Starting phenix.real_space_refine on Sun Aug 24 06:28:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pvq_20497/08_2025/6pvq_20497.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pvq_20497/08_2025/6pvq_20497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pvq_20497/08_2025/6pvq_20497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pvq_20497/08_2025/6pvq_20497.map" model { file = "/net/cci-nas-00/data/ceres_data/6pvq_20497/08_2025/6pvq_20497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pvq_20497/08_2025/6pvq_20497.cif" } resolution = 4.75 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 11348 2.51 5 N 2996 2.21 5 O 3196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17640 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4581 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 540} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 4239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4239 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 503} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4581 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 540} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 4239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4239 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 503} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 3.22, per 1000 atoms: 0.18 Number of scatterers: 17640 At special positions: 0 Unit cell: (138.86, 147.34, 129.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3196 8.00 N 2996 7.00 C 11348 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: 1.06 Conformation dependent library (CDL) restraints added in 636.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4156 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 4 sheets defined 56.3% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 116 through 130 Processing helix chain 'A' and resid 131 through 146 Processing helix chain 'A' and resid 153 through 163 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.789A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.575A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.911A pdb=" N ASN A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.725A pdb=" N GLU A 214 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.972A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.714A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.789A pdb=" N ALA A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.569A pdb=" N ASN A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.948A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 4.388A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 4.181A pdb=" N LEU A 333 " --> pdb=" O ASN A 330 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 334 " --> pdb=" O TRP A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 330 through 334' Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.533A pdb=" N LYS A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.672A pdb=" N ARG A 363 " --> pdb=" O TYR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 374 removed outlier: 3.629A pdb=" N LEU A 370 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N SER A 372 " --> pdb=" O PRO A 369 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 410 removed outlier: 3.543A pdb=" N ILE A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 436 removed outlier: 4.135A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 457 removed outlier: 3.789A pdb=" N PHE A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 482 through 505 removed outlier: 3.970A pdb=" N GLY A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 536 removed outlier: 3.522A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.717A pdb=" N LEU A 541 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 561 removed outlier: 4.054A pdb=" N ALA A 554 " --> pdb=" O CYS A 550 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 556 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 706 removed outlier: 3.543A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.549A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 147 Processing helix chain 'B' and resid 154 through 163 removed outlier: 3.763A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.705A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.662A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.840A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.735A pdb=" N LEU B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.786A pdb=" N ASN B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.913A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.898A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 336 Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.513A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.662A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.964A pdb=" N ARG B 371 " --> pdb=" O LYS B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 4.282A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.790A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 removed outlier: 3.687A pdb=" N SER B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS B 446 " --> pdb=" O PHE B 442 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 455 " --> pdb=" O TYR B 451 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 479 removed outlier: 3.684A pdb=" N LYS B 478 " --> pdb=" O ALA B 474 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 474 through 479' Processing helix chain 'B' and resid 483 through 501 removed outlier: 3.506A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE B 497 " --> pdb=" O TRP B 493 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 542 removed outlier: 4.107A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 530 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.617A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 551 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 706 removed outlier: 3.534A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 130 Processing helix chain 'C' and resid 131 through 146 Processing helix chain 'C' and resid 153 through 163 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.760A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.576A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.906A pdb=" N ASN C 205 " --> pdb=" O ASP C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 214 removed outlier: 3.725A pdb=" N GLU C 214 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.977A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.717A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 removed outlier: 3.890A pdb=" N ALA C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.568A pdb=" N ASN C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.946A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 4.390A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 removed outlier: 4.186A pdb=" N LEU C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU C 334 " --> pdb=" O TRP C 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 330 through 334' Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.524A pdb=" N LYS C 350 " --> pdb=" O GLN C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.515A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 374 removed outlier: 3.615A pdb=" N LEU C 370 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N SER C 372 " --> pdb=" O PRO C 369 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 410 removed outlier: 3.538A pdb=" N ILE C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 422 through 436 removed outlier: 4.131A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 457 removed outlier: 3.789A pdb=" N PHE C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 482 through 505 removed outlier: 3.964A pdb=" N GLY C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 536 removed outlier: 3.524A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 541 removed outlier: 3.724A pdb=" N LEU C 541 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 561 removed outlier: 4.057A pdb=" N ALA C 554 " --> pdb=" O CYS C 550 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA C 556 " --> pdb=" O VAL C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 706 removed outlier: 3.545A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 130 removed outlier: 3.548A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 147 Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.762A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR D 163 " --> pdb=" O MET D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.705A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.662A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.841A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 removed outlier: 3.735A pdb=" N LEU D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.786A pdb=" N ASN D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.909A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 removed outlier: 3.899A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 336 Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.514A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.658A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.964A pdb=" N ARG D 371 " --> pdb=" O LYS D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 removed outlier: 4.281A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.797A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 removed outlier: 3.686A pdb=" N SER D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS D 446 " --> pdb=" O PHE D 442 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE D 447 " --> pdb=" O LEU D 443 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 455 " --> pdb=" O TYR D 451 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 479 removed outlier: 3.686A pdb=" N LYS D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 474 through 479' Processing helix chain 'D' and resid 483 through 501 removed outlier: 3.501A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE D 497 " --> pdb=" O TRP D 493 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER D 498 " --> pdb=" O ALA D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 542 removed outlier: 4.113A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA D 530 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.615A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 551 " --> pdb=" O TYR D 547 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA D 556 " --> pdb=" O VAL D 552 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN D 561 " --> pdb=" O LEU D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 566 Processing helix chain 'D' and resid 688 through 706 removed outlier: 3.535A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AA2, first strand: chain 'B' and resid 381 through 382 Processing sheet with id=AA3, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AA4, first strand: chain 'D' and resid 381 through 382 removed outlier: 3.903A pdb=" N SER D 386 " --> pdb=" O ASN D 735 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN D 735 " --> pdb=" O SER D 386 " (cutoff:3.500A) 649 hydrogen bonds defined for protein. 1899 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: 2.28 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5002 1.33 - 1.45: 3739 1.45 - 1.57: 9123 1.57 - 1.70: 0 1.70 - 1.82: 164 Bond restraints: 18028 Sorted by residual: bond pdb=" C LEU D 469 " pdb=" N PRO D 470 " ideal model delta sigma weight residual 1.333 1.372 -0.039 1.20e-02 6.94e+03 1.07e+01 bond pdb=" C LEU B 469 " pdb=" N PRO B 470 " ideal model delta sigma weight residual 1.333 1.372 -0.039 1.20e-02 6.94e+03 1.04e+01 bond pdb=" N GLU D 257 " pdb=" CA GLU D 257 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.16e+00 bond pdb=" N GLU B 257 " pdb=" CA GLU B 257 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 8.97e+00 bond pdb=" C LEU A 707 " pdb=" N PRO A 708 " ideal model delta sigma weight residual 1.337 1.310 0.026 1.06e-02 8.90e+03 6.22e+00 ... (remaining 18023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 22753 2.31 - 4.63: 1310 4.63 - 6.94: 239 6.94 - 9.25: 69 9.25 - 11.57: 25 Bond angle restraints: 24396 Sorted by residual: angle pdb=" N ASP C 166 " pdb=" CA ASP C 166 " pdb=" C ASP C 166 " ideal model delta sigma weight residual 114.62 106.96 7.66 1.14e+00 7.69e-01 4.52e+01 angle pdb=" N ASP A 166 " pdb=" CA ASP A 166 " pdb=" C ASP A 166 " ideal model delta sigma weight residual 114.62 107.01 7.61 1.14e+00 7.69e-01 4.46e+01 angle pdb=" N ARG D 416 " pdb=" CA ARG D 416 " pdb=" C ARG D 416 " ideal model delta sigma weight residual 112.59 104.88 7.71 1.22e+00 6.72e-01 3.99e+01 angle pdb=" N ARG B 416 " pdb=" CA ARG B 416 " pdb=" C ARG B 416 " ideal model delta sigma weight residual 112.59 104.89 7.70 1.22e+00 6.72e-01 3.98e+01 angle pdb=" N LEU B 730 " pdb=" CA LEU B 730 " pdb=" C LEU B 730 " ideal model delta sigma weight residual 110.91 117.98 -7.07 1.17e+00 7.31e-01 3.65e+01 ... (remaining 24391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 9814 16.14 - 32.27: 817 32.27 - 48.41: 178 48.41 - 64.54: 13 64.54 - 80.68: 24 Dihedral angle restraints: 10846 sinusoidal: 4466 harmonic: 6380 Sorted by residual: dihedral pdb=" CA ARG D 729 " pdb=" C ARG D 729 " pdb=" N LEU D 730 " pdb=" CA LEU D 730 " ideal model delta harmonic sigma weight residual 180.00 136.48 43.52 0 5.00e+00 4.00e-02 7.58e+01 dihedral pdb=" CA ARG B 729 " pdb=" C ARG B 729 " pdb=" N LEU B 730 " pdb=" CA LEU B 730 " ideal model delta harmonic sigma weight residual 180.00 136.54 43.46 0 5.00e+00 4.00e-02 7.56e+01 dihedral pdb=" CA PRO C 89 " pdb=" C PRO C 89 " pdb=" N GLN C 90 " pdb=" CA GLN C 90 " ideal model delta harmonic sigma weight residual -180.00 -140.64 -39.36 0 5.00e+00 4.00e-02 6.20e+01 ... (remaining 10843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2096 0.070 - 0.140: 524 0.140 - 0.210: 93 0.210 - 0.279: 7 0.279 - 0.349: 8 Chirality restraints: 2728 Sorted by residual: chirality pdb=" CB THR A 94 " pdb=" CA THR A 94 " pdb=" OG1 THR A 94 " pdb=" CG2 THR A 94 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CB THR C 94 " pdb=" CA THR C 94 " pdb=" OG1 THR C 94 " pdb=" CG2 THR C 94 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA THR C 94 " pdb=" N THR C 94 " pdb=" C THR C 94 " pdb=" CB THR C 94 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 2725 not shown) Planarity restraints: 3092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 112 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.18e+00 pdb=" C GLN C 112 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN C 112 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG C 113 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 112 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.91e+00 pdb=" C GLN A 112 " 0.052 2.00e-02 2.50e+03 pdb=" O GLN A 112 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG A 113 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 754 " -0.048 5.00e-02 4.00e+02 7.26e-02 8.44e+00 pdb=" N PRO A 755 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 755 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 755 " -0.040 5.00e-02 4.00e+02 ... (remaining 3089 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4067 2.77 - 3.31: 17763 3.31 - 3.84: 28894 3.84 - 4.37: 32948 4.37 - 4.90: 51455 Nonbonded interactions: 135127 Sorted by model distance: nonbonded pdb=" OH TYR D 448 " pdb=" O GLY D 558 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR B 448 " pdb=" O GLY B 558 " model vdw 2.245 3.040 nonbonded pdb=" OD2 ASP D 391 " pdb=" OG1 THR D 393 " model vdw 2.253 3.040 nonbonded pdb=" OD2 ASP B 391 " pdb=" OG1 THR B 393 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP D 379 " pdb=" OG SER D 387 " model vdw 2.257 3.040 ... (remaining 135122 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.780 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 18028 Z= 0.417 Angle : 1.315 11.566 24396 Z= 0.729 Chirality : 0.064 0.349 2728 Planarity : 0.008 0.073 3092 Dihedral : 13.013 80.677 6690 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.37 % Allowed : 14.41 % Favored : 85.21 % Rotamer: Outliers : 1.15 % Allowed : 9.35 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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 aren not related in a simple way. whole: -5.23 (0.13), residues: 2144 helix: -3.14 (0.11), residues: 1018 sheet: -4.38 (0.49), residues: 60 loop : -3.82 (0.16), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG C 714 TYR 0.027 0.003 TYR A 359 PHE 0.043 0.004 PHE A 542 TRP 0.033 0.004 TRP B 692 HIS 0.016 0.003 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00813 (18028) covalent geometry : angle 1.31514 (24396) hydrogen bonds : bond 0.30611 ( 649) hydrogen bonds : angle 9.44966 ( 1899) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7805 (p0) cc_final: 0.7389 (t0) REVERT: A 156 ASP cc_start: 0.8870 (p0) cc_final: 0.8521 (p0) REVERT: A 187 VAL cc_start: 0.9716 (t) cc_final: 0.9480 (p) REVERT: A 293 ASP cc_start: 0.8454 (t70) cc_final: 0.8067 (t70) REVERT: A 311 LYS cc_start: 0.8928 (mttt) cc_final: 0.8699 (tptt) REVERT: A 313 GLN cc_start: 0.8884 (mt0) cc_final: 0.8488 (pp30) REVERT: A 350 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8812 (tppt) REVERT: A 353 LYS cc_start: 0.8977 (mmtt) cc_final: 0.8638 (mmmm) REVERT: A 364 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8141 (mm-30) REVERT: A 370 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9267 (mm) REVERT: A 392 LEU cc_start: 0.9190 (tp) cc_final: 0.8930 (tp) REVERT: A 408 VAL cc_start: 0.9148 (t) cc_final: 0.8948 (t) REVERT: A 417 HIS cc_start: 0.8274 (p-80) cc_final: 0.7789 (p-80) REVERT: A 436 PHE cc_start: 0.8630 (p90) cc_final: 0.8343 (p90) REVERT: A 440 MET cc_start: 0.7454 (mmm) cc_final: 0.7166 (mmt) REVERT: A 730 LEU cc_start: 0.8229 (mp) cc_final: 0.7805 (mp) outliers start: 4 outliers final: 0 residues processed: 143 average time/residue: 0.0789 time to fit residues: 13.5323 Evaluate side-chains 92 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.179 Evaluate side-chains 128 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7923 (mmp80) REVERT: B 146 CYS cc_start: 0.9158 (t) cc_final: 0.8936 (p) REVERT: B 158 LEU cc_start: 0.9710 (tp) cc_final: 0.9319 (mt) REVERT: B 174 LYS cc_start: 0.9171 (tptt) cc_final: 0.8279 (mptt) REVERT: B 193 PHE cc_start: 0.8671 (t80) cc_final: 0.8150 (t80) REVERT: B 213 TYR cc_start: 0.8836 (p90) cc_final: 0.8150 (p90) REVERT: B 220 ASN cc_start: 0.8880 (t160) cc_final: 0.8597 (t0) REVERT: B 298 ASN cc_start: 0.9073 (p0) cc_final: 0.8299 (p0) REVERT: B 301 HIS cc_start: 0.8827 (m-70) cc_final: 0.8098 (m-70) REVERT: B 351 MET cc_start: 0.8857 (mmm) cc_final: 0.8202 (mmm) REVERT: B 416 ARG cc_start: 0.7940 (mmt180) cc_final: 0.7585 (mmt180) REVERT: B 425 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8433 (tm) REVERT: B 440 MET cc_start: 0.8545 (mmt) cc_final: 0.7735 (mmt) REVERT: B 488 MET cc_start: -0.0015 (tpp) cc_final: -0.0289 (ppp) REVERT: B 698 ARG cc_start: 0.8943 (tpt90) cc_final: 0.8581 (tpt90) REVERT: B 701 LEU cc_start: 0.9443 (mt) cc_final: 0.9177 (mp) REVERT: B 703 PHE cc_start: 0.9080 (m-80) cc_final: 0.8807 (t80) REVERT: B 731 CYS cc_start: 0.8382 (p) cc_final: 0.6621 (p) outliers start: 7 outliers final: 1 residues processed: 126 average time/residue: 0.0875 time to fit residues: 13.0523 Evaluate side-chains 77 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 205 ASN C 242 ASN C 244 HIS Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 HIS B 251 ASN B 301 HIS B 401 ASN B 417 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.094151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.062915 restraints weight = 18298.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.064815 restraints weight = 12438.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.066167 restraints weight = 9429.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.067147 restraints weight = 7695.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.067705 restraints weight = 6626.452| |-----------------------------------------------------------------------------| r_work (final): 0.3109 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.099250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.065732 restraints weight = 17022.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.067448 restraints weight = 11808.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.068609 restraints weight = 9203.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.069581 restraints weight = 7732.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.070087 restraints weight = 6797.621| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18028 Z= 0.198 Angle : 0.814 13.630 24396 Z= 0.425 Chirality : 0.046 0.204 2728 Planarity : 0.006 0.064 3092 Dihedral : 6.994 39.713 2360 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.71 % Favored : 86.19 % Rotamer: Outliers : 0.42 % Allowed : 3.66 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -3.87 (0.15), residues: 2144 helix: -1.54 (0.13), residues: 1154 sheet: -4.29 (0.50), residues: 52 loop : -3.87 (0.17), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 712 TYR 0.023 0.002 TYR C 359 PHE 0.024 0.002 PHE A 542 TRP 0.020 0.002 TRP B 739 HIS 0.006 0.001 HIS C 745 Details of bonding type rmsd covalent geometry : bond 0.00418 (18028) covalent geometry : angle 0.81432 (24396) hydrogen bonds : bond 0.04944 ( 649) hydrogen bonds : angle 5.18694 ( 1899) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASN cc_start: 0.7784 (p0) cc_final: 0.7538 (p0) REVERT: C 139 LEU cc_start: 0.9641 (mm) cc_final: 0.9375 (pp) REVERT: C 156 ASP cc_start: 0.8773 (p0) cc_final: 0.8567 (p0) REVERT: C 159 MET cc_start: 0.9179 (mmt) cc_final: 0.8538 (mtp) REVERT: C 199 ILE cc_start: 0.7717 (tp) cc_final: 0.6303 (tp) REVERT: C 268 LEU cc_start: 0.9406 (tp) cc_final: 0.9170 (tp) REVERT: C 284 ASN cc_start: 0.8794 (t0) cc_final: 0.8536 (t0) REVERT: C 314 ASN cc_start: 0.8656 (m-40) cc_final: 0.8414 (p0) REVERT: C 320 MET cc_start: 0.9534 (tpp) cc_final: 0.9298 (mmt) REVERT: C 404 LEU cc_start: 0.9497 (mm) cc_final: 0.9059 (mt) REVERT: C 417 HIS cc_start: 0.8592 (p-80) cc_final: 0.8079 (p-80) REVERT: C 419 MET cc_start: 0.8431 (mtm) cc_final: 0.7828 (mtt) REVERT: C 436 PHE cc_start: 0.8731 (p90) cc_final: 0.8463 (p90) REVERT: C 440 MET cc_start: 0.7613 (mmm) cc_final: 0.7300 (mmt) REVERT: C 740 THR cc_start: 0.7120 (OUTLIER) cc_final: 0.6853 (t) outliers start: 2 outliers final: 0 residues processed: 110 average time/residue: 0.0758 time to fit residues: 10.3353 Evaluate side-chains 67 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.175 Evaluate side-chains 88 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 CYS cc_start: 0.9136 (t) cc_final: 0.8877 (p) REVERT: B 174 LYS cc_start: 0.9444 (tptt) cc_final: 0.8865 (tppt) REVERT: B 178 ASN cc_start: 0.9079 (t0) cc_final: 0.8742 (p0) REVERT: B 213 TYR cc_start: 0.8650 (p90) cc_final: 0.8253 (p90) REVERT: B 256 HIS cc_start: 0.8863 (m90) cc_final: 0.8449 (m90) REVERT: B 351 MET cc_start: 0.9160 (mmm) cc_final: 0.8740 (mmm) REVERT: B 419 MET cc_start: 0.8742 (mtt) cc_final: 0.8531 (mmm) REVERT: B 440 MET cc_start: 0.7883 (mmt) cc_final: 0.7261 (mmt) REVERT: B 695 GLN cc_start: 0.8903 (mt0) cc_final: 0.8609 (mm110) outliers start: 2 outliers final: 0 residues processed: 87 average time/residue: 0.0722 time to fit residues: 7.7401 Evaluate side-chains 65 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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: 66.8607 > 50: distance: 0 - 1: 43.019 distance: 1 - 2: 23.005 distance: 1 - 4: 35.383 distance: 2 - 3: 48.766 distance: 2 - 14: 48.550 distance: 4 - 5: 13.993 distance: 5 - 6: 8.551 distance: 5 - 7: 9.363 distance: 7 - 9: 19.678 distance: 7 - 10: 7.543 distance: 8 - 9: 20.454 distance: 9 - 11: 27.666 distance: 10 - 12: 4.975 distance: 11 - 13: 13.986 distance: 12 - 13: 5.620 distance: 14 - 15: 37.588 distance: 15 - 16: 46.868 distance: 15 - 18: 32.739 distance: 16 - 17: 36.236 distance: 16 - 23: 10.103 distance: 18 - 19: 49.725 distance: 19 - 20: 24.113 distance: 20 - 21: 3.630 distance: 21 - 22: 3.353 distance: 23 - 24: 9.343 distance: 24 - 25: 28.383 distance: 24 - 27: 34.807 distance: 25 - 26: 43.696 distance: 25 - 32: 39.338 distance: 27 - 28: 30.609 distance: 28 - 29: 25.858 distance: 29 - 30: 5.729 distance: 30 - 31: 3.356 distance: 32 - 33: 48.932 distance: 33 - 34: 45.255 distance: 33 - 36: 23.335 distance: 34 - 35: 41.578 distance: 34 - 43: 40.901 distance: 35 - 69: 53.836 distance: 36 - 37: 10.193 distance: 37 - 38: 14.078 distance: 37 - 39: 27.529 distance: 38 - 40: 23.768 distance: 39 - 41: 44.205 distance: 40 - 42: 8.724 distance: 41 - 42: 30.237 distance: 43 - 44: 29.600 distance: 44 - 45: 38.149 distance: 44 - 47: 53.313 distance: 45 - 46: 53.527 distance: 45 - 48: 46.561 distance: 46 - 77: 62.806 distance: 48 - 49: 23.087 distance: 49 - 50: 26.366 distance: 49 - 52: 44.345 distance: 50 - 51: 40.826 distance: 50 - 57: 24.006 distance: 52 - 53: 51.373 distance: 53 - 54: 51.166 distance: 54 - 55: 23.960 distance: 55 - 56: 8.206 distance: 57 - 58: 33.336 distance: 58 - 59: 51.656 distance: 58 - 61: 37.152 distance: 59 - 60: 39.658 distance: 59 - 69: 61.030 distance: 61 - 62: 46.328 distance: 62 - 63: 13.852 distance: 62 - 64: 17.494 distance: 63 - 65: 27.954 distance: 64 - 66: 37.176 distance: 66 - 67: 7.406 distance: 67 - 68: 12.991 distance: 69 - 70: 10.640 distance: 70 - 71: 50.704 distance: 70 - 73: 40.635 distance: 71 - 72: 56.606 distance: 71 - 77: 29.484 distance: 73 - 74: 47.410 distance: 74 - 75: 22.985 distance: 75 - 76: 5.333 distance: 77 - 78: 46.448 distance: 78 - 79: 29.670 distance: 78 - 81: 28.268 distance: 79 - 80: 15.404 distance: 79 - 88: 15.009 distance: 81 - 82: 24.945 distance: 82 - 83: 6.834 distance: 82 - 84: 10.466 distance: 83 - 85: 19.770 distance: 84 - 86: 46.281 distance: 85 - 87: 34.192 distance: 86 - 87: 52.993 distance: 88 - 89: 10.811 distance: 89 - 90: 3.933 distance: 90 - 91: 3.910 distance: 92 - 93: 5.706 distance: 93 - 94: 3.652 distance: 93 - 95: 3.017 distance: 94 - 96: 9.003 distance: 95 - 97: 3.173