tt0) cc_final: 0.8015 (tt0) REVERT: F 236 LYS cc_start: 0.7314 (ttmt) cc_final: 0.7060 (ttmt) REVERT: F 249 GLU cc_start: 0.7903 (mp0) cc_final: 0.7674 (mp0) REVERT: F 264 CYS cc_start: 0.8161 (m) cc_final: 0.7699 (m) REVERT: F 299 CYS cc_start: 0.7925 (t) cc_final: 0.7638 (t) REVERT: F 308 LYS cc_start: 0.8351 (mttp) cc_final: 0.8107 (ttmm) REVERT: G 33 GLN cc_start: 0.8599 (mt0) cc_final: 0.8223 (mt0) REVERT: G 54 GLU cc_start: 0.7369 (tp30) cc_final: 0.6846 (tp30) REVERT: G 92 GLN cc_start: 0.8464 (mt0) cc_final: 0.7992 (mp10) REVERT: G 93 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8093 (mm-40) REVERT: G 103 SER cc_start: 0.8511 (t) cc_final: 0.8151 (p) REVERT: G 107 ARG cc_start: 0.7313 (ptp90) cc_final: 0.6927 (ptp90) REVERT: G 199 LYS cc_start: 0.7803 (tttt) cc_final: 0.7600 (ttmt) REVERT: G 214 THR cc_start: 0.7665 (t) cc_final: 0.7227 (p) REVERT: G 217 LYS cc_start: 0.7867 (ttpt) cc_final: 0.7516 (tppt) REVERT: H 18 ASP cc_start: 0.8255 (p0) cc_final: 0.8047 (p0) REVERT: H 21 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7769 (mt-10) REVERT: H 58 LYS cc_start: 0.8115 (mttt) cc_final: 0.7739 (mttt) REVERT: I 31 VAL cc_start: 0.7273 (OUTLIER) cc_final: 0.6707 (t) REVERT: I 43 MET cc_start: 0.6372 (tmm) cc_final: 0.6154 (tmm) REVERT: I 128 PHE cc_start: 0.7497 (t80) cc_final: 0.7049 (t80) REVERT: I 146 ARG cc_start: 0.7190 (ptt180) cc_final: 0.6777 (ptt180) REVERT: I 147 ARG cc_start: 0.7604 (tpt90) cc_final: 0.7336 (mmm160) REVERT: I 210 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7711 (tm-30) REVERT: I 225 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.7915 (pt) REVERT: I 228 TYR cc_start: 0.7554 (t80) cc_final: 0.7084 (t80) REVERT: I 233 GLU cc_start: 0.7406 (pt0) cc_final: 0.6876 (pm20) REVERT: I 261 MET cc_start: 0.6191 (mpp) cc_final: 0.5404 (mpp) REVERT: I 265 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7046 (mt-10) REVERT: I 274 ARG cc_start: 0.7470 (ttp-170) cc_final: 0.7116 (ttp-170) REVERT: I 295 LEU cc_start: 0.7788 (tp) cc_final: 0.7467 (tp) REVERT: I 297 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6642 (tm-30) REVERT: I 300 LEU cc_start: 0.8405 (pt) cc_final: 0.8140 (pt) REVERT: I 322 MET cc_start: 0.7967 (mtt) cc_final: 0.7487 (ttm) REVERT: I 325 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7262 (mp) REVERT: I 365 MET cc_start: 0.7249 (mmm) cc_final: 0.6992 (mmm) REVERT: I 368 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7790 (mm-40) REVERT: I 376 LYS cc_start: 0.8455 (tttt) cc_final: 0.7905 (tptp) REVERT: I 420 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6498 (tm-30) REVERT: I 424 ARG cc_start: 0.7553 (mtp85) cc_final: 0.7103 (mtp85) REVERT: I 425 TYR cc_start: 0.7217 (t80) cc_final: 0.6859 (t80) REVERT: I 469 MET cc_start: 0.7179 (mpp) cc_final: 0.6863 (mtt) REVERT: I 472 LYS cc_start: 0.8279 (tptt) cc_final: 0.7830 (tptm) REVERT: I 638 GLN cc_start: 0.8447 (mp10) cc_final: 0.8239 (mt0) REVERT: I 680 LEU cc_start: 0.8577 (mt) cc_final: 0.8068 (pp) REVERT: L 14 PHE cc_start: 0.8417 (m-80) cc_final: 0.8167 (m-80) REVERT: L 57 LYS cc_start: 0.8333 (mmtt) cc_final: 0.8001 (tptt) REVERT: L 158 GLN cc_start: 0.7938 (tp-100) cc_final: 0.7606 (tp-100) REVERT: M 204 GLN cc_start: 0.7313 (mm-40) cc_final: 0.6797 (mm-40) REVERT: M 291 SER cc_start: 0.5828 (p) cc_final: 0.4794 (t) REVERT: M 298 GLN cc_start: 0.6888 (mp10) cc_final: 0.6186 (mp10) REVERT: M 312 LEU cc_start: 0.7371 (mt) cc_final: 0.7090 (mm) REVERT: M 320 SER cc_start: 0.7835 (m) cc_final: 0.7231 (p) REVERT: M 322 MET cc_start: 0.7235 (mmm) cc_final: 0.6823 (mpp) REVERT: M 362 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7910 (pp) REVERT: M 368 PHE cc_start: 0.7660 (m-80) cc_final: 0.7408 (m-10) REVERT: M 370 ILE cc_start: 0.8793 (pt) cc_final: 0.8541 (tt) REVERT: N 23 MET cc_start: 0.6740 (ttm) cc_final: 0.6530 (mtm) REVERT: N 38 MET cc_start: 0.7710 (ttm) cc_final: 0.7502 (ttm) REVERT: N 43 TRP cc_start: 0.7437 (p-90) cc_final: 0.7162 (p-90) REVERT: E 43 LYS cc_start: 0.8526 (mptt) cc_final: 0.7850 (mptt) REVERT: E 210 LYS cc_start: 0.7337 (mttm) cc_final: 0.6979 (mttt) REVERT: E 240 LEU cc_start: 0.7885 (tp) cc_final: 0.7592 (tt) REVERT: E 270 SER cc_start: 0.7551 (m) cc_final: 0.7180 (p) REVERT: E 277 GLU cc_start: 0.7686 (tt0) cc_final: 0.7399 (tt0) REVERT: E 305 ARG cc_start: 0.7448 (ttp-170) cc_final: 0.7141 (mtp180) outliers start: 164 outliers final: 106 residues processed: 1055 average time/residue: 0.1867 time to fit residues: 304.1140 Evaluate side-chains 1084 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 963 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 431 GLN Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 372 LYS Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 394 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 243 LYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 122 MET Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 165 LYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 47 HIS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 416 SER Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 436 ASN Chi-restraints excluded: chain I residue 502 SER Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 581 TRP Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain I residue 684 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain M residue 193 ILE Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 325 ASN Chi-restraints excluded: chain M residue 361 THR Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 409 ILE Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 325 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 128 optimal weight: 0.7980 chunk 356 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 281 optimal weight: 0.9990 chunk 286 optimal weight: 0.8980 chunk 354 optimal weight: 2.9990 chunk 347 optimal weight: 0.9990 chunk 213 optimal weight: 0.0270 chunk 66 optimal weight: 0.9980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 376 GLN B 210 ASN B 429 ASN B 432 ASN D 209 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN ** F 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 ASN ** F 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 GLN ** I 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 ASN M 236 ASN ** M 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.153247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.126126 restraints weight = 58143.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.129939 restraints weight = 30734.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.132429 restraints weight = 19124.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.134099 restraints weight = 13558.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.135215 restraints weight = 10627.038| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 30360 Z= 0.135 Angle : 0.667 26.117 41001 Z= 0.335 Chirality : 0.042 0.534 4630 Planarity : 0.004 0.061 5228 Dihedral : 5.240 57.204 4045 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.83 % Allowed : 26.02 % Favored : 69.15 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.14), residues: 3634 helix: 1.43 (0.11), residues: 2237 sheet: -0.66 (0.34), residues: 224 loop : -1.54 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 91 TYR 0.044 0.001 TYR D 148 PHE 0.016 0.001 PHE B 69 TRP 0.027 0.002 TRP I 545 HIS 0.017 0.001 HIS E 217 Details of bonding type rmsd covalent geometry : bond 0.00302 (30356) covalent geometry : angle 0.65963 (40997) SS BOND : bond 0.00315 ( 2) SS BOND : angle 10.11744 ( 4) hydrogen bonds : bond 0.04320 ( 1657) hydrogen bonds : angle 4.17292 ( 4854) metal coordination : bond 0.00267 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 962 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8227 (tt) REVERT: A 149 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8030 (tt) REVERT: A 172 TYR cc_start: 0.7140 (m-10) cc_final: 0.6659 (m-10) REVERT: A 174 ASP cc_start: 0.8098 (t0) cc_final: 0.7644 (t0) REVERT: A 180 ASN cc_start: 0.7638 (m-40) cc_final: 0.7189 (p0) REVERT: A 219 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7766 (mm) REVERT: A 224 LYS cc_start: 0.8336 (ttmt) cc_final: 0.8058 (mmtm) REVERT: A 226 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.5786 (mp0) REVERT: A 296 CYS cc_start: 0.8286 (m) cc_final: 0.7730 (m) REVERT: A 317 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8074 (mtmm) REVERT: A 356 MET cc_start: 0.7431 (ppp) cc_final: 0.7170 (ppp) REVERT: A 365 LEU cc_start: 0.7118 (mt) cc_final: 0.6741 (mt) REVERT: A 467 LYS cc_start: 0.8161 (tptt) cc_final: 0.7771 (tptt) REVERT: B 40 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.6230 (ttmt) REVERT: B 55 GLN cc_start: 0.6201 (OUTLIER) cc_final: 0.5866 (pp30) REVERT: B 88 MET cc_start: 0.5043 (mmt) cc_final: 0.4362 (mmm) REVERT: B 106 ASN cc_start: 0.8009 (OUTLIER) cc_final: 0.7539 (p0) REVERT: B 110 LYS cc_start: 0.8361 (mtmm) cc_final: 0.8013 (mttt) REVERT: B 111 SER cc_start: 0.8747 (m) cc_final: 0.8232 (p) REVERT: B 196 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7406 (mt-10) REVERT: B 220 GLN cc_start: 0.7692 (pt0) cc_final: 0.6886 (pp30) REVERT: B 234 MET cc_start: 0.6791 (mmm) cc_final: 0.6244 (mmm) REVERT: B 244 MET cc_start: 0.6789 (tmm) cc_final: 0.6326 (mmm) REVERT: B 264 ASN cc_start: 0.8502 (m110) cc_final: 0.8202 (m110) REVERT: B 278 LYS cc_start: 0.7447 (mtmm) cc_final: 0.7070 (mtmt) REVERT: B 318 TYR cc_start: 0.7108 (t80) cc_final: 0.6748 (t80) REVERT: B 361 LYS cc_start: 0.7619 (ttpt) cc_final: 0.7340 (tttp) REVERT: B 395 ASP cc_start: 0.7104 (m-30) cc_final: 0.6805 (t0) REVERT: B 404 GLN cc_start: 0.8101 (tt0) cc_final: 0.7774 (tt0) REVERT: B 426 LYS cc_start: 0.7904 (mttp) cc_final: 0.7476 (mtpp) REVERT: C 21 MET cc_start: 0.6789 (ttp) cc_final: 0.6148 (tpt) REVERT: C 68 MET cc_start: 0.7127 (tmm) cc_final: 0.6732 (tmm) REVERT: C 78 PHE cc_start: 0.7720 (t80) cc_final: 0.6998 (t80) REVERT: C 81 VAL cc_start: 0.8414 (m) cc_final: 0.8150 (p) REVERT: C 82 GLN cc_start: 0.8412 (tt0) cc_final: 0.8058 (pt0) REVERT: C 166 MET cc_start: 0.6566 (mmt) cc_final: 0.6140 (mmt) REVERT: C 186 TYR cc_start: 0.7943 (t80) cc_final: 0.7728 (t80) REVERT: C 192 TYR cc_start: 0.7222 (m-80) cc_final: 0.6993 (m-80) REVERT: C 214 MET cc_start: 0.7704 (mpp) cc_final: 0.6980 (mpp) REVERT: C 224 TYR cc_start: 0.7430 (t80) cc_final: 0.7017 (t80) REVERT: C 245 THR cc_start: 0.8693 (m) cc_final: 0.8428 (t) REVERT: C 247 GLN cc_start: 0.7846 (pp30) cc_final: 0.7496 (pp30) REVERT: C 292 MET cc_start: 0.7330 (tpt) cc_final: 0.7081 (mmm) REVERT: C 309 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7690 (ttp80) REVERT: C 316 THR cc_start: 0.8096 (m) cc_final: 0.7788 (p) REVERT: C 327 GLN cc_start: 0.8075 (mp10) cc_final: 0.7559 (mp10) REVERT: C 380 MET cc_start: 0.7238 (mtp) cc_final: 0.6909 (mtt) REVERT: C 405 GLN cc_start: 0.8038 (tp40) cc_final: 0.7813 (tp40) REVERT: D 203 GLU cc_start: 0.7434 (tp30) cc_final: 0.6838 (tp30) REVERT: D 218 HIS cc_start: 0.5628 (OUTLIER) cc_final: 0.5411 (t-90) REVERT: D 323 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6748 (mm-30) REVERT: D 341 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7096 (tt0) REVERT: D 349 ASN cc_start: 0.8159 (t0) cc_final: 0.7755 (m-40) REVERT: D 354 GLN cc_start: 0.7390 (tp40) cc_final: 0.6926 (tp40) REVERT: D 364 ARG cc_start: 0.6881 (mtm180) cc_final: 0.6549 (mtm-85) REVERT: D 386 GLU cc_start: 0.6977 (tm-30) cc_final: 0.6755 (tm-30) REVERT: F 137 HIS cc_start: 0.7262 (OUTLIER) cc_final: 0.6744 (t-90) REVERT: F 153 LYS cc_start: 0.8216 (tttp) cc_final: 0.7727 (tttp) REVERT: F 185 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7689 (tm-30) REVERT: F 186 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7610 (tt) REVERT: F 196 GLU cc_start: 0.8211 (tt0) cc_final: 0.8009 (tt0) REVERT: F 236 LYS cc_start: 0.7330 (ttmt) cc_final: 0.6996 (ttmt) REVERT: F 249 GLU cc_start: 0.7908 (mp0) cc_final: 0.7674 (mp0) REVERT: F 264 CYS cc_start: 0.8120 (m) cc_final: 0.7679 (m) REVERT: F 308 LYS cc_start: 0.8362 (mttp) cc_final: 0.8124 (ttmm) REVERT: G 33 GLN cc_start: 0.8589 (mt0) cc_final: 0.8195 (mt0) REVERT: G 54 GLU cc_start: 0.7367 (tp30) cc_final: 0.6826 (tp30) REVERT: G 72 TYR cc_start: 0.7353 (m-10) cc_final: 0.7054 (m-10) REVERT: G 92 GLN cc_start: 0.8446 (mt0) cc_final: 0.7986 (mp10) REVERT: G 103 SER cc_start: 0.8541 (t) cc_final: 0.8201 (p) REVERT: G 107 ARG cc_start: 0.7319 (ptp90) cc_final: 0.6939 (ptp90) REVERT: G 120 LEU cc_start: 0.8356 (mp) cc_final: 0.7911 (mt) REVERT: G 151 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6703 (mp) REVERT: G 199 LYS cc_start: 0.7779 (tttt) cc_final: 0.7564 (ttmt) REVERT: G 217 LYS cc_start: 0.7843 (ttpt) cc_final: 0.7525 (tppt) REVERT: H 18 ASP cc_start: 0.8275 (p0) cc_final: 0.7908 (p0) REVERT: H 21 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7755 (mt-10) REVERT: H 90 TYR cc_start: 0.6758 (m-10) cc_final: 0.6533 (m-10) REVERT: I 31 VAL cc_start: 0.7306 (OUTLIER) cc_final: 0.6745 (t) REVERT: I 43 MET cc_start: 0.6318 (tmm) cc_final: 0.6074 (tmm) REVERT: I 93 LYS cc_start: 0.8001 (pttm) cc_final: 0.7731 (ptpp) REVERT: I 128 PHE cc_start: 0.7550 (t80) cc_final: 0.7084 (t80) REVERT: I 148 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7611 (mm-30) REVERT: I 168 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7454 (mtp85) REVERT: I 225 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.7408 (pp) REVERT: I 228 TYR cc_start: 0.7502 (t80) cc_final: 0.6825 (t80) REVERT: I 229 LYS cc_start: 0.8602 (ptpp) cc_final: 0.8299 (pttm) REVERT: I 233 GLU cc_start: 0.7365 (pt0) cc_final: 0.6145 (pm20) REVERT: I 261 MET cc_start: 0.6063 (mpp) cc_final: 0.5477 (mpp) REVERT: I 265 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7147 (mt-10) REVERT: I 271 GLU cc_start: 0.7885 (pm20) cc_final: 0.7488 (pp20) REVERT: I 274 ARG cc_start: 0.7404 (ttp-170) cc_final: 0.7097 (ttm110) REVERT: I 284 GLN cc_start: 0.7632 (mp-120) cc_final: 0.7390 (mp10) REVERT: I 295 LEU cc_start: 0.7866 (tp) cc_final: 0.7547 (tp) REVERT: I 297 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6486 (tm-30) REVERT: I 300 LEU cc_start: 0.8402 (pt) cc_final: 0.8159 (pt) REVERT: I 322 MET cc_start: 0.7950 (mtt) cc_final: 0.7382 (ttm) REVERT: I 325 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7217 (mp) REVERT: I 365 MET cc_start: 0.7186 (mmm) cc_final: 0.6935 (mmm) REVERT: I 368 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7756 (mm-40) REVERT: I 420 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6466 (tm-30) REVERT: I 424 ARG cc_start: 0.7514 (mtp85) cc_final: 0.7099 (mtp85) REVERT: I 425 TYR cc_start: 0.7184 (t80) cc_final: 0.6828 (t80) REVERT: I 450 MET cc_start: 0.7160 (tpp) cc_final: 0.6870 (tpp) REVERT: I 469 MET cc_start: 0.7257 (mpp) cc_final: 0.6924 (mtt) REVERT: I 472 LYS cc_start: 0.8324 (tptt) cc_final: 0.7947 (tptm) REVERT: I 488 MET cc_start: 0.7975 (ppp) cc_final: 0.7615 (tmm) REVERT: I 525 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7997 (mm) REVERT: I 565 ARG cc_start: 0.8038 (mmt90) cc_final: 0.7783 (mmm-85) REVERT: I 638 GLN cc_start: 0.8457 (mt0) cc_final: 0.8248 (mt0) REVERT: I 680 LEU cc_start: 0.8742 (mt) cc_final: 0.8252 (pp) REVERT: L 14 PHE cc_start: 0.8402 (m-80) cc_final: 0.8160 (m-80) REVERT: L 158 GLN cc_start: 0.7923 (tp-100) cc_final: 0.7610 (tp-100) REVERT: M 119 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7459 (ptmt) REVERT: M 204 GLN cc_start: 0.7283 (mm-40) cc_final: 0.6748 (mm-40) REVERT: M 291 SER cc_start: 0.5717 (p) cc_final: 0.4709 (t) REVERT: M 312 LEU cc_start: 0.7375 (mt) cc_final: 0.7115 (mm) REVERT: M 320 SER cc_start: 0.7877 (m) cc_final: 0.7288 (p) REVERT: M 322 MET cc_start: 0.7378 (mmm) cc_final: 0.6934 (mpp) REVERT: M 368 PHE cc_start: 0.7652 (m-80) cc_final: 0.7425 (m-10) REVERT: M 370 ILE cc_start: 0.8782 (pt) cc_final: 0.8535 (tt) REVERT: N 23 MET cc_start: 0.6748 (ttm) cc_final: 0.6535 (mtm) REVERT: N 43 TRP cc_start: 0.7426 (p-90) cc_final: 0.7159 (p-90) REVERT: E 166 VAL cc_start: 0.7680 (p) cc_final: 0.7343 (m) REVERT: E 270 SER cc_start: 0.7550 (m) cc_final: 0.7222 (p) REVERT: E 277 GLU cc_start: 0.7703 (tt0) cc_final: 0.7433 (tt0) REVERT: E 305 ARG cc_start: 0.7477 (ttp-170) cc_final: 0.7122 (mtp180) REVERT: E 330 GLN cc_start: 0.8091 (mm110) cc_final: 0.7803 (mm-40) outliers start: 159 outliers final: 105 residues processed: 1040 average time/residue: 0.1892 time to fit residues: 304.9919 Evaluate side-chains 1079 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 955 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 431 GLN Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 36 TYR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 372 LYS Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 394 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 243 LYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 165 LYS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 47 HIS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 297 GLU Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 304 HIS Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 416 SER Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 525 LEU Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 581 TRP Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain I residue 684 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain M residue 193 ILE Chi-restraints excluded: chain M residue 202 LEU Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 409 ILE Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 325 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 250 optimal weight: 0.9980 chunk 270 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 288 optimal weight: 8.9990 chunk 268 optimal weight: 3.9990 chunk 203 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 197 HIS ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 564 GLN ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 ASN M 236 ASN ** M 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.153007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.125798 restraints weight = 58269.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129611 restraints weight = 30831.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.132104 restraints weight = 19238.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.133775 restraints weight = 13668.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.134900 restraints weight = 10705.558| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 30360 Z= 0.145 Angle : 0.693 25.326 41001 Z= 0.350 Chirality : 0.042 0.538 4630 Planarity : 0.005 0.066 5228 Dihedral : 5.267 56.970 4045 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.43 % Rotamer: Outliers : 4.47 % Allowed : 27.20 % Favored : 68.33 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3634 helix: 1.37 (0.11), residues: 2240 sheet: -0.44 (0.37), residues: 200 loop : -1.57 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 193 TYR 0.044 0.002 TYR D 148 PHE 0.013 0.001 PHE I 83 TRP 0.041 0.002 TRP I 545 HIS 0.011 0.001 HIS E 217 Details of bonding type rmsd covalent geometry : bond 0.00326 (30356) covalent geometry : angle 0.68588 (40997) SS BOND : bond 0.00706 ( 2) SS BOND : angle 10.19913 ( 4) hydrogen bonds : bond 0.04452 ( 1657) hydrogen bonds : angle 4.21364 ( 4854) metal coordination : bond 0.00295 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 966 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8107 (tt) REVERT: A 172 TYR cc_start: 0.7163 (m-10) cc_final: 0.6662 (m-10) REVERT: A 174 ASP cc_start: 0.8102 (t0) cc_final: 0.7634 (t0) REVERT: A 180 ASN cc_start: 0.7654 (m-40) cc_final: 0.7203 (p0) REVERT: A 207 LYS cc_start: 0.8495 (ttmt) cc_final: 0.8268 (ttmt) REVERT: A 219 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7772 (mm) REVERT: A 224 LYS cc_start: 0.8335 (ttmt) cc_final: 0.8070 (mmtm) REVERT: A 226 GLU cc_start: 0.5966 (OUTLIER) cc_final: 0.5737 (mp0) REVERT: A 296 CYS cc_start: 0.8250 (m) cc_final: 0.7748 (m) REVERT: A 317 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8056 (mtmm) REVERT: A 365 LEU cc_start: 0.7108 (mt) cc_final: 0.6776 (mt) REVERT: A 416 ARG cc_start: 0.8287 (mmt-90) cc_final: 0.7821 (mmt-90) REVERT: A 451 LYS cc_start: 0.7883 (mtmm) cc_final: 0.7181 (mtmm) REVERT: A 467 LYS cc_start: 0.8155 (tptt) cc_final: 0.7774 (tptt) REVERT: B 55 GLN cc_start: 0.6185 (OUTLIER) cc_final: 0.5847 (pp30) REVERT: B 88 MET cc_start: 0.5073 (mmt) cc_final: 0.4374 (mmm) REVERT: B 106 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7533 (p0) REVERT: B 110 LYS cc_start: 0.8418 (mtmm) cc_final: 0.8072 (mttt) REVERT: B 111 SER cc_start: 0.8795 (m) cc_final: 0.8283 (p) REVERT: B 196 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7407 (mt-10) REVERT: B 220 GLN cc_start: 0.7630 (pt0) cc_final: 0.6765 (pp30) REVERT: B 234 MET cc_start: 0.6825 (mmm) cc_final: 0.6256 (mmm) REVERT: B 244 MET cc_start: 0.6877 (tmm) cc_final: 0.6425 (mmm) REVERT: B 264 ASN cc_start: 0.8527 (m110) cc_final: 0.8252 (m110) REVERT: B 278 LYS cc_start: 0.7404 (mtmm) cc_final: 0.7077 (mtmt) REVERT: B 318 TYR cc_start: 0.7079 (t80) cc_final: 0.6576 (t80) REVERT: B 361 LYS cc_start: 0.7645 (ttpt) cc_final: 0.7370 (tttp) REVERT: B 395 ASP cc_start: 0.7011 (m-30) cc_final: 0.6765 (t0) REVERT: B 404 GLN cc_start: 0.8058 (tt0) cc_final: 0.7719 (tt0) REVERT: B 426 LYS cc_start: 0.7934 (mttp) cc_final: 0.7494 (mtpp) REVERT: C 21 MET cc_start: 0.6812 (ttp) cc_final: 0.6161 (tpt) REVERT: C 68 MET cc_start: 0.7061 (tmm) cc_final: 0.6649 (tmm) REVERT: C 78 PHE cc_start: 0.7715 (t80) cc_final: 0.7021 (t80) REVERT: C 82 GLN cc_start: 0.8377 (tt0) cc_final: 0.8072 (pt0) REVERT: C 166 MET cc_start: 0.6530 (mmt) cc_final: 0.6146 (mmt) REVERT: C 192 TYR cc_start: 0.7251 (m-80) cc_final: 0.7002 (m-80) REVERT: C 214 MET cc_start: 0.7686 (mpp) cc_final: 0.6968 (mpp) REVERT: C 224 TYR cc_start: 0.7457 (t80) cc_final: 0.7064 (t80) REVERT: C 245 THR cc_start: 0.8701 (m) cc_final: 0.8462 (t) REVERT: C 247 GLN cc_start: 0.7918 (pp30) cc_final: 0.7553 (pp30) REVERT: C 292 MET cc_start: 0.7291 (tpt) cc_final: 0.7064 (mmm) REVERT: C 309 ARG cc_start: 0.8237 (ttp80) cc_final: 0.7681 (ttp80) REVERT: C 316 THR cc_start: 0.8165 (m) cc_final: 0.7862 (p) REVERT: C 327 GLN cc_start: 0.8078 (mp10) cc_final: 0.7531 (mp10) REVERT: C 380 MET cc_start: 0.7245 (mtp) cc_final: 0.6929 (mtt) REVERT: C 405 GLN cc_start: 0.8054 (tp40) cc_final: 0.7823 (tp40) REVERT: D 203 GLU cc_start: 0.7486 (tp30) cc_final: 0.6896 (tp30) REVERT: D 206 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8342 (mm-40) REVERT: D 231 HIS cc_start: 0.8022 (m-70) cc_final: 0.7795 (m90) REVERT: D 241 GLN cc_start: 0.4773 (tm-30) cc_final: 0.4564 (tm-30) REVERT: D 323 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6745 (mm-30) REVERT: D 341 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6884 (tt0) REVERT: D 349 ASN cc_start: 0.8167 (t0) cc_final: 0.7838 (m-40) REVERT: D 354 GLN cc_start: 0.7418 (tp40) cc_final: 0.6955 (tp40) REVERT: D 364 ARG cc_start: 0.6906 (mtm180) cc_final: 0.6559 (mtm-85) REVERT: D 386 GLU cc_start: 0.6934 (tm-30) cc_final: 0.6544 (tm-30) REVERT: F 130 PRO cc_start: 0.8228 (Cg_exo) cc_final: 0.7984 (Cg_endo) REVERT: F 137 HIS cc_start: 0.7295 (OUTLIER) cc_final: 0.6764 (t-90) REVERT: F 153 LYS cc_start: 0.8234 (tttp) cc_final: 0.7685 (tttp) REVERT: F 196 GLU cc_start: 0.8206 (tt0) cc_final: 0.8004 (tt0) REVERT: F 234 ARG cc_start: 0.7687 (mtt-85) cc_final: 0.7406 (mmt180) REVERT: F 236 LYS cc_start: 0.7331 (ttmt) cc_final: 0.6992 (ttmt) REVERT: F 249 GLU cc_start: 0.7907 (mp0) cc_final: 0.7680 (mp0) REVERT: F 264 CYS cc_start: 0.8166 (m) cc_final: 0.7679 (m) REVERT: F 299 CYS cc_start: 0.7894 (t) cc_final: 0.7575 (t) REVERT: F 308 LYS cc_start: 0.8366 (mttp) cc_final: 0.8129 (ttmm) REVERT: G 33 GLN cc_start: 0.8589 (mt0) cc_final: 0.8013 (mt0) REVERT: G 54 GLU cc_start: 0.7408 (tp30) cc_final: 0.6840 (tp30) REVERT: G 72 TYR cc_start: 0.7458 (m-10) cc_final: 0.7167 (m-10) REVERT: G 103 SER cc_start: 0.8563 (t) cc_final: 0.8224 (p) REVERT: G 107 ARG cc_start: 0.7360 (ptp90) cc_final: 0.6988 (ptp90) REVERT: G 151 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6782 (mp) REVERT: G 199 LYS cc_start: 0.7780 (tttt) cc_final: 0.7565 (ttmt) REVERT: G 210 GLU cc_start: 0.6823 (pp20) cc_final: 0.6204 (pp20) REVERT: G 217 LYS cc_start: 0.7864 (ttpt) cc_final: 0.7555 (tppt) REVERT: H 18 ASP cc_start: 0.8277 (p0) cc_final: 0.7909 (p0) REVERT: H 21 GLU cc_start: 0.8495 (mt-10) cc_final: 0.7835 (mt-10) REVERT: I 31 VAL cc_start: 0.7319 (OUTLIER) cc_final: 0.6779 (t) REVERT: I 43 MET cc_start: 0.6267 (tmm) cc_final: 0.6035 (tmm) REVERT: I 91 ARG cc_start: 0.7425 (ptp-170) cc_final: 0.7215 (ptm160) REVERT: I 92 LEU cc_start: 0.8302 (mt) cc_final: 0.8015 (mm) REVERT: I 128 PHE cc_start: 0.7545 (t80) cc_final: 0.7097 (t80) REVERT: I 148 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7689 (mm-30) REVERT: I 210 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8046 (tm-30) REVERT: I 225 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8546 (pt) REVERT: I 228 TYR cc_start: 0.7605 (t80) cc_final: 0.6893 (t80) REVERT: I 233 GLU cc_start: 0.7455 (pt0) cc_final: 0.6334 (pm20) REVERT: I 261 MET cc_start: 0.6046 (mpp) cc_final: 0.5450 (mpp) REVERT: I 265 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7097 (mt-10) REVERT: I 274 ARG cc_start: 0.7413 (ttp-170) cc_final: 0.7100 (ttm110) REVERT: I 284 GLN cc_start: 0.7735 (mp-120) cc_final: 0.7293 (mp-120) REVERT: I 295 LEU cc_start: 0.7927 (tp) cc_final: 0.7565 (tp) REVERT: I 297 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6535 (tm-30) REVERT: I 300 LEU cc_start: 0.8440 (pt) cc_final: 0.8177 (pt) REVERT: I 322 MET cc_start: 0.7928 (mtt) cc_final: 0.7307 (ttm) REVERT: I 325 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7278 (mp) REVERT: I 365 MET cc_start: 0.7189 (mmm) cc_final: 0.6945 (mmm) REVERT: I 368 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7764 (mm-40) REVERT: I 420 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6507 (tm-30) REVERT: I 424 ARG cc_start: 0.7536 (mtp85) cc_final: 0.7084 (mtp85) REVERT: I 425 TYR cc_start: 0.7194 (t80) cc_final: 0.6840 (t80) REVERT: I 450 MET cc_start: 0.7136 (tpp) cc_final: 0.6866 (tpp) REVERT: I 452 VAL cc_start: 0.8689 (m) cc_final: 0.8389 (p) REVERT: I 469 MET cc_start: 0.7216 (mpp) cc_final: 0.6909 (mtt) REVERT: I 472 LYS cc_start: 0.8294 (tptt) cc_final: 0.7909 (tptp) REVERT: I 525 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8028 (mm) REVERT: I 638 GLN cc_start: 0.8419 (mt0) cc_final: 0.8034 (mt0) REVERT: I 680 LEU cc_start: 0.8721 (mt) cc_final: 0.8231 (pp) REVERT: L 14 PHE cc_start: 0.8403 (m-80) cc_final: 0.8164 (m-80) REVERT: L 57 LYS cc_start: 0.8334 (mmtt) cc_final: 0.8029 (tptp) REVERT: L 158 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7528 (tp-100) REVERT: M 105 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7898 (mt) REVERT: M 204 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6677 (mm-40) REVERT: M 291 SER cc_start: 0.5502 (p) cc_final: 0.4549 (t) REVERT: M 312 LEU cc_start: 0.7402 (mt) cc_final: 0.7112 (mm) REVERT: M 320 SER cc_start: 0.7881 (m) cc_final: 0.7277 (p) REVERT: M 322 MET cc_start: 0.7359 (mmm) cc_final: 0.6918 (mpp) REVERT: M 368 PHE cc_start: 0.7647 (m-80) cc_final: 0.7396 (m-10) REVERT: M 370 ILE cc_start: 0.8785 (pt) cc_final: 0.8504 (tt) REVERT: N 23 MET cc_start: 0.6753 (ttm) cc_final: 0.6528 (mtm) REVERT: N 38 MET cc_start: 0.7738 (ttm) cc_final: 0.7455 (ttm) REVERT: N 43 TRP cc_start: 0.7409 (p-90) cc_final: 0.7110 (p-90) REVERT: E 166 VAL cc_start: 0.7692 (p) cc_final: 0.7346 (m) REVERT: E 210 LYS cc_start: 0.7371 (mttm) cc_final: 0.6976 (mttt) REVERT: E 240 LEU cc_start: 0.7821 (tp) cc_final: 0.7547 (tt) REVERT: E 270 SER cc_start: 0.7552 (m) cc_final: 0.7188 (p) REVERT: E 277 GLU cc_start: 0.7701 (tt0) cc_final: 0.7431 (tt0) REVERT: E 305 ARG cc_start: 0.7495 (ttp-170) cc_final: 0.7069 (mtp180) REVERT: E 330 GLN cc_start: 0.8083 (mm110) cc_final: 0.7839 (mm-40) outliers start: 147 outliers final: 104 residues processed: 1039 average time/residue: 0.1893 time to fit residues: 303.5984 Evaluate side-chains 1058 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 940 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 431 GLN Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 36 TYR Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 372 LYS Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 394 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 243 LYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 165 LYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 47 HIS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 302 ILE Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 416 SER Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 436 ASN Chi-restraints excluded: chain I residue 502 SER Chi-restraints excluded: chain I residue 525 LEU Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 581 TRP Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain I residue 684 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain M residue 202 LEU Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 325 ASN Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 409 ILE Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 325 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 296 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 323 optimal weight: 2.9990 chunk 352 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 355 optimal weight: 0.6980 chunk 250 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 197 HIS A 376 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN B 432 ASN F 67 GLN ** F 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 ASN H 52 ASN ** I 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 564 GLN ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 641 GLN M 229 ASN M 236 ASN M 273 HIS ** M 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.151948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.124737 restraints weight = 58379.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.128510 restraints weight = 31132.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.130976 restraints weight = 19479.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.132653 restraints weight = 13885.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.133747 restraints weight = 10882.825| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 30360 Z= 0.162 Angle : 0.723 25.036 41001 Z= 0.364 Chirality : 0.043 0.541 4630 Planarity : 0.005 0.068 5228 Dihedral : 5.320 57.868 4045 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.16 % Rotamer: Outliers : 4.26 % Allowed : 28.02 % Favored : 67.72 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3634 helix: 1.31 (0.11), residues: 2242 sheet: -0.56 (0.35), residues: 211 loop : -1.58 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 193 TYR 0.046 0.002 TYR D 148 PHE 0.023 0.001 PHE H 133 TRP 0.037 0.002 TRP I 545 HIS 0.010 0.001 HIS E 217 Details of bonding type rmsd covalent geometry : bond 0.00362 (30356) covalent geometry : angle 0.71656 (40997) SS BOND : bond 0.00662 ( 2) SS BOND : angle 10.12649 ( 4) hydrogen bonds : bond 0.04703 ( 1657) hydrogen bonds : angle 4.28853 ( 4854) metal coordination : bond 0.00373 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 958 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8129 (tt) REVERT: A 172 TYR cc_start: 0.7154 (m-10) cc_final: 0.6644 (m-10) REVERT: A 174 ASP cc_start: 0.8129 (t0) cc_final: 0.7705 (t0) REVERT: A 180 ASN cc_start: 0.7667 (m-40) cc_final: 0.7176 (p0) REVERT: A 219 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7746 (mm) REVERT: A 224 LYS cc_start: 0.8339 (ttmt) cc_final: 0.8098 (mmtm) REVERT: A 226 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5708 (mp0) REVERT: A 296 CYS cc_start: 0.8262 (m) cc_final: 0.7715 (m) REVERT: A 317 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8060 (mtmm) REVERT: A 365 LEU cc_start: 0.7142 (mt) cc_final: 0.6831 (mt) REVERT: A 416 ARG cc_start: 0.8291 (mmt-90) cc_final: 0.7796 (mmt-90) REVERT: A 451 LYS cc_start: 0.7898 (mtmm) cc_final: 0.7160 (mtmm) REVERT: A 467 LYS cc_start: 0.8176 (tptt) cc_final: 0.7813 (tptt) REVERT: B 55 GLN cc_start: 0.6172 (OUTLIER) cc_final: 0.5849 (pp30) REVERT: B 88 MET cc_start: 0.5119 (mmt) cc_final: 0.4413 (mmm) REVERT: B 106 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7501 (p0) REVERT: B 110 LYS cc_start: 0.8440 (mtmm) cc_final: 0.8070 (mttt) REVERT: B 111 SER cc_start: 0.8853 (m) cc_final: 0.8336 (p) REVERT: B 196 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7462 (mt-10) REVERT: B 220 GLN cc_start: 0.7672 (pt0) cc_final: 0.6893 (pp30) REVERT: B 234 MET cc_start: 0.6705 (mmm) cc_final: 0.6138 (mmm) REVERT: B 244 MET cc_start: 0.6905 (tmm) cc_final: 0.6478 (mmm) REVERT: B 264 ASN cc_start: 0.8522 (m110) cc_final: 0.8254 (m110) REVERT: B 318 TYR cc_start: 0.7211 (t80) cc_final: 0.6747 (t80) REVERT: B 338 MET cc_start: 0.6486 (mmp) cc_final: 0.5991 (mmp) REVERT: B 361 LYS cc_start: 0.7643 (ttpt) cc_final: 0.7380 (tttp) REVERT: B 377 GLU cc_start: 0.7024 (tp30) cc_final: 0.6775 (tp30) REVERT: B 395 ASP cc_start: 0.7027 (m-30) cc_final: 0.6739 (t0) REVERT: B 404 GLN cc_start: 0.8047 (tt0) cc_final: 0.7754 (tt0) REVERT: B 426 LYS cc_start: 0.7945 (mttp) cc_final: 0.7485 (mtpp) REVERT: C 21 MET cc_start: 0.6842 (ttp) cc_final: 0.6185 (tpt) REVERT: C 68 MET cc_start: 0.7047 (tmm) cc_final: 0.6619 (tmm) REVERT: C 82 GLN cc_start: 0.8377 (tt0) cc_final: 0.8085 (pt0) REVERT: C 166 MET cc_start: 0.6457 (mmt) cc_final: 0.6124 (mmt) REVERT: C 192 TYR cc_start: 0.7319 (m-80) cc_final: 0.7101 (m-80) REVERT: C 214 MET cc_start: 0.7655 (mpp) cc_final: 0.6930 (mpp) REVERT: C 224 TYR cc_start: 0.7437 (t80) cc_final: 0.7024 (t80) REVERT: C 245 THR cc_start: 0.8692 (m) cc_final: 0.8453 (t) REVERT: C 247 GLN cc_start: 0.7975 (pp30) cc_final: 0.7653 (pp30) REVERT: C 248 ILE cc_start: 0.8402 (tt) cc_final: 0.7919 (tt) REVERT: C 292 MET cc_start: 0.7290 (tpt) cc_final: 0.7051 (mmm) REVERT: C 309 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7693 (ttp80) REVERT: C 316 THR cc_start: 0.8198 (m) cc_final: 0.7896 (p) REVERT: C 327 GLN cc_start: 0.8092 (mp10) cc_final: 0.7539 (mp10) REVERT: C 380 MET cc_start: 0.7191 (mtp) cc_final: 0.6965 (mtt) REVERT: C 405 GLN cc_start: 0.8072 (tp40) cc_final: 0.7860 (tp40) REVERT: D 203 GLU cc_start: 0.7495 (tp30) cc_final: 0.6941 (tp30) REVERT: D 231 HIS cc_start: 0.8053 (m-70) cc_final: 0.7800 (m90) REVERT: D 267 MET cc_start: 0.7688 (mmt) cc_final: 0.7466 (mmm) REVERT: D 323 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6742 (mm-30) REVERT: D 341 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.7179 (tt0) REVERT: D 349 ASN cc_start: 0.8190 (t0) cc_final: 0.7868 (m-40) REVERT: D 354 GLN cc_start: 0.7504 (tp40) cc_final: 0.7016 (tp40) REVERT: D 386 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6568 (tm-30) REVERT: F 130 PRO cc_start: 0.8239 (Cg_exo) cc_final: 0.8034 (Cg_endo) REVERT: F 137 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.6779 (t-90) REVERT: F 153 LYS cc_start: 0.8189 (tttp) cc_final: 0.7631 (tttp) REVERT: F 166 SER cc_start: 0.8252 (m) cc_final: 0.7288 (p) REVERT: F 236 LYS cc_start: 0.7376 (ttmt) cc_final: 0.7014 (ttmt) REVERT: F 249 GLU cc_start: 0.7911 (mp0) cc_final: 0.7692 (mp0) REVERT: F 264 CYS cc_start: 0.8200 (m) cc_final: 0.7712 (m) REVERT: F 299 CYS cc_start: 0.7868 (t) cc_final: 0.7601 (t) REVERT: F 308 LYS cc_start: 0.8400 (mttp) cc_final: 0.8144 (ttmm) REVERT: G 33 GLN cc_start: 0.8597 (mt0) cc_final: 0.8027 (mt0) REVERT: G 54 GLU cc_start: 0.7398 (tp30) cc_final: 0.6841 (tp30) REVERT: G 72 TYR cc_start: 0.7494 (m-10) cc_final: 0.7201 (m-10) REVERT: G 103 SER cc_start: 0.8582 (t) cc_final: 0.8221 (p) REVERT: G 107 ARG cc_start: 0.7374 (ptp90) cc_final: 0.6972 (ptp90) REVERT: G 113 TYR cc_start: 0.7792 (m-10) cc_final: 0.7151 (m-80) REVERT: G 210 GLU cc_start: 0.6789 (pp20) cc_final: 0.6093 (pp20) REVERT: G 217 LYS cc_start: 0.7845 (ttpt) cc_final: 0.7545 (tppt) REVERT: H 18 ASP cc_start: 0.8261 (p0) cc_final: 0.7889 (p0) REVERT: H 21 GLU cc_start: 0.8494 (mt-10) cc_final: 0.7772 (mt-10) REVERT: I 31 VAL cc_start: 0.7285 (OUTLIER) cc_final: 0.6768 (t) REVERT: I 43 MET cc_start: 0.6278 (tmm) cc_final: 0.6015 (tmm) REVERT: I 91 ARG cc_start: 0.7430 (ptp-170) cc_final: 0.7201 (ptm160) REVERT: I 92 LEU cc_start: 0.8319 (mt) cc_final: 0.8022 (mm) REVERT: I 128 PHE cc_start: 0.7501 (t80) cc_final: 0.7047 (t80) REVERT: I 148 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7877 (mm-30) REVERT: I 228 TYR cc_start: 0.7646 (t80) cc_final: 0.6874 (t80) REVERT: I 233 GLU cc_start: 0.7470 (pt0) cc_final: 0.6396 (pm20) REVERT: I 261 MET cc_start: 0.5798 (mpp) cc_final: 0.5224 (mpp) REVERT: I 265 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7176 (mt-10) REVERT: I 271 GLU cc_start: 0.7979 (pm20) cc_final: 0.7544 (pp20) REVERT: I 274 ARG cc_start: 0.7443 (ttp-170) cc_final: 0.7114 (ttm110) REVERT: I 284 GLN cc_start: 0.7861 (mp-120) cc_final: 0.7173 (mp10) REVERT: I 297 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6391 (tm-30) REVERT: I 300 LEU cc_start: 0.8426 (pt) cc_final: 0.8113 (pt) REVERT: I 322 MET cc_start: 0.7917 (mtt) cc_final: 0.7389 (ttm) REVERT: I 325 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7263 (mp) REVERT: I 365 MET cc_start: 0.7201 (mmm) cc_final: 0.6924 (mmm) REVERT: I 368 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7746 (mm-40) REVERT: I 420 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6793 (tm-30) REVERT: I 425 TYR cc_start: 0.7154 (t80) cc_final: 0.6849 (t80) REVERT: I 472 LYS cc_start: 0.8293 (tptt) cc_final: 0.7938 (tptp) REVERT: I 507 MET cc_start: 0.7835 (mmp) cc_final: 0.7478 (tpp) REVERT: I 525 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8033 (mm) REVERT: I 680 LEU cc_start: 0.8535 (mt) cc_final: 0.8103 (pp) REVERT: L 14 PHE cc_start: 0.8422 (m-80) cc_final: 0.8180 (m-80) REVERT: L 57 LYS cc_start: 0.8344 (mmtt) cc_final: 0.8044 (tptp) REVERT: L 158 GLN cc_start: 0.7824 (tp-100) cc_final: 0.7500 (tp-100) REVERT: M 105 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7783 (mt) REVERT: M 119 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7444 (ptmt) REVERT: M 204 GLN cc_start: 0.7238 (mm-40) cc_final: 0.6659 (mm-40) REVERT: M 216 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6696 (tt) REVERT: M 291 SER cc_start: 0.5625 (p) cc_final: 0.4716 (t) REVERT: M 312 LEU cc_start: 0.7418 (mt) cc_final: 0.7152 (mm) REVERT: M 320 SER cc_start: 0.7890 (m) cc_final: 0.7342 (p) REVERT: M 368 PHE cc_start: 0.7687 (m-80) cc_final: 0.7412 (m-10) REVERT: M 370 ILE cc_start: 0.8766 (pt) cc_final: 0.8481 (tt) REVERT: M 383 LEU cc_start: 0.8270 (mt) cc_final: 0.7918 (tt) REVERT: N 23 MET cc_start: 0.6766 (ttm) cc_final: 0.6546 (mtm) REVERT: N 43 TRP cc_start: 0.7435 (p-90) cc_final: 0.7189 (p-90) REVERT: E 166 VAL cc_start: 0.7711 (p) cc_final: 0.7319 (m) REVERT: E 210 LYS cc_start: 0.7411 (mttm) cc_final: 0.7002 (mttt) REVERT: E 230 LYS cc_start: 0.8364 (pttm) cc_final: 0.8125 (pttm) REVERT: E 270 SER cc_start: 0.7552 (m) cc_final: 0.7204 (p) REVERT: E 277 GLU cc_start: 0.7709 (tt0) cc_final: 0.7425 (tt0) REVERT: E 305 ARG cc_start: 0.7481 (ttp-170) cc_final: 0.7038 (mtp180) REVERT: E 330 GLN cc_start: 0.8116 (mm110) cc_final: 0.7895 (mm-40) outliers start: 140 outliers final: 104 residues processed: 1025 average time/residue: 0.1898 time to fit residues: 301.7827 Evaluate side-chains 1055 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 937 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 431 GLN Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 36 TYR Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 372 LYS Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 394 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 243 LYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 165 LYS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 47 HIS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 168 ARG Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 416 SER Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain I residue 502 SER Chi-restraints excluded: chain I residue 525 LEU Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 581 TRP Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain I residue 641 GLN Chi-restraints excluded: chain I residue 684 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain M residue 202 LEU Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 325 ASN Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 409 ILE Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 325 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 139 optimal weight: 6.9990 chunk 181 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 307 optimal weight: 7.9990 chunk 116 optimal weight: 0.0030 chunk 10 optimal weight: 2.9990 chunk 253 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 128 optimal weight: 0.2980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 376 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN C 378 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN ** F 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** I 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 ASN I 564 GLN ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 641 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 ASN M 236 ASN ** M 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 406 ASN E 110 GLN ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.153391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.126169 restraints weight = 58020.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.130009 restraints weight = 30907.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132522 restraints weight = 19317.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134183 restraints weight = 13660.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.135303 restraints weight = 10748.171| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 30360 Z= 0.137 Angle : 0.736 24.589 41001 Z= 0.370 Chirality : 0.042 0.527 4630 Planarity : 0.005 0.063 5228 Dihedral : 5.225 59.356 4043 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.18 % Favored : 95.79 % Rotamer: Outliers : 3.65 % Allowed : 29.12 % Favored : 67.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.14), residues: 3634 helix: 1.32 (0.11), residues: 2244 sheet: -0.61 (0.35), residues: 216 loop : -1.56 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG I 424 TYR 0.048 0.001 TYR D 148 PHE 0.014 0.001 PHE I 118 TRP 0.030 0.002 TRP I 545 HIS 0.011 0.001 HIS E 217 Details of bonding type rmsd covalent geometry : bond 0.00310 (30356) covalent geometry : angle 0.72909 (40997) SS BOND : bond 0.00603 ( 2) SS BOND : angle 10.21501 ( 4) hydrogen bonds : bond 0.04322 ( 1657) hydrogen bonds : angle 4.24589 ( 4854) metal coordination : bond 0.00265 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 950 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8081 (tt) REVERT: A 172 TYR cc_start: 0.7157 (m-10) cc_final: 0.6623 (m-10) REVERT: A 174 ASP cc_start: 0.8078 (t0) cc_final: 0.7606 (t0) REVERT: A 180 ASN cc_start: 0.7606 (m-40) cc_final: 0.7156 (p0) REVERT: A 219 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7736 (mm) REVERT: A 224 LYS cc_start: 0.8349 (ttmt) cc_final: 0.8100 (mmtm) REVERT: A 226 GLU cc_start: 0.5872 (OUTLIER) cc_final: 0.5650 (mp0) REVERT: A 296 CYS cc_start: 0.8222 (m) cc_final: 0.7686 (m) REVERT: A 317 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8003 (mtmm) REVERT: A 343 LYS cc_start: 0.7246 (mmmm) cc_final: 0.7024 (mmmm) REVERT: A 365 LEU cc_start: 0.7100 (mt) cc_final: 0.6744 (mt) REVERT: A 416 ARG cc_start: 0.8285 (mmt-90) cc_final: 0.7808 (mmt-90) REVERT: A 451 LYS cc_start: 0.7884 (mtmm) cc_final: 0.7167 (mtmm) REVERT: B 43 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7915 (mmtt) REVERT: B 55 GLN cc_start: 0.6146 (OUTLIER) cc_final: 0.5836 (pp30) REVERT: B 88 MET cc_start: 0.5086 (mmt) cc_final: 0.4397 (mmm) REVERT: B 106 ASN cc_start: 0.7965 (OUTLIER) cc_final: 0.7413 (p0) REVERT: B 110 LYS cc_start: 0.8447 (mtmm) cc_final: 0.8066 (mttt) REVERT: B 111 SER cc_start: 0.8835 (m) cc_final: 0.8326 (p) REVERT: B 196 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7364 (mt-10) REVERT: B 220 GLN cc_start: 0.7677 (pt0) cc_final: 0.6875 (pp30) REVERT: B 234 MET cc_start: 0.6792 (mmm) cc_final: 0.6084 (mmm) REVERT: B 244 MET cc_start: 0.6920 (tmm) cc_final: 0.6472 (mmm) REVERT: B 264 ASN cc_start: 0.8513 (m110) cc_final: 0.8201 (m110) REVERT: B 278 LYS cc_start: 0.7493 (mtmm) cc_final: 0.7175 (mtmt) REVERT: B 297 GLN cc_start: 0.7284 (tt0) cc_final: 0.6949 (tm-30) REVERT: B 318 TYR cc_start: 0.7091 (t80) cc_final: 0.6692 (t80) REVERT: B 361 LYS cc_start: 0.7642 (ttpt) cc_final: 0.7397 (tttp) REVERT: B 377 GLU cc_start: 0.7022 (tp30) cc_final: 0.6730 (tp30) REVERT: B 395 ASP cc_start: 0.6978 (m-30) cc_final: 0.6712 (t0) REVERT: B 404 GLN cc_start: 0.7980 (tt0) cc_final: 0.7697 (tt0) REVERT: B 426 LYS cc_start: 0.7923 (mttp) cc_final: 0.7467 (mtpp) REVERT: C 21 MET cc_start: 0.6825 (ttp) cc_final: 0.6180 (tpt) REVERT: C 68 MET cc_start: 0.6993 (tmm) cc_final: 0.6551 (tmm) REVERT: C 82 GLN cc_start: 0.8362 (tt0) cc_final: 0.8056 (pt0) REVERT: C 166 MET cc_start: 0.6399 (mmt) cc_final: 0.6092 (mmt) REVERT: C 192 TYR cc_start: 0.7186 (m-80) cc_final: 0.6919 (m-80) REVERT: C 214 MET cc_start: 0.7640 (mpp) cc_final: 0.6908 (mpp) REVERT: C 224 TYR cc_start: 0.7422 (t80) cc_final: 0.6985 (t80) REVERT: C 245 THR cc_start: 0.8659 (m) cc_final: 0.8426 (t) REVERT: C 247 GLN cc_start: 0.7955 (pp30) cc_final: 0.7575 (pp30) REVERT: C 248 ILE cc_start: 0.8338 (tt) cc_final: 0.7823 (tt) REVERT: C 292 MET cc_start: 0.7276 (tpt) cc_final: 0.6985 (mmm) REVERT: C 309 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7751 (ttp80) REVERT: C 327 GLN cc_start: 0.8087 (mp10) cc_final: 0.7550 (mp10) REVERT: C 380 MET cc_start: 0.7190 (mtp) cc_final: 0.6862 (mtt) REVERT: C 405 GLN cc_start: 0.8062 (tp40) cc_final: 0.7848 (tp40) REVERT: D 203 GLU cc_start: 0.7397 (tp30) cc_final: 0.6960 (tp30) REVERT: D 256 GLN cc_start: 0.7277 (mm-40) cc_final: 0.7052 (mm-40) REVERT: D 267 MET cc_start: 0.7632 (mmt) cc_final: 0.7412 (mmm) REVERT: D 323 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6745 (mm-30) REVERT: D 341 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.7167 (tt0) REVERT: D 349 ASN cc_start: 0.8174 (t0) cc_final: 0.7854 (m-40) REVERT: D 386 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6476 (tm-30) REVERT: F 97 LYS cc_start: 0.7990 (ptpp) cc_final: 0.7450 (ptpp) REVERT: F 130 PRO cc_start: 0.8258 (Cg_exo) cc_final: 0.8046 (Cg_endo) REVERT: F 153 LYS cc_start: 0.8238 (tttp) cc_final: 0.7652 (tttp) REVERT: F 166 SER cc_start: 0.8277 (m) cc_final: 0.7269 (p) REVERT: F 234 ARG cc_start: 0.7461 (mtt90) cc_final: 0.7221 (mmt180) REVERT: F 236 LYS cc_start: 0.7330 (ttmt) cc_final: 0.7027 (ttmt) REVERT: F 249 GLU cc_start: 0.7904 (mp0) cc_final: 0.7692 (mp0) REVERT: F 264 CYS cc_start: 0.8125 (m) cc_final: 0.7678 (m) REVERT: F 308 LYS cc_start: 0.8357 (mttp) cc_final: 0.8139 (ttmm) REVERT: G 33 GLN cc_start: 0.8587 (mt0) cc_final: 0.7995 (mt0) REVERT: G 54 GLU cc_start: 0.7390 (tp30) cc_final: 0.6831 (tp30) REVERT: G 72 TYR cc_start: 0.7461 (m-10) cc_final: 0.7163 (m-10) REVERT: G 103 SER cc_start: 0.8576 (t) cc_final: 0.8202 (p) REVERT: G 107 ARG cc_start: 0.7336 (ptp90) cc_final: 0.6947 (ptp90) REVERT: G 113 TYR cc_start: 0.7727 (m-10) cc_final: 0.7259 (m-80) REVERT: G 199 LYS cc_start: 0.7857 (ttmt) cc_final: 0.7486 (ttmt) REVERT: G 210 GLU cc_start: 0.6778 (pp20) cc_final: 0.6091 (pp20) REVERT: G 217 LYS cc_start: 0.7828 (ttpt) cc_final: 0.7524 (tppt) REVERT: H 18 ASP cc_start: 0.8261 (p0) cc_final: 0.7870 (p0) REVERT: H 21 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7727 (mt-10) REVERT: I 31 VAL cc_start: 0.7226 (OUTLIER) cc_final: 0.6698 (t) REVERT: I 91 ARG cc_start: 0.7434 (ptp-170) cc_final: 0.7228 (ptm160) REVERT: I 92 LEU cc_start: 0.8298 (mt) cc_final: 0.8016 (mm) REVERT: I 128 PHE cc_start: 0.7571 (t80) cc_final: 0.7118 (t80) REVERT: I 148 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7873 (mm-30) REVERT: I 210 GLU cc_start: 0.8543 (tm-30) cc_final: 0.7970 (tm-30) REVERT: I 228 TYR cc_start: 0.7620 (t80) cc_final: 0.6799 (t80) REVERT: I 229 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8361 (ptpp) REVERT: I 233 GLU cc_start: 0.7427 (pt0) cc_final: 0.6345 (mp0) REVERT: I 237 LEU cc_start: 0.8978 (pp) cc_final: 0.8512 (tt) REVERT: I 259 GLU cc_start: 0.6829 (tp30) cc_final: 0.6613 (tp30) REVERT: I 261 MET cc_start: 0.5895 (mpp) cc_final: 0.5425 (mpp) REVERT: I 274 ARG cc_start: 0.7418 (ttp-170) cc_final: 0.7127 (ttm110) REVERT: I 284 GLN cc_start: 0.7711 (mp-120) cc_final: 0.7176 (mp10) REVERT: I 297 GLU cc_start: 0.6796 (tm-30) cc_final: 0.6341 (tm-30) REVERT: I 300 LEU cc_start: 0.8339 (pt) cc_final: 0.8075 (pt) REVERT: I 322 MET cc_start: 0.7883 (mtt) cc_final: 0.7482 (ttm) REVERT: I 325 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7274 (mp) REVERT: I 365 MET cc_start: 0.7252 (mmm) cc_final: 0.6972 (mmm) REVERT: I 368 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7726 (mm-40) REVERT: I 376 LYS cc_start: 0.8410 (tttt) cc_final: 0.7912 (tptp) REVERT: I 397 LYS cc_start: 0.8247 (tptt) cc_final: 0.8044 (tptt) REVERT: I 425 TYR cc_start: 0.7272 (t80) cc_final: 0.6883 (t80) REVERT: I 450 MET cc_start: 0.7098 (tpp) cc_final: 0.6843 (tpp) REVERT: I 452 VAL cc_start: 0.8655 (m) cc_final: 0.8394 (p) REVERT: I 463 GLN cc_start: 0.8109 (mm110) cc_final: 0.7854 (mm-40) REVERT: I 507 MET cc_start: 0.7854 (mmp) cc_final: 0.7543 (tpp) REVERT: I 525 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8082 (mm) REVERT: I 680 LEU cc_start: 0.8550 (mt) cc_final: 0.8105 (pp) REVERT: L 14 PHE cc_start: 0.8375 (m-80) cc_final: 0.8140 (m-80) REVERT: L 57 LYS cc_start: 0.8400 (mmtt) cc_final: 0.8091 (tptt) REVERT: L 158 GLN cc_start: 0.7782 (tp-100) cc_final: 0.7456 (tp-100) REVERT: M 105 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7750 (mt) REVERT: M 119 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7432 (ptmt) REVERT: M 204 GLN cc_start: 0.7199 (mm-40) cc_final: 0.6613 (mm-40) REVERT: M 216 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6428 (tt) REVERT: M 291 SER cc_start: 0.5483 (p) cc_final: 0.4575 (t) REVERT: M 312 LEU cc_start: 0.7408 (mt) cc_final: 0.7161 (mm) REVERT: M 320 SER cc_start: 0.7885 (m) cc_final: 0.7286 (p) REVERT: M 322 MET cc_start: 0.7323 (mmm) cc_final: 0.6777 (mpp) REVERT: M 368 PHE cc_start: 0.7607 (m-80) cc_final: 0.7359 (m-10) REVERT: M 370 ILE cc_start: 0.8711 (pt) cc_final: 0.8428 (tt) REVERT: M 383 LEU cc_start: 0.8297 (mt) cc_final: 0.7979 (tt) REVERT: N 23 MET cc_start: 0.6737 (ttm) cc_final: 0.6516 (mtm) REVERT: N 43 TRP cc_start: 0.7402 (p-90) cc_final: 0.7198 (p-90) REVERT: E 166 VAL cc_start: 0.7687 (p) cc_final: 0.7274 (m) REVERT: E 210 LYS cc_start: 0.7394 (mttm) cc_final: 0.6981 (mttt) REVERT: E 240 LEU cc_start: 0.7887 (tp) cc_final: 0.7684 (tt) REVERT: E 270 SER cc_start: 0.7525 (m) cc_final: 0.7217 (p) REVERT: E 277 GLU cc_start: 0.7699 (tt0) cc_final: 0.7429 (tt0) REVERT: E 305 ARG cc_start: 0.7478 (ttp-170) cc_final: 0.7046 (mtp180) REVERT: E 330 GLN cc_start: 0.8130 (mm110) cc_final: 0.7878 (mm-40) outliers start: 120 outliers final: 97 residues processed: 1011 average time/residue: 0.1901 time to fit residues: 297.9527 Evaluate side-chains 1049 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 939 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 431 GLN Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 36 TYR Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 370 HIS Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 372 LYS Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 394 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 243 LYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 168 ARG Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 416 SER Chi-restraints excluded: chain I residue 525 LEU Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 564 GLN Chi-restraints excluded: chain I residue 581 TRP Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 641 GLN Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 155 LEU Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 325 ASN Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 409 ILE Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 39 SER Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 268 ASP Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 325 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 153 optimal weight: 2.9990 chunk 345 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 302 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 197 HIS A 376 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN B 432 ASN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN F 67 GLN ** F 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 GLN ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 613 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 ASN ** M 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 ASN E 265 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.150169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.122876 restraints weight = 58546.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.126619 restraints weight = 31365.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.129055 restraints weight = 19681.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.130686 restraints weight = 14037.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.131780 restraints weight = 11037.206| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 30360 Z= 0.209 Angle : 0.784 25.082 41001 Z= 0.399 Chirality : 0.045 0.547 4630 Planarity : 0.005 0.095 5228 Dihedral : 5.410 58.455 4043 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.95 % Favored : 95.02 % Rotamer: Outliers : 3.74 % Allowed : 28.84 % Favored : 67.42 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3634 helix: 1.16 (0.11), residues: 2233 sheet: -0.69 (0.35), residues: 210 loop : -1.64 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 289 TYR 0.044 0.002 TYR D 148 PHE 0.026 0.002 PHE I 402 TRP 0.024 0.003 TRP M 97 HIS 0.009 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00464 (30356) covalent geometry : angle 0.77801 (40997) SS BOND : bond 0.00638 ( 2) SS BOND : angle 10.14491 ( 4) hydrogen bonds : bond 0.05196 ( 1657) hydrogen bonds : angle 4.47926 ( 4854) metal coordination : bond 0.00525 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6655.22 seconds wall clock time: 115 minutes 3.20 seconds (6903.20 seconds total)