Starting phenix.real_space_refine on Sat Sep 12 18:49:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pvq_20497/09_2026/6pvq_20497.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pvq_20497/09_2026/6pvq_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_20497/09_2026/6pvq_20497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pvq_20497/09_2026/6pvq_20497.map" model { file = "/net/cci-nas-00/data/ceres_data/6pvq_20497/09_2026/6pvq_20497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pvq_20497/09_2026/6pvq_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 4.06, per 1000 atoms: 0.23 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: 1.99 Conformation dependent library (CDL) restraints added in 791.6 milliseconds 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: 0.49 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: 2.60 Time building geometry restraints manager: 2.47 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: 0.04 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.150 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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 are 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/Z covalent geometry : bond 0.00813 / 0.42 (18028) covalent geometry : angle 1.31514 / 0.73 (24396) hydrogen bonds : bond 0.30611 / 20.14 ( 649) hydrogen bonds : angle 9.44966 / 6.52 ( 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 : 0.195 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: 0.8637 (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: 0.7804 (mp) outliers start: 4 outliers final: 0 residues processed: 143 average time/residue: 0.0901 time to fit residues: 15.7297 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 : 0.174 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 : 0.163 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: 0.8434 (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: 0.9178 (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: 0.0968 time to fit residues: 14.5074 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 : 0.183 ------------------------------------------------------------------------------- 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... A 205 ASN A 242 ASN A 244 HIS B 244 HIS B 251 ASN B 301 HIS B 401 ASN B 417 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.094071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.062846 restraints weight = 18309.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.064745 restraints weight = 12416.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.066054 restraints weight = 9409.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.066895 restraints weight = 7714.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.067569 restraints weight = 6704.880| |-----------------------------------------------------------------------------| r_work (final): 0.3105 |-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: 0.7647 moved from start: 0.3736 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 : 12.40 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 are 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/Z covalent geometry : bond 0.00418 / 0.20 (18028) covalent geometry : angle 0.81432 / 0.43 (24396) hydrogen bonds : bond 0.04944 / 3.29 ( 649) hydrogen bonds : angle 5.18694 / 3.63 ( 1899) *********************** REFINEMENT MACRO_CYCLE 2 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 109 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASN cc_start: 0.7786 (p0) cc_final: 0.7544 (p0) REVERT: C 139 LEU cc_start: 0.9640 (mm) cc_final: 0.9376 (pp) REVERT: C 156 ASP cc_start: 0.8772 (p0) cc_final: 0.8567 (p0) REVERT: C 159 MET cc_start: 0.9181 (mmt) cc_final: 0.8544 (mtp) REVERT: C 199 ILE cc_start: 0.7709 (tp) cc_final: 0.6289 (tp) REVERT: C 268 LEU cc_start: 0.9403 (tp) cc_final: 0.9176 (tp) REVERT: C 284 ASN cc_start: 0.8792 (t0) cc_final: 0.8523 (t0) REVERT: C 320 MET cc_start: 0.9538 (tpp) cc_final: 0.9294 (mmt) REVERT: C 404 LEU cc_start: 0.9496 (mm) cc_final: 0.9059 (mt) REVERT: C 417 HIS cc_start: 0.8590 (p-80) cc_final: 0.8078 (p-80) REVERT: C 419 MET cc_start: 0.8432 (mtm) cc_final: 0.7830 (mtt) REVERT: C 436 PHE cc_start: 0.8734 (p90) cc_final: 0.8467 (p90) REVERT: C 440 MET cc_start: 0.7613 (mmm) cc_final: 0.7303 (mmt) REVERT: C 740 THR cc_start: 0.7120 (OUTLIER) cc_final: 0.6853 (t) outliers start: 2 outliers final: 0 residues processed: 108 average time/residue: 0.0733 time to fit residues: 9.9128 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 : 0.189 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 : 0.157 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: 0.8530 (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: 0.0729 time to fit residues: 7.9383 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 : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 138 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 167 optimal weight: 0.0170 chunk 147 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 313 GLN C 205 ASN C 242 ASN C 244 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.094812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.063323 restraints weight = 18008.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.065140 restraints weight = 12392.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.066322 restraints weight = 9458.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.067355 restraints weight = 7828.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.067923 restraints weight = 6791.246| |-----------------------------------------------------------------------------| r_work (final): 0.3101 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.099627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.065929 restraints weight = 16338.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.067720 restraints weight = 11010.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.068936 restraints weight = 8422.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.069931 restraints weight = 6983.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.070528 restraints weight = 6101.252| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18028 Z= 0.151 Angle : 0.756 12.047 24396 Z= 0.387 Chirality : 0.044 0.285 2728 Planarity : 0.005 0.074 3092 Dihedral : 6.411 37.201 2360 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.78 % Favored : 86.94 % Rotamer: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.26 (0.16), residues: 2144 helix: -0.78 (0.14), residues: 1136 sheet: -4.17 (0.50), residues: 62 loop : -3.90 (0.17), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 122 TYR 0.019 0.001 TYR A 359 PHE 0.018 0.001 PHE A 542 TRP 0.012 0.002 TRP D 521 HIS 0.005 0.001 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (18028) covalent geometry : angle 0.75565 / 0.39 (24396) hydrogen bonds : bond 0.04286 / 2.86 ( 649) hydrogen bonds : angle 4.81451 / 3.41 ( 1899) *********************** REFINEMENT MACRO_CYCLE 3 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 87 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7954 (p0) cc_final: 0.7698 (p0) REVERT: A 159 MET cc_start: 0.9175 (mmt) cc_final: 0.8640 (mtp) REVERT: A 320 MET cc_start: 0.9440 (tpp) cc_final: 0.9183 (mmt) REVERT: A 351 MET cc_start: 0.9445 (mmm) cc_final: 0.9223 (mmm) REVERT: A 401 ASN cc_start: 0.8568 (t0) cc_final: 0.8345 (t0) REVERT: A 404 LEU cc_start: 0.9563 (mm) cc_final: 0.9010 (mt) REVERT: A 405 GLU cc_start: 0.8530 (pt0) cc_final: 0.8199 (pp20) REVERT: A 417 HIS cc_start: 0.8552 (p-80) cc_final: 0.8074 (p-80) REVERT: A 419 MET cc_start: 0.8429 (mtm) cc_final: 0.7908 (mtt) REVERT: A 436 PHE cc_start: 0.8665 (p90) cc_final: 0.8323 (p90) REVERT: A 440 MET cc_start: 0.7631 (mmm) cc_final: 0.7291 (mmt) REVERT: A 694 LEU cc_start: 0.9470 (mp) cc_final: 0.9076 (pp) REVERT: A 730 LEU cc_start: 0.8238 (mp) cc_final: 0.7899 (mp) REVERT: A 740 THR cc_start: 0.7014 (p) cc_final: 0.6566 (t) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0767 time to fit residues: 8.4664 Evaluate side-chains 67 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.259 Evaluate side-chains 86 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.167 Fit side-chains REVERT: D 174 LYS cc_start: 0.9417 (tptt) cc_final: 0.8806 (mptt) REVERT: D 178 ASN cc_start: 0.9126 (t0) cc_final: 0.8829 (p0) REVERT: D 213 TYR cc_start: 0.8471 (p90) cc_final: 0.8251 (p90) REVERT: D 256 HIS cc_start: 0.8796 (m90) cc_final: 0.8428 (m90) REVERT: D 351 MET cc_start: 0.9310 (mmm) cc_final: 0.9023 (mmm) REVERT: D 417 HIS cc_start: 0.8191 (p-80) cc_final: 0.7966 (p-80) REVERT: D 440 MET cc_start: 0.8031 (mmt) cc_final: 0.7651 (mmt) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.0718 time to fit residues: 7.8230 Evaluate side-chains 62 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 124 optimal weight: 9.9990 chunk 23 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 132 optimal weight: 0.0570 chunk 72 optimal weight: 2.9990 overall best weight: 1.2504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN A 452 ASN D 143 GLN D 313 GLN D 523 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 = 0.3655 r_free = 0.3655 target = 0.097370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.064822 restraints weight = 17755.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.066648 restraints weight = 12259.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.068159 restraints weight = 9382.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.069135 restraints weight = 7706.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.069768 restraints weight = 6695.746| |-----------------------------------------------------------------------------| r_work (final): 0.3133 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.101298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.066955 restraints weight = 16608.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.068947 restraints weight = 10997.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.070368 restraints weight = 8254.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.071280 restraints weight = 6755.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.072028 restraints weight = 5877.089| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18028 Z= 0.125 Angle : 0.707 9.217 24396 Z= 0.364 Chirality : 0.043 0.365 2728 Planarity : 0.005 0.061 3092 Dihedral : 5.913 37.239 2360 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.25 % Favored : 86.57 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.89 (0.17), residues: 2144 helix: -0.37 (0.15), residues: 1134 sheet: -4.22 (0.47), residues: 62 loop : -3.85 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 319 TYR 0.017 0.001 TYR A 359 PHE 0.034 0.001 PHE B 193 TRP 0.010 0.001 TRP B 742 HIS 0.004 0.001 HIS D 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (18028) covalent geometry : angle 0.70652 / 0.36 (24396) hydrogen bonds : bond 0.03622 / 2.42 ( 649) hydrogen bonds : angle 4.42880 / 3.12 ( 1899) *********************** REFINEMENT MACRO_CYCLE 4 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 93 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8103 (p0) cc_final: 0.7875 (p0) REVERT: A 159 MET cc_start: 0.9114 (mmt) cc_final: 0.8569 (mtt) REVERT: A 268 LEU cc_start: 0.9570 (tp) cc_final: 0.9242 (tp) REVERT: A 320 MET cc_start: 0.9309 (tpp) cc_final: 0.8950 (mmt) REVERT: A 401 ASN cc_start: 0.8529 (t0) cc_final: 0.8329 (t0) REVERT: A 404 LEU cc_start: 0.9543 (mm) cc_final: 0.9321 (mt) REVERT: A 405 GLU cc_start: 0.8341 (pt0) cc_final: 0.7987 (pp20) REVERT: A 417 HIS cc_start: 0.8616 (p-80) cc_final: 0.8153 (p-80) REVERT: A 419 MET cc_start: 0.8447 (mtm) cc_final: 0.7902 (mtt) REVERT: A 440 MET cc_start: 0.7767 (mmm) cc_final: 0.7554 (mmt) REVERT: A 694 LEU cc_start: 0.9505 (mp) cc_final: 0.9103 (pp) REVERT: A 729 ARG cc_start: 0.8304 (mpt180) cc_final: 0.7813 (mpt180) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0583 time to fit residues: 6.9940 Evaluate side-chains 64 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.175 Evaluate side-chains 89 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: D 178 ASN cc_start: 0.9107 (t0) cc_final: 0.8814 (p0) REVERT: D 255 GLN cc_start: 0.8501 (mp10) cc_final: 0.7809 (tt0) REVERT: D 256 HIS cc_start: 0.8711 (m90) cc_final: 0.8281 (m90) REVERT: D 351 MET cc_start: 0.9289 (mmm) cc_final: 0.9023 (mmm) REVERT: D 408 VAL cc_start: 0.8834 (t) cc_final: 0.8504 (t) REVERT: D 416 ARG cc_start: 0.7085 (mmt180) cc_final: 0.4933 (mmp-170) REVERT: D 417 HIS cc_start: 0.8122 (p-80) cc_final: 0.7885 (p-80) REVERT: D 419 MET cc_start: 0.9142 (tpp) cc_final: 0.8286 (mmm) REVERT: D 440 MET cc_start: 0.8029 (mmt) cc_final: 0.7660 (mmm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0626 time to fit residues: 7.1931 Evaluate side-chains 62 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 73 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 78 optimal weight: 0.0980 chunk 177 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 32 optimal weight: 0.0670 chunk 162 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.098196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.065633 restraints weight = 17720.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.067620 restraints weight = 11938.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.069044 restraints weight = 8991.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.069992 restraints weight = 7341.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.070569 restraints weight = 6401.538| |-----------------------------------------------------------------------------| r_work (final): 0.3144 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.100607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.068824 restraints weight = 15855.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.070718 restraints weight = 10482.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.072261 restraints weight = 7897.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.073223 restraints weight = 6357.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.073955 restraints weight = 5462.185| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18028 Z= 0.116 Angle : 0.689 9.694 24396 Z= 0.352 Chirality : 0.043 0.256 2728 Planarity : 0.004 0.061 3092 Dihedral : 5.677 37.078 2360 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.13 % Favored : 87.78 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.55 (0.17), residues: 2144 helix: -0.03 (0.15), residues: 1130 sheet: -4.17 (0.46), residues: 62 loop : -3.76 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 733 TYR 0.016 0.001 TYR A 359 PHE 0.016 0.001 PHE A 249 TRP 0.026 0.001 TRP B 742 HIS 0.003 0.001 HIS A 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (18028) covalent geometry : angle 0.68873 / 0.35 (24396) hydrogen bonds : bond 0.03304 / 2.22 ( 649) hydrogen bonds : angle 4.11712 / 2.89 ( 1899) *********************** REFINEMENT MACRO_CYCLE 5 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 88 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.9085 (mmt) cc_final: 0.8545 (mtt) REVERT: A 268 LEU cc_start: 0.9551 (tp) cc_final: 0.9229 (tp) REVERT: A 320 MET cc_start: 0.9301 (tpp) cc_final: 0.8903 (mmt) REVERT: A 401 ASN cc_start: 0.8635 (t0) cc_final: 0.8415 (t0) REVERT: A 404 LEU cc_start: 0.9544 (mm) cc_final: 0.9271 (mt) REVERT: A 405 GLU cc_start: 0.8429 (pt0) cc_final: 0.8038 (pp20) REVERT: A 417 HIS cc_start: 0.8720 (p-80) cc_final: 0.8245 (p-80) REVERT: A 419 MET cc_start: 0.8483 (mtm) cc_final: 0.8009 (mtt) REVERT: A 436 PHE cc_start: 0.8567 (p90) cc_final: 0.8354 (p90) REVERT: A 694 LEU cc_start: 0.9500 (mp) cc_final: 0.9111 (pp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0609 time to fit residues: 7.1284 Evaluate side-chains 68 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.179 Evaluate side-chains 88 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 178 ASN cc_start: 0.9065 (t0) cc_final: 0.8824 (p0) REVERT: D 201 ASP cc_start: 0.8530 (p0) cc_final: 0.7947 (m-30) REVERT: D 255 GLN cc_start: 0.8388 (mp10) cc_final: 0.7753 (tt0) REVERT: D 256 HIS cc_start: 0.8612 (m90) cc_final: 0.8230 (m90) REVERT: D 351 MET cc_start: 0.9347 (mmm) cc_final: 0.9047 (mmm) REVERT: D 408 VAL cc_start: 0.8866 (t) cc_final: 0.8592 (t) REVERT: D 416 ARG cc_start: 0.6875 (mmt180) cc_final: 0.4778 (mmp-170) REVERT: D 417 HIS cc_start: 0.7965 (p-80) cc_final: 0.7720 (p-80) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0684 time to fit residues: 7.6441 Evaluate side-chains 63 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 181 optimal weight: 0.0570 chunk 77 optimal weight: 0.0070 chunk 50 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 198 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 37 optimal weight: 0.0570 chunk 159 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 overall best weight: 1.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN A 256 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.098530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.066422 restraints weight = 17387.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.068365 restraints weight = 11766.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.069750 restraints weight = 8963.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.070836 restraints weight = 7362.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.071451 restraints weight = 6370.403| |-----------------------------------------------------------------------------| r_work (final): 0.3164 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.101435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.067875 restraints weight = 16424.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.069712 restraints weight = 11258.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.071108 restraints weight = 8606.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.072112 restraints weight = 7128.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.072664 restraints weight = 6205.117| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18028 Z= 0.124 Angle : 0.692 9.293 24396 Z= 0.355 Chirality : 0.042 0.173 2728 Planarity : 0.005 0.073 3092 Dihedral : 5.576 36.611 2360 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.13 % Favored : 87.78 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.47 (0.17), residues: 2144 helix: 0.05 (0.15), residues: 1126 sheet: -4.05 (0.43), residues: 70 loop : -3.72 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 225 TYR 0.016 0.001 TYR A 359 PHE 0.018 0.001 PHE D 193 TRP 0.021 0.001 TRP B 742 HIS 0.007 0.001 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (18028) covalent geometry : angle 0.69187 / 0.36 (24396) hydrogen bonds : bond 0.03239 / 2.19 ( 649) hydrogen bonds : angle 4.11497 / 2.89 ( 1899) *********************** REFINEMENT MACRO_CYCLE 6 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 90 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.8742 (p0) cc_final: 0.8163 (t0) REVERT: A 159 MET cc_start: 0.8998 (mmt) cc_final: 0.8390 (mtt) REVERT: A 320 MET cc_start: 0.9240 (tpp) cc_final: 0.8843 (mmt) REVERT: A 401 ASN cc_start: 0.8601 (t0) cc_final: 0.8383 (t0) REVERT: A 404 LEU cc_start: 0.9552 (mm) cc_final: 0.9277 (mt) REVERT: A 405 GLU cc_start: 0.8288 (pt0) cc_final: 0.7864 (pp20) REVERT: A 417 HIS cc_start: 0.8671 (p-80) cc_final: 0.8282 (p-80) REVERT: A 419 MET cc_start: 0.8570 (mtm) cc_final: 0.8102 (mtt) REVERT: A 694 LEU cc_start: 0.9517 (mp) cc_final: 0.9138 (pp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.0554 time to fit residues: 6.7994 Evaluate side-chains 68 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.186 Evaluate side-chains 82 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 178 ASN cc_start: 0.9143 (t0) cc_final: 0.8838 (p0) REVERT: D 201 ASP cc_start: 0.8497 (p0) cc_final: 0.7903 (m-30) REVERT: D 255 GLN cc_start: 0.8381 (mp10) cc_final: 0.7733 (tt0) REVERT: D 256 HIS cc_start: 0.8601 (m90) cc_final: 0.8255 (m90) REVERT: D 346 GLN cc_start: 0.9365 (mt0) cc_final: 0.9027 (mt0) REVERT: D 351 MET cc_start: 0.9427 (mmm) cc_final: 0.9185 (mmm) REVERT: D 408 VAL cc_start: 0.8868 (t) cc_final: 0.8495 (t) REVERT: D 416 ARG cc_start: 0.7129 (mmt180) cc_final: 0.4616 (mmp-170) REVERT: D 417 HIS cc_start: 0.8000 (p-80) cc_final: 0.7022 (t70) REVERT: D 729 ARG cc_start: 0.7673 (mmt90) cc_final: 0.7465 (mmt90) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0628 time to fit residues: 6.6898 Evaluate side-chains 64 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 4.9990 chunk 68 optimal weight: 0.0170 chunk 167 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 chunk 67 optimal weight: 0.2980 chunk 154 optimal weight: 5.9990 chunk 157 optimal weight: 0.0980 chunk 129 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 overall best weight: 0.3220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN A 274 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 ASN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.099936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.066673 restraints weight = 17754.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.068701 restraints weight = 11980.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.070124 restraints weight = 9076.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.070985 restraints weight = 7462.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.071726 restraints weight = 6533.090| |-----------------------------------------------------------------------------| r_work (final): 0.3175 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.102761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.069038 restraints weight = 16378.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.070996 restraints weight = 11153.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.072418 restraints weight = 8519.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.073338 restraints weight = 7055.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.074046 restraints weight = 6159.845| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18028 Z= 0.122 Angle : 0.691 8.782 24396 Z= 0.351 Chirality : 0.041 0.163 2728 Planarity : 0.004 0.062 3092 Dihedral : 5.423 36.418 2360 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.47 % Favored : 88.43 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.31 (0.17), residues: 2144 helix: 0.17 (0.15), residues: 1126 sheet: -3.94 (0.44), residues: 70 loop : -3.63 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 202 TYR 0.021 0.001 TYR D 208 PHE 0.015 0.001 PHE A 542 TRP 0.023 0.001 TRP A 739 HIS 0.007 0.001 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (18028) covalent geometry : angle 0.69075 / 0.35 (24396) hydrogen bonds : bond 0.03176 / 2.14 ( 649) hydrogen bonds : angle 3.98874 / 2.81 ( 1899) *********************** REFINEMENT MACRO_CYCLE 7 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 89 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.8821 (p0) cc_final: 0.8235 (t0) REVERT: A 159 MET cc_start: 0.8953 (mmt) cc_final: 0.8291 (mtt) REVERT: A 313 GLN cc_start: 0.8216 (mt0) cc_final: 0.7956 (pt0) REVERT: A 320 MET cc_start: 0.9164 (tpp) cc_final: 0.8944 (mmt) REVERT: A 401 ASN cc_start: 0.8587 (t0) cc_final: 0.8378 (t0) REVERT: A 404 LEU cc_start: 0.9543 (mm) cc_final: 0.9092 (mt) REVERT: A 405 GLU cc_start: 0.8267 (pt0) cc_final: 0.7843 (pp20) REVERT: A 417 HIS cc_start: 0.8603 (p-80) cc_final: 0.8225 (p-80) REVERT: A 419 MET cc_start: 0.8634 (mtm) cc_final: 0.8206 (mtt) REVERT: A 694 LEU cc_start: 0.9525 (mp) cc_final: 0.9139 (pp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0607 time to fit residues: 7.2704 Evaluate side-chains 66 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.184 Evaluate side-chains 82 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 159 MET cc_start: 0.9154 (mmt) cc_final: 0.8928 (ttm) REVERT: D 178 ASN cc_start: 0.9158 (t0) cc_final: 0.8920 (p0) REVERT: D 201 ASP cc_start: 0.8413 (p0) cc_final: 0.7826 (m-30) REVERT: D 255 GLN cc_start: 0.8313 (mp10) cc_final: 0.7744 (tt0) REVERT: D 256 HIS cc_start: 0.8568 (m90) cc_final: 0.8205 (m90) REVERT: D 346 GLN cc_start: 0.9290 (mt0) cc_final: 0.8967 (mt0) REVERT: D 351 MET cc_start: 0.9501 (mmm) cc_final: 0.9227 (mmm) REVERT: D 391 ASP cc_start: 0.7033 (t70) cc_final: 0.6669 (t70) REVERT: D 408 VAL cc_start: 0.8799 (t) cc_final: 0.8436 (t) REVERT: D 416 ARG cc_start: 0.7058 (mmt180) cc_final: 0.4861 (mmp-170) REVERT: D 417 HIS cc_start: 0.7833 (p-80) cc_final: 0.6886 (t70) REVERT: D 440 MET cc_start: 0.8056 (mmp) cc_final: 0.7745 (mmm) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0751 time to fit residues: 7.8340 Evaluate side-chains 62 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 74 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 106 optimal weight: 0.0670 chunk 37 optimal weight: 0.1980 chunk 98 optimal weight: 7.9990 chunk 75 optimal weight: 0.1980 chunk 145 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.100440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.068154 restraints weight = 17615.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.070097 restraints weight = 11807.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.071471 restraints weight = 8963.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.072425 restraints weight = 7371.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.072974 restraints weight = 6442.543| |-----------------------------------------------------------------------------| r_work (final): 0.3195 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.102566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.069171 restraints weight = 16309.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.071115 restraints weight = 11237.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.072377 restraints weight = 8663.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.073398 restraints weight = 7191.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.074011 restraints weight = 6295.340| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.6362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18028 Z= 0.118 Angle : 0.692 9.019 24396 Z= 0.350 Chirality : 0.042 0.195 2728 Planarity : 0.005 0.063 3092 Dihedral : 5.318 35.840 2360 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.75 % Favored : 88.15 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.20 (0.18), residues: 2144 helix: 0.25 (0.15), residues: 1126 sheet: -3.71 (0.48), residues: 62 loop : -3.59 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 202 TYR 0.018 0.001 TYR B 213 PHE 0.030 0.001 PHE B 193 TRP 0.024 0.001 TRP C 739 HIS 0.005 0.000 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (18028) covalent geometry : angle 0.69174 / 0.35 (24396) hydrogen bonds : bond 0.03161 / 2.13 ( 649) hydrogen bonds : angle 3.98094 / 2.81 ( 1899) *********************** REFINEMENT MACRO_CYCLE 8 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 86 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 156 ASP cc_start: 0.8811 (p0) cc_final: 0.8162 (t0) REVERT: C 159 MET cc_start: 0.8779 (mmt) cc_final: 0.8261 (mtt) REVERT: C 176 LEU cc_start: 0.9483 (mm) cc_final: 0.8536 (tt) REVERT: C 221 ILE cc_start: 0.9565 (mp) cc_final: 0.8953 (mp) REVERT: C 293 ASP cc_start: 0.8452 (t0) cc_final: 0.7143 (t70) REVERT: C 313 GLN cc_start: 0.8294 (mt0) cc_final: 0.8052 (pt0) REVERT: C 401 ASN cc_start: 0.8518 (t0) cc_final: 0.8305 (t0) REVERT: C 405 GLU cc_start: 0.8237 (pt0) cc_final: 0.7820 (pp20) REVERT: C 417 HIS cc_start: 0.8547 (p-80) cc_final: 0.8131 (p-80) REVERT: C 419 MET cc_start: 0.8635 (mtm) cc_final: 0.8220 (mtt) REVERT: C 694 LEU cc_start: 0.9523 (mp) cc_final: 0.9164 (pp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0595 time to fit residues: 7.0177 Evaluate side-chains 64 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.218 Evaluate side-chains 79 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 MET cc_start: 0.9165 (mmt) cc_final: 0.8910 (ttm) REVERT: D 178 ASN cc_start: 0.9164 (t0) cc_final: 0.8916 (p0) REVERT: D 256 HIS cc_start: 0.8445 (m90) cc_final: 0.8167 (m90) REVERT: D 318 LYS cc_start: 0.9333 (ttmt) cc_final: 0.9022 (ttpt) REVERT: D 351 MET cc_start: 0.9524 (mmm) cc_final: 0.9304 (mmm) REVERT: D 391 ASP cc_start: 0.7100 (t70) cc_final: 0.6842 (t70) REVERT: D 408 VAL cc_start: 0.8834 (t) cc_final: 0.8492 (t) REVERT: D 416 ARG cc_start: 0.7076 (mmt180) cc_final: 0.5792 (mmp-170) REVERT: D 417 HIS cc_start: 0.7810 (p-80) cc_final: 0.6961 (t70) REVERT: D 729 ARG cc_start: 0.7711 (mpt180) cc_final: 0.7463 (mmt90) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0720 time to fit residues: 7.3591 Evaluate side-chains 61 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 170 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 189 optimal weight: 3.9990 chunk 91 optimal weight: 0.0170 chunk 101 optimal weight: 0.0870 chunk 165 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 21 optimal weight: 0.0070 chunk 52 optimal weight: 7.9990 chunk 2 optimal weight: 40.0000 chunk 210 optimal weight: 4.9990 overall best weight: 0.8016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 242 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.100246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.068070 restraints weight = 17650.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.070145 restraints weight = 11661.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.071583 restraints weight = 8751.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.072434 restraints weight = 7169.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.073086 restraints weight = 6269.321| |-----------------------------------------------------------------------------| r_work (final): 0.3198 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.102184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.070566 restraints weight = 15915.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.072510 restraints weight = 10805.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.073810 restraints weight = 8168.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.074920 restraints weight = 6730.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.075598 restraints weight = 5814.595| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.6522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18028 Z= 0.119 Angle : 0.696 9.169 24396 Z= 0.350 Chirality : 0.042 0.180 2728 Planarity : 0.005 0.068 3092 Dihedral : 5.289 35.666 2360 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.82 % Favored : 89.09 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.14 (0.18), residues: 2144 helix: 0.27 (0.15), residues: 1130 sheet: -3.69 (0.49), residues: 62 loop : -3.54 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 733 TYR 0.021 0.001 TYR B 213 PHE 0.015 0.001 PHE C 542 TRP 0.018 0.001 TRP C 739 HIS 0.008 0.001 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (18028) covalent geometry : angle 0.69618 / 0.35 (24396) hydrogen bonds : bond 0.02990 / 2.01 ( 649) hydrogen bonds : angle 3.89453 / 2.72 ( 1899) *********************** REFINEMENT MACRO_CYCLE 9 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 82 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASP cc_start: 0.8725 (p0) cc_final: 0.8116 (t0) REVERT: A 159 MET cc_start: 0.8743 (mmt) cc_final: 0.8224 (mtt) REVERT: A 401 ASN cc_start: 0.8558 (t0) cc_final: 0.8326 (t0) REVERT: A 405 GLU cc_start: 0.8242 (pt0) cc_final: 0.7795 (pp20) REVERT: A 417 HIS cc_start: 0.8630 (p-80) cc_final: 0.8223 (p-80) REVERT: A 419 MET cc_start: 0.8698 (mtm) cc_final: 0.8243 (mtt) REVERT: A 694 LEU cc_start: 0.9549 (mp) cc_final: 0.9179 (pp) REVERT: A 706 MET cc_start: 0.8346 (ttp) cc_final: 0.7047 (tpt) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0579 time to fit residues: 6.5326 Evaluate side-chains 61 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.189 Evaluate side-chains 80 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.9140 (mmt) cc_final: 0.8879 (ttm) REVERT: B 178 ASN cc_start: 0.9147 (t0) cc_final: 0.8936 (p0) REVERT: B 201 ASP cc_start: 0.8463 (p0) cc_final: 0.7661 (m-30) REVERT: B 256 HIS cc_start: 0.8352 (m90) cc_final: 0.8108 (m90) REVERT: B 318 LYS cc_start: 0.9292 (ttmt) cc_final: 0.9049 (ttpt) REVERT: B 351 MET cc_start: 0.9567 (mmm) cc_final: 0.9307 (mmm) REVERT: B 391 ASP cc_start: 0.7106 (t70) cc_final: 0.6820 (t70) REVERT: B 408 VAL cc_start: 0.8836 (t) cc_final: 0.8619 (t) REVERT: B 416 ARG cc_start: 0.6843 (mmt180) cc_final: 0.6390 (mmp-170) REVERT: B 419 MET cc_start: 0.8975 (tpt) cc_final: 0.8546 (tpp) REVERT: B 729 ARG cc_start: 0.7808 (mpt180) cc_final: 0.7591 (mmt180) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0739 time to fit residues: 7.5313 Evaluate side-chains 63 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 147 optimal weight: 8.9990 chunk 197 optimal weight: 50.0000 chunk 65 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 185 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 ASN A 242 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.096408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.064292 restraints weight = 18206.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.066152 restraints weight = 12264.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067442 restraints weight = 9339.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.068286 restraints weight = 7741.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.068731 restraints weight = 6793.498| |-----------------------------------------------------------------------------| r_work (final): 0.3102 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.098484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.064626 restraints weight = 16779.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.066456 restraints weight = 11524.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.067654 restraints weight = 8905.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.068622 restraints weight = 7448.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.069215 restraints weight = 6548.525| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.6621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18028 Z= 0.184 Angle : 0.743 10.169 24396 Z= 0.379 Chirality : 0.044 0.214 2728 Planarity : 0.005 0.068 3092 Dihedral : 5.442 36.640 2360 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.59 % Favored : 87.31 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.09 (0.17), residues: 2144 helix: 0.34 (0.15), residues: 1122 sheet: -3.44 (0.52), residues: 60 loop : -3.53 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 733 TYR 0.026 0.002 TYR C 390 PHE 0.032 0.001 PHE D 193 TRP 0.025 0.002 TRP B 739 HIS 0.011 0.001 HIS D 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (18028) covalent geometry : angle 0.74336 / 0.38 (24396) hydrogen bonds : bond 0.03091 / 2.08 ( 649) hydrogen bonds : angle 4.16592 / 2.91 ( 1899) ********************** REFINEMENT MACRO_CYCLE 10 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 76 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 156 ASP cc_start: 0.8779 (p0) cc_final: 0.8198 (t0) REVERT: C 159 MET cc_start: 0.8880 (mmt) cc_final: 0.8413 (mtt) REVERT: C 263 GLU cc_start: 0.7472 (pt0) cc_final: 0.7233 (pt0) REVERT: C 405 GLU cc_start: 0.8440 (pt0) cc_final: 0.8068 (pt0) REVERT: C 417 HIS cc_start: 0.8869 (p-80) cc_final: 0.8461 (p-80) REVERT: C 419 MET cc_start: 0.8816 (mtm) cc_final: 0.8263 (mtt) REVERT: C 694 LEU cc_start: 0.9558 (mp) cc_final: 0.9192 (pp) REVERT: C 702 GLU cc_start: 0.9325 (mp0) cc_final: 0.9050 (mp0) REVERT: C 706 MET cc_start: 0.8472 (ttp) cc_final: 0.7356 (tpt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0669 time to fit residues: 6.7122 Evaluate side-chains 54 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.180 Evaluate side-chains 72 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 159 MET cc_start: 0.9180 (mmt) cc_final: 0.8880 (ttm) REVERT: D 178 ASN cc_start: 0.9195 (t0) cc_final: 0.8818 (p0) REVERT: D 201 ASP cc_start: 0.8566 (p0) cc_final: 0.7788 (m-30) REVERT: D 255 GLN cc_start: 0.8407 (mp10) cc_final: 0.7869 (tt0) REVERT: D 256 HIS cc_start: 0.8398 (m90) cc_final: 0.8039 (m90) REVERT: D 351 MET cc_start: 0.9605 (mmm) cc_final: 0.9368 (mmm) REVERT: D 416 ARG cc_start: 0.7181 (mmt180) cc_final: 0.6586 (mmp-170) REVERT: D 417 HIS cc_start: 0.7825 (p-80) cc_final: 0.6945 (t70) REVERT: D 419 MET cc_start: 0.9183 (tpt) cc_final: 0.8725 (tpp) REVERT: D 420 LEU cc_start: 0.9469 (mt) cc_final: 0.9238 (mt) REVERT: D 440 MET cc_start: 0.7889 (mmp) cc_final: 0.7551 (mmm) REVERT: D 729 ARG cc_start: 0.7919 (mpt180) cc_final: 0.7633 (mmt180) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0676 time to fit residues: 6.3550 Evaluate side-chains 59 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 60 optimal weight: 0.0270 chunk 20 optimal weight: 9.9990 chunk 202 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 213 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 84 optimal weight: 0.0970 chunk 109 optimal weight: 7.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 242 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.099302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.067305 restraints weight = 17822.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.069304 restraints weight = 11960.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.070562 restraints weight = 9006.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.071599 restraints weight = 7412.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.072146 restraints weight = 6453.162| |-----------------------------------------------------------------------------| r_work (final): 0.3169 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.101550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.068286 restraints weight = 16098.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.070108 restraints weight = 11258.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.071308 restraints weight = 8766.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.072309 restraints weight = 7344.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.072916 restraints weight = 6462.389| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.6824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18028 Z= 0.124 Angle : 0.728 9.793 24396 Z= 0.365 Chirality : 0.043 0.184 2728 Planarity : 0.005 0.095 3092 Dihedral : 5.347 35.946 2360 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.05 (0.18), residues: 2144 helix: 0.31 (0.15), residues: 1136 sheet: -3.52 (0.51), residues: 60 loop : -3.47 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 714 TYR 0.020 0.001 TYR C 390 PHE 0.015 0.001 PHE C 715 TRP 0.017 0.001 TRP B 742 HIS 0.007 0.001 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (18028) covalent geometry : angle 0.72828 / 0.36 (24396) hydrogen bonds : bond 0.03124 / 2.13 ( 649) hydrogen bonds : angle 3.87300 / 2.71 ( 1899) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2020.65 seconds wall clock time: 36 minutes 8.32 seconds (2168.32 seconds total)