core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: command: /home/a1love/rosetta_src_2021.16.61629_bundle/main/source/bin/match.linuxgccrelease -extra_res_fa ./FAD.params -extra_res_fa ./LCA.params -match:geometric_constraint_file ./ACL_CBGA_CST_2.cst -match:lig_name FAD -match:lig_name LCA -match:scaffold_active_site_residues_for_geomcsts /home/a1love/Projects/clz_tcz/input/CBGA_docking/ACL_pos.pos -out:path:all /home/a1love/Projects/clz_tcz/output/RosettaDock/CBGA_docking -s ./tcz_af_no_flavin_rlx_0001.pdb @general_match.flags basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1065699182 seed_offset=0 real_seed=1065699182 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1065699182 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch N_acetylated as requested core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 986 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.91 seconds. core.import_pose.import_pose: File './tcz_af_no_flavin_rlx_0001.pdb' automatically determined to be of type PDB apps.public.match.match: Selecting orientation atoms: C6 C5 C18 protocols.match.MatcherTask: [ WARNING ] no grid file specified for option -grid_boundary. The bounding grid will be generated from the dimensions of the pose. This is experimental at the moment. protocols.match.MatcherTask: Bounding box lower corner set to (-24.661,-10.892,18.503), upper corner set to to (44.555,42.204,64.674). protocols.toolbox.match_enzdes_util.EnzConstraintIO: read enzyme constraints from ./ACL_CBGA_CST_2.cst ... done, 2 cst blocks were read. protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst: Reading match::scaffold_active_site_residues_for_geomcsts /home/a1love/Projects/clz_tcz/input/CBGA_docking/ACL_pos.pos protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst: protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst: 1 : 67 protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst: 2 :All pose positions requested, using 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 protocols.BumpGrid: Atom type CNH2 with ProbeRadius 5 = 1.65 protocols.BumpGrid: Atom type COO with ProbeRadius 5 = 1.65 protocols.BumpGrid: Atom type CH0 with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type CH1 with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type CH2 with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type CH3 with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type aroC with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type Ntrp with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Nhis with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type NtrR with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type NH2O with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Nlys with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Narg with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Npro with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type OH with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type OW with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type ONH2 with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type OOC with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Oaro with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Oet2 with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Oet3 with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type S with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type SH1 with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Nbb with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type CAbb with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type CObb with ProbeRadius 5 = 1.65 protocols.BumpGrid: Atom type OCbb with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Phos with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Pbb with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Hpol with ProbeRadius 1 = 1 protocols.BumpGrid: Atom type HS with ProbeRadius 1 = 1 protocols.BumpGrid: Atom type Hapo with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Haro with ProbeRadius 1 = 1 protocols.BumpGrid: Atom type HNbb with ProbeRadius 1 = 1 protocols.BumpGrid: Atom type Hwat with ProbeRadius 1 = 1 protocols.BumpGrid: Atom type Owat with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Opoint with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type HOH with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Bsp2 with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type F with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Cl with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type Br with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type I with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Zn2p with ProbeRadius 0 = 0 protocols.BumpGrid: Atom type Co2p with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Cu2p with ProbeRadius 0 = 0 protocols.BumpGrid: Atom type Fe2p with ProbeRadius 0 = 0 protocols.BumpGrid: Atom type Fe3p with ProbeRadius 0 = 0 protocols.BumpGrid: Atom type Mg2p with ProbeRadius 1 = 1 protocols.BumpGrid: Atom type Ca2p with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Pha with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type OPha with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type OHha with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Hha with ProbeRadius 1 = 1 protocols.BumpGrid: Atom type CO3 with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type OC3 with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Si with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type OSi with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Oice with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Hice with ProbeRadius 1 = 1 protocols.BumpGrid: Atom type Na1p with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type K1p with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type He with ProbeRadius 1 = 1 protocols.BumpGrid: Atom type Li with ProbeRadius 1 = 1 protocols.BumpGrid: Atom type Be with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Ne with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Al with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Ar with ProbeRadius 5 = 1.65 protocols.BumpGrid: Atom type Sc with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Ti with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type V with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Cr with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Mn with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Ni with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Ga with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Ge with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type As with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Se with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Kr with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type Rb with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type Sr with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Y with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Zr with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Nb with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Mo with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Tc with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Ru with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Rh with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Pd with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Ag with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Cd with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type In with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Sn with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Sb with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Te with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Xe with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Cs with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Ba with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type La with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Ce with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Pr with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Nd with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Pm with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Sm with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Eu with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Gd with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Tb with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Dy with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Ho with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Er with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Tm with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Yb with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Lu with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Hf with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Ta with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type W with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Re with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Os with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Ir with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Pt with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Au with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Hg with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Tl with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Pb with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Bi with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Po with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type At with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Rn with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Fr with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Ra with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Ac with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Th with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Pa with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type U with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Np with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Pu with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Am with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Cm with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Bk with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Cf with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Es with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Fm with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Md with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type No with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Lr with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type SUCK with ProbeRadius 0 = 0 protocols.BumpGrid: Atom type REPL with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type REPLS with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type HREPS with ProbeRadius 0 = 0 protocols.BumpGrid: Atom type VIRT with ProbeRadius 0 = 0 protocols.BumpGrid: Atom type MPct with ProbeRadius 0 = 0 protocols.BumpGrid: Atom type MPnm with ProbeRadius 0 = 0 protocols.BumpGrid: Atom type MPdp with ProbeRadius 0 = 0 protocols.BumpGrid: Atom type MPtk with ProbeRadius 0 = 0 protocols.match.Matcher: Set occupied space bounding box: Lower (-24.661, -10.892, 18.503) Upper (44.555, 42.204, 64.674) protocols.match.Matcher: Matcher::initialize_from_file: n geometric constraints: 2 protocols.match.Matcher: Begin constraint1 protocols.match.Matcher: Upstream residue type HIS for geometric constraint #1 protocols.match.Matcher: Did not locate ALGORITHM_INFO:: match for constraint 1 protocols.match.Matcher: HIS FAD protocols.match.Matcher: U3: CD2 U2: CG U1: ND1 D1: C8M D2: C8 D3: C9 protocols.match.Matcher: Adding Classical Match Algorithm with geometry samples: protocols.match.Matcher: tor_U3D1: 84 94 104 protocols.match.Matcher: ang_U2D1: 82.1 92.1 102.1 protocols.match.Matcher: dis_U1D1: 1.1 1.6 2.1 protocols.match.Matcher: tor_U2D2: 240.3 250.3 260.3 protocols.match.Matcher: ang_U1D2: 115.2 125.2 135.2 protocols.match.Matcher: tor_U1D3: 353.3 3.3 13.3 protocols.match.downstream.LigandConformerBuilder: Initializing from residue LCA protocols.match.downstream.LigandConformerBuilder: No ligand rotamer library found, matching with geometry specified form .params file. protocols.match.downstream.LigandConformerBuilder: Ligand conformers were split up into 1 match-redundant groups. protocols.match.Matcher: Upstream residue type HIS_D for geometric constraint #1 protocols.match.Matcher: Did not locate ALGORITHM_INFO:: match for constraint 1 protocols.match.Matcher: HIS_D FAD protocols.match.Matcher: U3: ND1 U2: CE1 U1: NE2 D1: C8M D2: C8 D3: C9 protocols.match.Matcher: Adding Classical Match Algorithm with geometry samples: protocols.match.Matcher: tor_U3D1: 84 94 104 protocols.match.Matcher: ang_U2D1: 82.1 92.1 102.1 protocols.match.Matcher: dis_U1D1: 1.1 1.6 2.1 protocols.match.Matcher: tor_U2D2: 240.3 250.3 260.3 protocols.match.Matcher: ang_U1D2: 115.2 125.2 135.2 protocols.match.Matcher: tor_U1D3: 353.3 3.3 13.3 protocols.match.downstream.LigandConformerBuilder: Initializing from residue LCA protocols.match.downstream.LigandConformerBuilder: No ligand rotamer library found, matching with geometry specified form .params file. protocols.match.downstream.LigandConformerBuilder: Ligand conformers were split up into 1 match-redundant groups. protocols.match.Matcher: Begin constraint2 protocols.match.Matcher: Upstream residue type FAD for geometric constraint #2 protocols.match.Matcher: FAD LCA protocols.match.Matcher: U3: C6 U2: C5X U1: N5 D1: C8 D2: C17 D3: C12 protocols.match.output.ProcessorFactory: Matches will be consolidated before output. Created UpstreamCollisionFilter Created UpstreamDownstreamCollisionFilter protocols.match.Matcher: Initializing BumpGrids... protocols.match.Matcher: ...done protocols.match.Matcher: TIMING: Bump grids took 7.54 seconds to compute core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/a1love/rosetta_src_2021.16.61629_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/a1love/rosetta_src_2021.16.61629_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.16 seconds to load from binary protocols.match.upstream.ProteinUpstreamBuilder: Considered 250047 downstream conformations at residue 67 and found 799 hits. protocols.match.downstream.ClassicMatchAlgorithm: Finished round 1 with 799 hits. protocols.match.downstream.SecondaryMatcherToDownstreamResidue: Preparing for hit generation protocols.match.downstream.SecondaryMatcherToDownstreamResidue: Preparing to examine geomcst-1's hits built from scaffold build point 67 protocols.match.downstream.SecondaryMatcherToDownstreamResidue: Examining 799 hits built from scaffold build point 67 representing 799 unique upstream rotamers protocols.match.downstream.SecondaryMatcherToDownstreamResidue: Secondary matching against geomcst 1 hits from build point 67