Starting phenix.real_space_refine on Fri Feb 6 20:28:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e81_47698/02_2026/9e81_47698.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e81_47698/02_2026/9e81_47698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e81_47698/02_2026/9e81_47698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e81_47698/02_2026/9e81_47698.map" model { file = "/net/cci-nas-00/data/ceres_data/9e81_47698/02_2026/9e81_47698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e81_47698/02_2026/9e81_47698.cif" } resolution = 3.3 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= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12281 atoms to isotropic. 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 S 105 5.16 5 C 11386 2.51 5 N 3056 2.21 5 O 3363 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17913 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3271 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 8, 'TRANS': 400} Chain breaks: 1 Chain: "B" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1722 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "C" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3216 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 13, 'TRANS': 390} Chain: "D" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2093 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 254} Chain breaks: 1 Chain: "E" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2321 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 281} Chain breaks: 2 Chain: "F" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2182 Classifications: {'peptide': 272} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 261} Chain breaks: 1 Chain: "G" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1687 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain: "H" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1383 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 162} Chain breaks: 1 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {' ZN': 1, '6LT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.92, per 1000 atoms: 0.22 Number of scatterers: 17913 At special positions: 0 Unit cell: (122.13, 148.68, 171.69, 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 105 16.00 F 2 9.00 O 3363 8.00 N 3056 7.00 C 11386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.47 Conformation dependent library (CDL) restraints added in 748.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" NE2 HIS E 138 " pdb="ZN ZN E 402 " - pdb=" NE2 HIS E 140 " 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4278 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 5 sheets defined 69.9% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 43 through 51 removed outlier: 3.957A pdb=" N TYR A 51 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.781A pdb=" N GLU A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 Processing helix chain 'A' and resid 88 through 102 Processing helix chain 'A' and resid 127 through 156 Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 178 through 190 removed outlier: 4.087A pdb=" N ASP A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 213 Processing helix chain 'A' and resid 214 through 228 Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 244 through 260 removed outlier: 3.557A pdb=" N LYS A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 271 Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.783A pdb=" N HIS A 277 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 301 removed outlier: 3.595A pdb=" N ALA A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 316 through 323 removed outlier: 3.976A pdb=" N LEU A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 323 " --> pdb=" O PHE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.641A pdb=" N ARG A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 353 removed outlier: 3.550A pdb=" N CYS A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 4.594A 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 Processing helix chain 'A' and resid 386 through 393 Processing helix chain 'A' and resid 396 through 411 removed outlier: 3.711A pdb=" N GLU A 410 " --> pdb=" O GLN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 463 Processing helix chain 'B' and resid 232 through 247 Processing helix chain 'B' and resid 250 through 266 Processing helix chain 'B' and resid 269 through 288 removed outlier: 3.803A pdb=" N ARG B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR B 275 " --> pdb=" O PRO B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 309 through 321 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 340 through 363 removed outlier: 3.550A pdb=" N ARG B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU B 349 " --> pdb=" O GLU B 345 " (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 418 through 442 removed outlier: 4.087A pdb=" N LEU B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 16 Processing helix chain 'C' and resid 20 through 30 removed outlier: 3.776A pdb=" N LEU C 24 " --> pdb=" O GLN C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 removed outlier: 4.194A pdb=" N LEU C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR C 44 " --> pdb=" O SER C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 65 removed outlier: 3.839A pdb=" N LYS C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 73 through 88 removed outlier: 3.803A pdb=" N LEU C 77 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 97 removed outlier: 3.708A pdb=" N THR C 97 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 115 Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.964A pdb=" N GLN C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 152 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 177 through 195 removed outlier: 4.121A pdb=" N PHE C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY C 189 " --> pdb=" O TYR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 removed outlier: 4.007A pdb=" N TYR C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 235 removed outlier: 3.553A pdb=" N TYR C 224 " --> pdb=" O MET C 220 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS C 226 " --> pdb=" O GLU C 222 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 229 " --> pdb=" O LYS C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 4.136A pdb=" N LEU C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 257' Processing helix chain 'C' and resid 258 through 267 Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 294 through 311 removed outlier: 3.650A pdb=" N CYS C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 326 removed outlier: 3.732A pdb=" N SER C 324 " --> pdb=" O GLN C 320 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG C 325 " --> pdb=" O ASP C 321 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 326 " --> pdb=" O MET C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 344 Processing helix chain 'C' and resid 369 through 399 removed outlier: 3.549A pdb=" N LEU C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 399 " --> pdb=" O GLN C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 404 Processing helix chain 'D' and resid 142 through 158 Processing helix chain 'D' and resid 160 through 176 removed outlier: 3.834A pdb=" N ALA D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU D 173 " --> pdb=" O ASN D 169 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 198 Processing helix chain 'D' and resid 200 through 212 removed outlier: 3.683A pdb=" N ALA D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 235 Processing helix chain 'D' and resid 239 through 251 Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.610A pdb=" N GLN D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 258 " --> pdb=" O CYS D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 274 through 285 removed outlier: 3.562A pdb=" N LEU D 278 " --> pdb=" O ARG D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 298 through 313 Processing helix chain 'D' and resid 321 through 328 Processing helix chain 'D' and resid 331 through 345 Processing helix chain 'D' and resid 365 through 392 removed outlier: 3.508A pdb=" N THR D 369 " --> pdb=" O GLU D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 406 removed outlier: 3.740A pdb=" N ALA D 399 " --> pdb=" O TRP D 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 30 removed outlier: 3.774A pdb=" N ILE E 28 " --> pdb=" O ILE E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 42 removed outlier: 3.586A pdb=" N GLN E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 73 removed outlier: 3.649A pdb=" N GLY E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 126 removed outlier: 4.139A pdb=" N GLN E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 162 Processing helix chain 'E' and resid 171 through 179 removed outlier: 4.067A pdb=" N ILE E 176 " --> pdb=" O PRO E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 210 through 217 removed outlier: 3.750A pdb=" N HIS E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 251 removed outlier: 3.951A pdb=" N ASN E 243 " --> pdb=" O GLU E 239 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS E 244 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRP E 246 " --> pdb=" O TRP E 242 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL E 247 " --> pdb=" O ASN E 243 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASN E 248 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR E 249 " --> pdb=" O TYR E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 removed outlier: 4.090A pdb=" N THR E 257 " --> pdb=" O SER E 253 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 253 through 258' Processing helix chain 'E' and resid 259 through 282 removed outlier: 3.640A pdb=" N THR E 263 " --> pdb=" O ALA E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 329 removed outlier: 3.737A pdb=" N LYS E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN E 321 " --> pdb=" O GLY E 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 63 removed outlier: 3.795A pdb=" N ILE F 48 " --> pdb=" O HIS F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 116 removed outlier: 3.872A pdb=" N VAL F 115 " --> pdb=" O GLN F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 144 removed outlier: 3.864A pdb=" N GLU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 206 Processing helix chain 'F' and resid 216 through 221 Processing helix chain 'F' and resid 222 through 248 removed outlier: 3.663A pdb=" N ALA F 227 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET F 230 " --> pdb=" O SER F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 266 removed outlier: 3.563A pdb=" N LEU F 257 " --> pdb=" O ASN F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 313 Processing helix chain 'G' and resid 11 through 19 Processing helix chain 'G' and resid 24 through 37 Processing helix chain 'G' and resid 49 through 54 Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 60 through 73 removed outlier: 3.612A pdb=" N LEU G 64 " --> pdb=" O ASN G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 81 removed outlier: 3.750A pdb=" N ALA G 80 " --> pdb=" O PRO G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.823A pdb=" N ARG G 107 " --> pdb=" O SER G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 124 through 138 removed outlier: 3.635A pdb=" N LEU G 128 " --> pdb=" O ASN G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 221 removed outlier: 3.564A pdb=" N ILE G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 27 removed outlier: 3.828A pdb=" N LEU H 16 " --> pdb=" O SER H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 47 Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 61 through 68 Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.769A pdb=" N GLY H 73 " --> pdb=" O SER H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 94 removed outlier: 3.832A pdb=" N ASN H 94 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 124 removed outlier: 3.796A pdb=" N ARG H 110 " --> pdb=" O MET H 106 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'H' and resid 140 through 148 removed outlier: 3.829A pdb=" N ILE H 148 " --> pdb=" O ALA H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 208 Processing sheet with id=AA1, first strand: chain 'G' and resid 110 through 112 removed outlier: 6.727A pdb=" N GLN G 142 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N THR B 367 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 382 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU C 315 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VAL A 417 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU C 317 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU C 315 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N THR H 126 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE C 351 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE H 128 " --> pdb=" O ILE C 351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 137 through 138 Processing sheet with id=AA3, first strand: chain 'E' and resid 54 through 58 removed outlier: 7.267A pdb=" N ASP E 94 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU E 82 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N SER E 95 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU E 80 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ALA E 97 " --> pdb=" O MET E 78 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N MET E 78 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY E 79 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TRP E 136 " --> pdb=" O GLY E 79 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET E 81 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN E 132 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N LEU E 183 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL E 226 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA E 185 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 178 through 186 removed outlier: 4.633A pdb=" N VAL F 167 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N LEU F 150 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU F 122 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N LEU F 152 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP F 124 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N LEU F 154 " --> pdb=" O TRP F 124 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR F 126 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE F 121 " --> pdb=" O GLY F 74 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLY F 74 " --> pdb=" O PHE F 121 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY F 123 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR F 125 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA F 71 " --> pdb=" O SER F 86 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N SER F 86 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE F 73 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER F 40 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL F 83 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA F 42 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ASN F 85 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 91 through 94 1131 hydrogen bonds defined for protein. 3324 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: 2.54 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3022 1.31 - 1.44: 4641 1.44 - 1.56: 10408 1.56 - 1.68: 0 1.68 - 1.81: 169 Bond restraints: 18240 Sorted by residual: bond pdb=" C25 6LT E 401 " pdb=" N13 6LT E 401 " ideal model delta sigma weight residual 1.361 1.465 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" CA MET C 68 " pdb=" CB MET C 68 " ideal model delta sigma weight residual 1.522 1.545 -0.022 7.00e-03 2.04e+04 1.02e+01 bond pdb=" C1 6LT E 401 " pdb=" N2 6LT E 401 " ideal model delta sigma weight residual 1.380 1.321 0.059 2.00e-02 2.50e+03 8.77e+00 bond pdb=" C10 6LT E 401 " pdb=" N13 6LT E 401 " ideal model delta sigma weight residual 1.405 1.459 -0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" C1 6LT E 401 " pdb=" C15 6LT E 401 " ideal model delta sigma weight residual 1.488 1.541 -0.053 2.00e-02 2.50e+03 7.08e+00 ... (remaining 18235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 24406 2.31 - 4.62: 202 4.62 - 6.93: 32 6.93 - 9.24: 7 9.24 - 11.55: 2 Bond angle restraints: 24649 Sorted by residual: angle pdb=" C MET C 68 " pdb=" CA MET C 68 " pdb=" CB MET C 68 " ideal model delta sigma weight residual 111.00 115.51 -4.51 8.70e-01 1.32e+00 2.69e+01 angle pdb=" N CYS E 218 " pdb=" CA CYS E 218 " pdb=" C CYS E 218 " ideal model delta sigma weight residual 114.56 109.41 5.15 1.27e+00 6.20e-01 1.64e+01 angle pdb=" C3 6LT E 401 " pdb=" N2 6LT E 401 " pdb=" C6 6LT E 401 " ideal model delta sigma weight residual 128.07 116.52 11.55 3.00e+00 1.11e-01 1.48e+01 angle pdb=" CA MET C 68 " pdb=" CB MET C 68 " pdb=" CG MET C 68 " ideal model delta sigma weight residual 114.10 121.70 -7.60 2.00e+00 2.50e-01 1.45e+01 angle pdb=" CB MET A 201 " pdb=" CG MET A 201 " pdb=" SD MET A 201 " ideal model delta sigma weight residual 112.70 122.67 -9.97 3.00e+00 1.11e-01 1.10e+01 ... (remaining 24644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.78: 10445 31.78 - 63.57: 635 63.57 - 95.35: 58 95.35 - 127.13: 1 127.13 - 158.92: 1 Dihedral angle restraints: 11140 sinusoidal: 4545 harmonic: 6595 Sorted by residual: dihedral pdb=" C1 6LT E 401 " pdb=" C15 6LT E 401 " pdb=" C16 6LT E 401 " pdb=" C17 6LT E 401 " ideal model delta sinusoidal sigma weight residual -74.55 84.37 -158.92 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C15 6LT E 401 " pdb=" C16 6LT E 401 " pdb=" C17 6LT E 401 " pdb=" C18 6LT E 401 " ideal model delta sinusoidal sigma weight residual 61.76 -63.88 125.64 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" CA GLU C 222 " pdb=" C GLU C 222 " pdb=" N SER C 223 " pdb=" CA SER C 223 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 11137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2201 0.045 - 0.090: 481 0.090 - 0.136: 99 0.136 - 0.181: 3 0.181 - 0.226: 3 Chirality restraints: 2787 Sorted by residual: chirality pdb=" CB VAL C 71 " pdb=" CA VAL C 71 " pdb=" CG1 VAL C 71 " pdb=" CG2 VAL C 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU D 309 " pdb=" CB LEU D 309 " pdb=" CD1 LEU D 309 " pdb=" CD2 LEU D 309 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" C6 6LT E 401 " pdb=" C18 6LT E 401 " pdb=" C7 6LT E 401 " pdb=" N2 6LT E 401 " both_signs ideal model delta sigma weight residual False 2.30 2.48 -0.18 2.00e-01 2.50e+01 8.19e-01 ... (remaining 2784 not shown) Planarity restraints: 3156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 71 " 0.047 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO C 72 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 72 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 72 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 400 " 0.034 5.00e-02 4.00e+02 5.28e-02 4.45e+00 pdb=" N PRO C 401 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 401 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 401 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 44 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO F 45 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 45 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 45 " -0.026 5.00e-02 4.00e+02 ... (remaining 3153 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 60 2.48 - 3.08: 12149 3.08 - 3.69: 26276 3.69 - 4.29: 37574 4.29 - 4.90: 65403 Nonbonded interactions: 141462 Sorted by model distance: nonbonded pdb=" OD2 ASP E 151 " pdb="ZN ZN E 402 " model vdw 1.871 2.230 nonbonded pdb=" N4 6LT E 401 " pdb="ZN ZN E 402 " model vdw 1.963 2.310 nonbonded pdb=" O THR C 76 " pdb=" OG SER C 79 " model vdw 2.197 3.040 nonbonded pdb=" O ASP C 73 " pdb=" OG1 THR C 76 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASP C 377 " pdb=" OH TYR H 203 " model vdw 2.215 3.040 ... (remaining 141457 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.250 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 0.104 18242 Z= 0.159 Angle : 0.563 11.551 24649 Z= 0.291 Chirality : 0.039 0.226 2787 Planarity : 0.004 0.072 3156 Dihedral : 18.941 158.919 6862 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.62 % Favored : 94.29 % Rotamer: Outliers : 0.31 % Allowed : 26.04 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.38 (0.19), residues: 2208 helix: 2.05 (0.14), residues: 1468 sheet: -0.21 (0.48), residues: 121 loop : -1.72 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 198 TYR 0.014 0.001 TYR C 267 PHE 0.014 0.001 PHE E 96 TRP 0.007 0.001 TRP H 75 HIS 0.008 0.001 HIS D 288 Details of bonding type rmsd covalent geometry : bond 0.00351 (18240) covalent geometry : angle 0.56281 (24649) hydrogen bonds : bond 0.11469 ( 1131) hydrogen bonds : angle 4.65200 ( 3324) metal coordination : bond 0.00435 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 172 time to evaluate : 0.525 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 176 average time/residue: 0.1256 time to fit residues: 34.6237 Evaluate side-chains 171 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 169 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain E residue 225 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN B 436 GLN F 160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.169979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126613 restraints weight = 19464.942| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.19 r_work: 0.3072 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.0503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18242 Z= 0.140 Angle : 0.516 7.814 24649 Z= 0.268 Chirality : 0.039 0.242 2787 Planarity : 0.004 0.072 3156 Dihedral : 6.374 142.767 2458 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.62 % Favored : 94.29 % Rotamer: Outliers : 2.35 % Allowed : 24.19 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.59 (0.19), residues: 2208 helix: 2.15 (0.14), residues: 1493 sheet: -0.13 (0.48), residues: 119 loop : -1.63 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 199 TYR 0.016 0.001 TYR E 143 PHE 0.015 0.001 PHE E 96 TRP 0.006 0.001 TRP E 136 HIS 0.005 0.001 HIS D 288 Details of bonding type rmsd covalent geometry : bond 0.00325 (18240) covalent geometry : angle 0.51649 (24649) hydrogen bonds : bond 0.04450 ( 1131) hydrogen bonds : angle 3.75397 ( 3324) metal coordination : bond 0.00557 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 67 CYS cc_start: 0.5435 (OUTLIER) cc_final: 0.4320 (t) REVERT: A 302 ASP cc_start: 0.7736 (p0) cc_final: 0.7481 (p0) REVERT: D 355 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8010 (mp) REVERT: D 391 THR cc_start: 0.6539 (OUTLIER) cc_final: 0.6292 (m) REVERT: G 163 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.6208 (mtt180) REVERT: G 204 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7023 (ttp80) REVERT: H 69 SER cc_start: 0.6420 (OUTLIER) cc_final: 0.5682 (p) outliers start: 46 outliers final: 24 residues processed: 209 average time/residue: 0.1221 time to fit residues: 39.0544 Evaluate side-chains 192 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain E residue 321 GLN Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 197 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 138 optimal weight: 0.0070 chunk 36 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 166 optimal weight: 0.0470 chunk 188 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 141 optimal weight: 0.5980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 436 GLN C 320 GLN G 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.171601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.130867 restraints weight = 19615.492| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.98 r_work: 0.3128 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18242 Z= 0.111 Angle : 0.479 8.767 24649 Z= 0.248 Chirality : 0.038 0.228 2787 Planarity : 0.004 0.071 3156 Dihedral : 6.005 134.182 2453 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.66 % Rotamer: Outliers : 2.56 % Allowed : 24.45 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.74 (0.19), residues: 2208 helix: 2.30 (0.14), residues: 1485 sheet: -0.03 (0.48), residues: 119 loop : -1.63 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 187 TYR 0.014 0.001 TYR E 143 PHE 0.015 0.001 PHE C 84 TRP 0.006 0.001 TRP E 136 HIS 0.007 0.001 HIS D 288 Details of bonding type rmsd covalent geometry : bond 0.00249 (18240) covalent geometry : angle 0.47914 (24649) hydrogen bonds : bond 0.03836 ( 1131) hydrogen bonds : angle 3.53586 ( 3324) metal coordination : bond 0.00370 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 302 ASP cc_start: 0.7742 (p0) cc_final: 0.7484 (p0) REVERT: A 350 ASP cc_start: 0.8558 (t0) cc_final: 0.8318 (t0) REVERT: A 463 GLN cc_start: 0.8555 (mm110) cc_final: 0.8229 (mt0) REVERT: C 145 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8227 (tp) REVERT: C 287 THR cc_start: 0.8015 (t) cc_final: 0.7768 (t) REVERT: D 280 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6279 (mp0) REVERT: D 309 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8434 (tt) REVERT: D 355 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8063 (mp) REVERT: E 74 ASN cc_start: 0.8374 (t0) cc_final: 0.8166 (t0) REVERT: E 210 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7245 (mttm) REVERT: F 314 ASP cc_start: 0.6121 (OUTLIER) cc_final: 0.5866 (t0) REVERT: G 161 ASP cc_start: 0.8721 (m-30) cc_final: 0.8461 (m-30) REVERT: G 163 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.6239 (mtt180) REVERT: G 208 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.6489 (mp10) REVERT: H 69 SER cc_start: 0.6537 (OUTLIER) cc_final: 0.5804 (p) REVERT: H 143 GLU cc_start: 0.6760 (tp30) cc_final: 0.6554 (tp30) outliers start: 50 outliers final: 26 residues processed: 223 average time/residue: 0.1312 time to fit residues: 44.9931 Evaluate side-chains 211 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 132 ASN Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 321 GLN Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 208 GLN Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 197 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 195 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 138 optimal weight: 0.4980 chunk 49 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 142 optimal weight: 0.0670 chunk 50 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.171334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.131612 restraints weight = 19583.959| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.12 r_work: 0.3093 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18242 Z= 0.119 Angle : 0.482 8.863 24649 Z= 0.248 Chirality : 0.038 0.173 2787 Planarity : 0.004 0.073 3156 Dihedral : 5.945 131.263 2453 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.62 % Favored : 94.29 % Rotamer: Outliers : 3.53 % Allowed : 23.84 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.74 (0.19), residues: 2208 helix: 2.27 (0.14), residues: 1497 sheet: 0.05 (0.48), residues: 119 loop : -1.64 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 187 TYR 0.015 0.001 TYR E 143 PHE 0.013 0.001 PHE E 96 TRP 0.006 0.001 TRP E 136 HIS 0.007 0.001 HIS D 288 Details of bonding type rmsd covalent geometry : bond 0.00275 (18240) covalent geometry : angle 0.48169 (24649) hydrogen bonds : bond 0.03859 ( 1131) hydrogen bonds : angle 3.48660 ( 3324) metal coordination : bond 0.00432 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 172 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 201 MET cc_start: 0.7525 (ppp) cc_final: 0.7059 (ppp) REVERT: A 302 ASP cc_start: 0.7810 (p0) cc_final: 0.7480 (p0) REVERT: A 350 ASP cc_start: 0.8544 (t0) cc_final: 0.8303 (t0) REVERT: A 447 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8567 (mt0) REVERT: C 145 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8232 (tp) REVERT: C 287 THR cc_start: 0.8015 (t) cc_final: 0.7782 (t) REVERT: D 309 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8421 (tt) REVERT: D 328 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8279 (mp) REVERT: D 355 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8086 (mp) REVERT: E 74 ASN cc_start: 0.8399 (t0) cc_final: 0.8187 (t0) REVERT: E 210 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7237 (mttm) REVERT: F 66 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.8089 (t) REVERT: F 314 ASP cc_start: 0.6218 (OUTLIER) cc_final: 0.5981 (t0) REVERT: G 161 ASP cc_start: 0.8765 (m-30) cc_final: 0.8509 (m-30) REVERT: G 204 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6651 (tmm160) REVERT: G 208 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.6437 (mp10) REVERT: H 69 SER cc_start: 0.6574 (OUTLIER) cc_final: 0.5854 (p) REVERT: H 143 GLU cc_start: 0.6848 (tp30) cc_final: 0.6639 (tp30) outliers start: 69 outliers final: 35 residues processed: 231 average time/residue: 0.1187 time to fit residues: 42.5280 Evaluate side-chains 218 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain E residue 132 ASN Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 153 GLU Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 208 GLN Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 197 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 166 optimal weight: 0.0570 chunk 63 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.171987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132184 restraints weight = 19473.828| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.03 r_work: 0.3103 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18242 Z= 0.112 Angle : 0.481 9.049 24649 Z= 0.247 Chirality : 0.038 0.245 2787 Planarity : 0.004 0.075 3156 Dihedral : 5.875 128.381 2453 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 3.38 % Allowed : 24.19 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.79 (0.19), residues: 2208 helix: 2.30 (0.14), residues: 1498 sheet: 0.08 (0.48), residues: 119 loop : -1.64 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 198 TYR 0.014 0.001 TYR E 143 PHE 0.012 0.001 PHE E 96 TRP 0.006 0.001 TRP E 136 HIS 0.007 0.001 HIS D 288 Details of bonding type rmsd covalent geometry : bond 0.00257 (18240) covalent geometry : angle 0.48113 (24649) hydrogen bonds : bond 0.03717 ( 1131) hydrogen bonds : angle 3.44197 ( 3324) metal coordination : bond 0.00363 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 184 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ASP cc_start: 0.7815 (p0) cc_final: 0.7519 (p0) REVERT: A 350 ASP cc_start: 0.8534 (t0) cc_final: 0.8278 (t0) REVERT: A 463 GLN cc_start: 0.8543 (mm110) cc_final: 0.8210 (mt0) REVERT: B 287 MET cc_start: 0.6467 (ptt) cc_final: 0.6246 (ptt) REVERT: C 145 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8215 (tp) REVERT: C 287 THR cc_start: 0.7940 (t) cc_final: 0.7710 (t) REVERT: D 264 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7930 (tp) REVERT: D 280 GLU cc_start: 0.7194 (mp0) cc_final: 0.6969 (mp0) REVERT: D 309 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8419 (tt) REVERT: D 355 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8072 (mp) REVERT: E 74 ASN cc_start: 0.8389 (t0) cc_final: 0.8170 (t0) REVERT: E 210 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7250 (mttm) REVERT: F 314 ASP cc_start: 0.6209 (OUTLIER) cc_final: 0.5961 (t0) REVERT: G 161 ASP cc_start: 0.8747 (m-30) cc_final: 0.8530 (m-30) REVERT: G 204 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.6648 (tmm160) REVERT: G 208 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.6411 (mp10) REVERT: H 69 SER cc_start: 0.6585 (OUTLIER) cc_final: 0.5839 (p) outliers start: 66 outliers final: 40 residues processed: 239 average time/residue: 0.1211 time to fit residues: 45.1729 Evaluate side-chains 222 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain E residue 132 ASN Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 208 GLN Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 197 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 174 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 177 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 186 optimal weight: 0.0980 chunk 124 optimal weight: 0.5980 chunk 155 optimal weight: 0.3980 chunk 80 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN C 320 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.172525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.131328 restraints weight = 19403.168| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.02 r_work: 0.3117 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18242 Z= 0.105 Angle : 0.475 9.288 24649 Z= 0.244 Chirality : 0.038 0.248 2787 Planarity : 0.004 0.076 3156 Dihedral : 5.811 126.061 2453 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.30 % Favored : 94.57 % Rotamer: Outliers : 3.38 % Allowed : 24.14 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.87 (0.19), residues: 2208 helix: 2.40 (0.14), residues: 1486 sheet: 0.12 (0.48), residues: 119 loop : -1.62 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 56 TYR 0.014 0.001 TYR E 143 PHE 0.011 0.001 PHE E 96 TRP 0.005 0.001 TRP H 82 HIS 0.006 0.001 HIS D 288 Details of bonding type rmsd covalent geometry : bond 0.00236 (18240) covalent geometry : angle 0.47507 (24649) hydrogen bonds : bond 0.03550 ( 1131) hydrogen bonds : angle 3.37471 ( 3324) metal coordination : bond 0.00309 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 178 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.7665 (ppp) cc_final: 0.7275 (ppp) REVERT: A 350 ASP cc_start: 0.8467 (t0) cc_final: 0.8187 (t0) REVERT: A 447 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8559 (mt0) REVERT: A 463 GLN cc_start: 0.8503 (mm110) cc_final: 0.8152 (mt0) REVERT: C 145 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8200 (tp) REVERT: C 265 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7459 (mm-40) REVERT: C 287 THR cc_start: 0.7911 (t) cc_final: 0.7683 (t) REVERT: D 264 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7911 (tp) REVERT: D 280 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: D 309 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8416 (tt) REVERT: D 355 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8064 (mp) REVERT: E 74 ASN cc_start: 0.8387 (t0) cc_final: 0.8186 (t0) REVERT: E 210 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7208 (mttm) REVERT: F 66 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.8065 (t) REVERT: F 314 ASP cc_start: 0.6116 (OUTLIER) cc_final: 0.5869 (t0) REVERT: G 161 ASP cc_start: 0.8738 (m-30) cc_final: 0.8534 (m-30) REVERT: G 204 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.6832 (ttp80) REVERT: G 208 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6486 (mp10) REVERT: H 69 SER cc_start: 0.6597 (OUTLIER) cc_final: 0.5858 (p) outliers start: 66 outliers final: 41 residues processed: 232 average time/residue: 0.1212 time to fit residues: 44.1238 Evaluate side-chains 229 residues out of total 1955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 176 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 288 HIS Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain E residue 132 ASN Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 208 GLN Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 197 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.9999 > 50: distance: 21 - 43: 19.679 distance: 27 - 54: 30.826 distance: 30 - 35: 5.203 distance: 31 - 59: 21.909 distance: 35 - 36: 4.857 distance: 36 - 37: 7.835 distance: 36 - 39: 14.712 distance: 37 - 38: 7.357 distance: 37 - 43: 12.033 distance: 38 - 71: 13.501 distance: 39 - 40: 21.754 distance: 40 - 41: 14.032 distance: 40 - 42: 26.892 distance: 43 - 44: 16.956 distance: 44 - 45: 8.832 distance: 44 - 47: 11.622 distance: 45 - 46: 27.412 distance: 45 - 54: 43.864 distance: 47 - 48: 19.518 distance: 48 - 49: 16.412 distance: 48 - 50: 22.394 distance: 49 - 51: 15.290 distance: 50 - 52: 15.401 distance: 51 - 53: 16.731 distance: 52 - 53: 23.448 distance: 54 - 55: 18.166 distance: 55 - 56: 36.706 distance: 55 - 58: 17.299 distance: 56 - 57: 15.340 distance: 56 - 59: 16.646 distance: 59 - 60: 8.637 distance: 60 - 61: 12.050 distance: 60 - 63: 12.279 distance: 61 - 62: 12.953 distance: 61 - 71: 8.024 distance: 63 - 64: 13.282 distance: 64 - 65: 6.856 distance: 64 - 66: 10.939 distance: 65 - 67: 20.163 distance: 66 - 68: 15.011 distance: 67 - 69: 18.834 distance: 68 - 69: 17.711 distance: 69 - 70: 18.400 distance: 71 - 72: 29.428 distance: 72 - 73: 18.136 distance: 73 - 74: 11.458 distance: 73 - 75: 13.389 distance: 75 - 76: 8.191 distance: 76 - 77: 12.789 distance: 76 - 79: 20.899 distance: 77 - 78: 21.424 distance: 77 - 82: 12.753 distance: 79 - 80: 15.163 distance: 79 - 81: 14.756 distance: 82 - 83: 5.825 distance: 83 - 84: 15.263 distance: 83 - 86: 13.564 distance: 84 - 85: 7.805 distance: 84 - 94: 10.694 distance: 86 - 87: 6.464 distance: 87 - 88: 11.587 distance: 87 - 89: 4.855 distance: 88 - 90: 3.087 distance: 89 - 91: 5.267 distance: 90 - 92: 5.621 distance: 91 - 92: 5.023 distance: 92 - 93: 17.181 distance: 94 - 95: 4.441 distance: 94 - 100: 10.736 distance: 95 - 96: 9.450 distance: 95 - 98: 13.624 distance: 96 - 97: 9.734 distance: 96 - 101: 5.487 distance: 98 - 99: 15.509 distance: 99 - 100: 20.046 distance: 101 - 102: 7.389 distance: 102 - 103: 6.653 distance: 102 - 105: 6.703 distance: 103 - 104: 5.866 distance: 103 - 109: 3.755 distance: 105 - 106: 6.711 distance: 106 - 107: 5.643 distance: 106 - 108: 10.390 distance: 110 - 111: 4.705 distance: 111 - 112: 7.547 distance: 111 - 121: 3.056 distance: 113 - 114: 5.978 distance: 114 - 115: 4.737 distance: 114 - 116: 9.617 distance: 116 - 118: 9.244 distance: 117 - 119: 7.859 distance: 118 - 119: 8.879 distance: 119 - 120: 3.114