Starting phenix.real_space_refine on Mon Aug 25 05:04:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ria_53991/08_2025/9ria_53991.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ria_53991/08_2025/9ria_53991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ria_53991/08_2025/9ria_53991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ria_53991/08_2025/9ria_53991.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ria_53991/08_2025/9ria_53991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ria_53991/08_2025/9ria_53991.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 101 5.16 5 C 15739 2.51 5 N 4256 2.21 5 O 4616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24721 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6757 Classifications: {'peptide': 845} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 807} Chain breaks: 3 Chain: "B" Number of atoms: 6758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6758 Classifications: {'peptide': 845} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 807} Chain breaks: 3 Chain: "C" Number of atoms: 6738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 6738 Classifications: {'peptide': 843} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 805} Chain breaks: 3 Chain: "G" Number of atoms: 4375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4375 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 516} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.28, per 1000 atoms: 0.25 Number of scatterers: 24721 At special positions: 0 Unit cell: (134.964, 129.168, 177.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 101 16.00 P 9 15.00 O 4616 8.00 N 4256 7.00 C 15739 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: 2.15 Conformation dependent library (CDL) restraints added in 809.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5824 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 24 sheets defined 55.8% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 25 through 49 removed outlier: 3.923A pdb=" N GLY A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 87 Processing helix chain 'A' and resid 98 through 125 Processing helix chain 'A' and resid 125 through 134 removed outlier: 3.825A pdb=" N ILE A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 171 Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.619A pdb=" N PHE A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.500A pdb=" N GLN A 237 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP A 239 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 269 through 278 removed outlier: 3.528A pdb=" N TRP A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 332 through 346 removed outlier: 4.305A pdb=" N LEU A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 3.529A pdb=" N SER A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 363 Processing helix chain 'A' and resid 366 through 376 Processing helix chain 'A' and resid 376 through 382 removed outlier: 3.606A pdb=" N HIS A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 400 removed outlier: 3.897A pdb=" N LEU A 392 " --> pdb=" O ASN A 388 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 411 removed outlier: 4.082A pdb=" N ALA A 406 " --> pdb=" O TYR A 402 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS A 411 " --> pdb=" O CYS A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 433 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 508 through 513 Processing helix chain 'A' and resid 523 through 530 removed outlier: 4.004A pdb=" N MET A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 removed outlier: 3.564A pdb=" N ILE A 555 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 562 Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 602 through 608 Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 671 through 675 Processing helix chain 'A' and resid 676 through 683 Processing helix chain 'A' and resid 695 through 700 Processing helix chain 'A' and resid 709 through 715 removed outlier: 3.703A pdb=" N ASN A 713 " --> pdb=" O GLY A 709 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 715 " --> pdb=" O PHE A 711 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 709 through 715' Processing helix chain 'A' and resid 740 through 744 Processing helix chain 'A' and resid 761 through 769 removed outlier: 3.747A pdb=" N SER A 764 " --> pdb=" O LYS A 761 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE A 765 " --> pdb=" O ASP A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 817 removed outlier: 3.590A pdb=" N PHE A 817 " --> pdb=" O SER A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 841 Processing helix chain 'A' and resid 853 through 873 Processing helix chain 'B' and resid 26 through 50 Processing helix chain 'B' and resid 55 through 88 Processing helix chain 'B' and resid 100 through 125 Processing helix chain 'B' and resid 125 through 134 removed outlier: 3.527A pdb=" N LEU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA B 131 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 134 " --> pdb=" O GLN B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 171 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 199 through 206 Processing helix chain 'B' and resid 219 through 230 Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.527A pdb=" N TYR B 238 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP B 239 " --> pdb=" O LYS B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 255 Processing helix chain 'B' and resid 269 through 277 removed outlier: 3.508A pdb=" N TRP B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 313 through 327 Processing helix chain 'B' and resid 332 through 346 removed outlier: 4.432A pdb=" N LEU B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) Proline residue: B 338 - end of helix removed outlier: 3.556A pdb=" N SER B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 364 removed outlier: 3.548A pdb=" N ALA B 359 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 376 removed outlier: 3.538A pdb=" N TRP B 370 " --> pdb=" O THR B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 382 Processing helix chain 'B' and resid 388 through 398 removed outlier: 3.605A pdb=" N LEU B 392 " --> pdb=" O ASN B 388 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 411 removed outlier: 4.277A pdb=" N ALA B 406 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS B 411 " --> pdb=" O CYS B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 422 through 432 Processing helix chain 'B' and resid 442 through 457 removed outlier: 3.635A pdb=" N ASP B 449 " --> pdb=" O ASP B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 491 Processing helix chain 'B' and resid 508 through 513 Processing helix chain 'B' and resid 523 through 530 removed outlier: 3.646A pdb=" N MET B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 562 removed outlier: 3.701A pdb=" N LYS B 560 " --> pdb=" O PRO B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 585 removed outlier: 3.679A pdb=" N LEU B 585 " --> pdb=" O PHE B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 608 Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 671 through 675 Processing helix chain 'B' and resid 676 through 683 Processing helix chain 'B' and resid 695 through 700 removed outlier: 3.523A pdb=" N LEU B 699 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 715 removed outlier: 3.642A pdb=" N ILE B 714 " --> pdb=" O LEU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 744 Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 835 through 841 removed outlier: 3.655A pdb=" N LEU B 838 " --> pdb=" O PRO B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 872 Processing helix chain 'C' and resid 26 through 49 Processing helix chain 'C' and resid 55 through 88 removed outlier: 3.653A pdb=" N ASP C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 125 Processing helix chain 'C' and resid 125 through 134 removed outlier: 3.503A pdb=" N GLN C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'C' and resid 188 through 198 Processing helix chain 'C' and resid 199 through 206 Processing helix chain 'C' and resid 219 through 232 removed outlier: 3.661A pdb=" N PHE C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE C 231 " --> pdb=" O ILE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 239 Processing helix chain 'C' and resid 242 through 257 removed outlier: 3.574A pdb=" N GLY C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 278 removed outlier: 3.863A pdb=" N ILE C 278 " --> pdb=" O ASP C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 313 through 326 Processing helix chain 'C' and resid 332 through 346 removed outlier: 4.210A pdb=" N LEU C 337 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Proline residue: C 338 - end of helix removed outlier: 3.534A pdb=" N SER C 341 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 363 Processing helix chain 'C' and resid 366 through 376 Processing helix chain 'C' and resid 376 through 383 Processing helix chain 'C' and resid 388 through 399 removed outlier: 3.848A pdb=" N LEU C 392 " --> pdb=" O ASN C 388 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 399 " --> pdb=" O MET C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 411 removed outlier: 3.900A pdb=" N ALA C 406 " --> pdb=" O TYR C 402 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS C 411 " --> pdb=" O CYS C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 422 through 433 Processing helix chain 'C' and resid 442 through 457 Processing helix chain 'C' and resid 477 through 488 Processing helix chain 'C' and resid 508 through 513 Processing helix chain 'C' and resid 523 through 530 Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 556 through 562 Processing helix chain 'C' and resid 602 through 608 Processing helix chain 'C' and resid 628 through 632 Processing helix chain 'C' and resid 671 through 675 Processing helix chain 'C' and resid 676 through 682 removed outlier: 3.661A pdb=" N PHE C 680 " --> pdb=" O THR C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 700 Processing helix chain 'C' and resid 710 through 716 removed outlier: 3.548A pdb=" N ILE C 714 " --> pdb=" O LEU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 744 Processing helix chain 'C' and resid 762 through 767 removed outlier: 3.858A pdb=" N LEU C 766 " --> pdb=" O ASP C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 817 removed outlier: 4.011A pdb=" N PHE C 817 " --> pdb=" O SER C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 841 removed outlier: 3.640A pdb=" N LEU C 838 " --> pdb=" O PRO C 835 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 841 " --> pdb=" O LEU C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 873 Processing helix chain 'G' and resid 139 through 144 removed outlier: 3.791A pdb=" N LEU G 144 " --> pdb=" O THR G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 159 removed outlier: 3.973A pdb=" N LEU G 159 " --> pdb=" O GLN G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'G' and resid 163 through 182 Processing helix chain 'G' and resid 184 through 192 removed outlier: 3.728A pdb=" N VAL G 188 " --> pdb=" O ASP G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 202 removed outlier: 3.708A pdb=" N ILE G 201 " --> pdb=" O GLY G 198 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE G 202 " --> pdb=" O ILE G 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 198 through 202' Processing helix chain 'G' and resid 204 through 218 removed outlier: 3.628A pdb=" N SER G 208 " --> pdb=" O LYS G 204 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL G 214 " --> pdb=" O TRP G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 238 Processing helix chain 'G' and resid 245 through 257 removed outlier: 3.730A pdb=" N LEU G 251 " --> pdb=" O VAL G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 279 removed outlier: 3.532A pdb=" N LYS G 267 " --> pdb=" O THR G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 292 Processing helix chain 'G' and resid 295 through 301 Processing helix chain 'G' and resid 302 through 319 removed outlier: 4.193A pdb=" N LYS G 306 " --> pdb=" O SER G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 334 Processing helix chain 'G' and resid 335 through 349 removed outlier: 3.732A pdb=" N ASP G 341 " --> pdb=" O ALA G 337 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR G 342 " --> pdb=" O GLN G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 370 Processing helix chain 'G' and resid 373 through 386 removed outlier: 3.755A pdb=" N SER G 383 " --> pdb=" O ASN G 379 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N SER G 384 " --> pdb=" O ARG G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 392 Processing helix chain 'G' and resid 394 through 410 Processing helix chain 'G' and resid 413 through 425 removed outlier: 3.555A pdb=" N LEU G 419 " --> pdb=" O ASP G 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 438 removed outlier: 3.637A pdb=" N VAL G 433 " --> pdb=" O ARG G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 442 removed outlier: 6.808A pdb=" N ASN G 442 " --> pdb=" O LYS G 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 439 through 442' Processing helix chain 'G' and resid 443 through 460 removed outlier: 3.568A pdb=" N LEU G 458 " --> pdb=" O LYS G 454 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA G 460 " --> pdb=" O SER G 456 " (cutoff:3.500A) Processing helix chain 'G' and resid 464 through 472 removed outlier: 3.682A pdb=" N LYS G 470 " --> pdb=" O GLU G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 473 through 477 removed outlier: 3.584A pdb=" N ASN G 476 " --> pdb=" O ALA G 473 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL G 477 " --> pdb=" O LEU G 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 473 through 477' Processing helix chain 'G' and resid 480 through 483 Processing helix chain 'G' and resid 484 through 501 removed outlier: 3.545A pdb=" N HIS G 488 " --> pdb=" O ASN G 484 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 531 removed outlier: 3.743A pdb=" N LEU G 512 " --> pdb=" O TRP G 508 " (cutoff:3.500A) Proline residue: G 518 - end of helix removed outlier: 3.641A pdb=" N ASN G 531 " --> pdb=" O THR G 527 " (cutoff:3.500A) Processing helix chain 'G' and resid 534 through 552 removed outlier: 3.529A pdb=" N LEU G 550 " --> pdb=" O HIS G 546 " (cutoff:3.500A) Processing helix chain 'G' and resid 555 through 563 removed outlier: 4.168A pdb=" N ARG G 561 " --> pdb=" O LYS G 557 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 574 removed outlier: 3.873A pdb=" N ALA G 574 " --> pdb=" O LYS G 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 571 through 574' Processing helix chain 'G' and resid 575 through 592 removed outlier: 3.695A pdb=" N ASN G 579 " --> pdb=" O ASP G 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 598 through 607 Processing helix chain 'G' and resid 608 through 621 removed outlier: 4.106A pdb=" N ASN G 621 " --> pdb=" O SER G 617 " (cutoff:3.500A) Processing helix chain 'G' and resid 625 through 643 removed outlier: 3.974A pdb=" N ALA G 643 " --> pdb=" O LYS G 639 " (cutoff:3.500A) Processing helix chain 'G' and resid 646 through 654 Processing helix chain 'G' and resid 660 through 677 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 6.834A pdb=" N THR A 208 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL A 263 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL A 210 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP A 265 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A 212 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR A 260 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU A 290 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE A 262 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR A 292 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU A 264 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N HIS A 307 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 420 through 421 removed outlier: 6.894A pdb=" N ILE A 471 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG A 465 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR A 473 " --> pdb=" O THR A 463 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498 removed outlier: 5.607A pdb=" N GLU A 571 " --> pdb=" O CYS A 542 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE A 548 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 5.607A pdb=" N GLU A 571 " --> pdb=" O CYS A 542 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 594 " --> pdb=" O ALA A 570 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N SER A 572 " --> pdb=" O SER A 594 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A 591 " --> pdb=" O ILE A 615 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLU A 617 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU A 593 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 614 " --> pdb=" O CYS A 639 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 600 through 601 removed outlier: 7.367A pdb=" N LEU A 623 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 666 through 670 removed outlier: 4.642A pdb=" N THR A 666 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLY A 690 " --> pdb=" O THR A 666 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N SER A 668 " --> pdb=" O GLY A 690 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG A 692 " --> pdb=" O SER A 668 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ILE A 670 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 758 through 759 removed outlier: 5.909A pdb=" N PHE A 758 " --> pdb=" O LYS A 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 786 through 787 Processing sheet with id=AA9, first strand: chain 'B' and resid 288 through 293 removed outlier: 7.751A pdb=" N HIS B 307 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 208 through 213 removed outlier: 6.441A pdb=" N THR B 208 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL B 263 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL B 210 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP B 265 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 212 " --> pdb=" O ASP B 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 420 through 421 removed outlier: 6.904A pdb=" N ILE B 471 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG B 465 " --> pdb=" O ILE B 471 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR B 473 " --> pdb=" O THR B 463 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 496 through 498 removed outlier: 6.203A pdb=" N GLN B 496 " --> pdb=" O CYS B 519 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 518 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N GLU B 571 " --> pdb=" O CYS B 542 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 548 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 496 through 498 removed outlier: 6.203A pdb=" N GLN B 496 " --> pdb=" O CYS B 519 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 518 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N GLU B 571 " --> pdb=" O CYS B 542 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU B 568 " --> pdb=" O ALA B 592 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER B 594 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ALA B 570 " --> pdb=" O SER B 594 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU B 614 " --> pdb=" O CYS B 639 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B 638 " --> pdb=" O SER B 668 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE B 670 " --> pdb=" O VAL B 638 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N THR B 640 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS B 688 " --> pdb=" O THR B 666 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N SER B 668 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLY B 690 " --> pdb=" O SER B 668 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 800 " --> pdb=" O ALA B 824 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 823 " --> pdb=" O GLU B 848 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 600 through 601 removed outlier: 6.969A pdb=" N LEU B 623 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 758 through 759 removed outlier: 5.963A pdb=" N PHE B 758 " --> pdb=" O LYS B 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 786 through 788 removed outlier: 6.871A pdb=" N TRP B 787 " --> pdb=" O LYS B 811 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 208 through 213 removed outlier: 6.382A pdb=" N THR C 208 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL C 263 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL C 210 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP C 265 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C 212 " --> pdb=" O ASP C 265 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N TYR C 260 " --> pdb=" O ARG C 288 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU C 290 " --> pdb=" O TYR C 260 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE C 262 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR C 292 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU C 264 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 420 through 421 removed outlier: 6.879A pdb=" N ILE C 471 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG C 465 " --> pdb=" O ILE C 471 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR C 473 " --> pdb=" O THR C 463 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 496 through 498 removed outlier: 5.944A pdb=" N GLN C 496 " --> pdb=" O CYS C 519 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 518 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU C 571 " --> pdb=" O CYS C 542 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE C 548 " --> pdb=" O LYS C 574 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 496 through 498 removed outlier: 5.944A pdb=" N GLN C 496 " --> pdb=" O CYS C 519 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 518 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU C 571 " --> pdb=" O CYS C 542 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 568 " --> pdb=" O ALA C 592 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N SER C 594 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 9.464A pdb=" N ALA C 570 " --> pdb=" O SER C 594 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE C 591 " --> pdb=" O ILE C 615 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU C 614 " --> pdb=" O CYS C 639 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 600 through 601 removed outlier: 3.587A pdb=" N LEU C 623 " --> pdb=" O SER C 643 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 691 through 693 removed outlier: 6.172A pdb=" N VAL C 691 " --> pdb=" O VAL C 726 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU C 800 " --> pdb=" O ALA C 824 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE C 826 " --> pdb=" O LEU C 800 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE C 802 " --> pdb=" O ILE C 826 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 758 through 759 removed outlier: 5.773A pdb=" N PHE C 758 " --> pdb=" O LYS C 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 786 through 788 removed outlier: 6.416A pdb=" N TRP C 787 " --> pdb=" O LYS C 811 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 1169 hydrogen bonds defined for protein. 3300 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: 6.28 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8090 1.35 - 1.47: 5462 1.47 - 1.59: 11504 1.59 - 1.70: 5 1.70 - 1.82: 151 Bond restraints: 25212 Sorted by residual: bond pdb=" N VAL A 210 " pdb=" CA VAL A 210 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.30e+00 bond pdb=" N ASN G 369 " pdb=" CA ASN G 369 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.81e+00 bond pdb=" N ARG A 209 " pdb=" CA ARG A 209 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.21e-02 6.83e+03 6.72e+00 bond pdb=" N PHE A 207 " pdb=" CA PHE A 207 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.17e-02 7.31e+03 5.85e+00 bond pdb=" N MET G 368 " pdb=" CA MET G 368 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.57e+00 ... (remaining 25207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 33793 2.35 - 4.69: 234 4.69 - 7.04: 24 7.04 - 9.39: 1 9.39 - 11.74: 2 Bond angle restraints: 34054 Sorted by residual: angle pdb=" CB MET G 511 " pdb=" CG MET G 511 " pdb=" SD MET G 511 " ideal model delta sigma weight residual 112.70 124.44 -11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" N VAL A 214 " pdb=" CA VAL A 214 " pdb=" C VAL A 214 " ideal model delta sigma weight residual 110.05 106.34 3.71 1.09e+00 8.42e-01 1.16e+01 angle pdb=" C LEU C 523 " pdb=" N ILE C 524 " pdb=" CA ILE C 524 " ideal model delta sigma weight residual 120.33 123.03 -2.70 8.00e-01 1.56e+00 1.14e+01 angle pdb=" CA LEU C 689 " pdb=" CB LEU C 689 " pdb=" CG LEU C 689 " ideal model delta sigma weight residual 116.30 127.86 -11.56 3.50e+00 8.16e-02 1.09e+01 angle pdb=" CA LYS B 761 " pdb=" CB LYS B 761 " pdb=" CG LYS B 761 " ideal model delta sigma weight residual 114.10 120.51 -6.41 2.00e+00 2.50e-01 1.03e+01 ... (remaining 34049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13736 17.94 - 35.87: 1368 35.87 - 53.81: 315 53.81 - 71.75: 40 71.75 - 89.68: 31 Dihedral angle restraints: 15490 sinusoidal: 6535 harmonic: 8955 Sorted by residual: dihedral pdb=" CA LYS B 499 " pdb=" C LYS B 499 " pdb=" N GLN B 500 " pdb=" CA GLN B 500 " ideal model delta harmonic sigma weight residual 180.00 161.34 18.66 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ASP B 449 " pdb=" C ASP B 449 " pdb=" N HIS B 450 " pdb=" CA HIS B 450 " ideal model delta harmonic sigma weight residual 180.00 161.79 18.21 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA LYS C 734 " pdb=" C LYS C 734 " pdb=" N PRO C 735 " pdb=" CA PRO C 735 " ideal model delta harmonic sigma weight residual 180.00 162.43 17.57 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 15487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2755 0.037 - 0.074: 785 0.074 - 0.111: 219 0.111 - 0.148: 38 0.148 - 0.185: 1 Chirality restraints: 3798 Sorted by residual: chirality pdb=" CA VAL A 210 " pdb=" N VAL A 210 " pdb=" C VAL A 210 " pdb=" CB VAL A 210 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" CG LEU A 349 " pdb=" CB LEU A 349 " pdb=" CD1 LEU A 349 " pdb=" CD2 LEU A 349 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA MET G 368 " pdb=" N MET G 368 " pdb=" C MET G 368 " pdb=" CB MET G 368 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 3795 not shown) Planarity restraints: 4344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 209 " -0.415 9.50e-02 1.11e+02 1.86e-01 2.13e+01 pdb=" NE ARG A 209 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG A 209 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 209 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 209 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 787 " 0.016 2.00e-02 2.50e+03 1.67e-02 6.96e+00 pdb=" CG TRP C 787 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 787 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 787 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C 787 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP C 787 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 787 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 787 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 787 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 787 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 177 " 0.012 2.00e-02 2.50e+03 1.98e-02 6.86e+00 pdb=" CG PHE G 177 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE G 177 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE G 177 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE G 177 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE G 177 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE G 177 " -0.002 2.00e-02 2.50e+03 ... (remaining 4341 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 12700 3.01 - 3.49: 25415 3.49 - 3.96: 39489 3.96 - 4.43: 47669 4.43 - 4.90: 74796 Nonbonded interactions: 200069 Sorted by model distance: nonbonded pdb=" N GLU G 662 " pdb=" OE1 GLU G 662 " model vdw 2.542 3.120 nonbonded pdb=" N GLU G 165 " pdb=" OE1 GLU G 165 " model vdw 2.556 3.120 nonbonded pdb=" O THR C 683 " pdb=" OG1 THR C 683 " model vdw 2.574 3.040 nonbonded pdb=" NH2 ARG A 209 " pdb=" O ILE G 514 " model vdw 2.577 3.120 nonbonded pdb=" C THR C 292 " pdb=" OG1 THR C 292 " model vdw 2.579 2.616 ... (remaining 200064 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 87 or resid 99 through 135 or resid 143 through \ 649 or resid 658 through 1001)) selection = (chain 'B' and (resid 25 through 87 or resid 99 through 649 or resid 658 through \ 1001)) selection = (chain 'C' and (resid 25 through 87 or resid 99 through 135 or resid 143 through \ 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.320 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: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.660 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.002 0.037 25212 Z= 0.118 Angle : 0.522 11.736 34054 Z= 0.297 Chirality : 0.038 0.185 3798 Planarity : 0.004 0.186 4344 Dihedral : 15.121 89.683 9666 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.96 % Allowed : 11.66 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.15), residues: 3049 helix: -0.17 (0.13), residues: 1501 sheet: -0.39 (0.33), residues: 290 loop : 0.17 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 182 TYR 0.023 0.001 TYR G 402 PHE 0.045 0.001 PHE G 177 TRP 0.040 0.001 TRP C 787 HIS 0.002 0.000 HIS G 221 Details of bonding type rmsd covalent geometry : bond 0.00220 (25212) covalent geometry : angle 0.52212 (34054) hydrogen bonds : bond 0.21446 ( 1154) hydrogen bonds : angle 7.15614 ( 3300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 364 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ASP cc_start: 0.7111 (t0) cc_final: 0.6843 (t0) REVERT: B 27 ILE cc_start: 0.7997 (mt) cc_final: 0.7763 (tt) REVERT: C 593 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7797 (pp) REVERT: C 723 LEU cc_start: 0.8826 (tp) cc_final: 0.8548 (tt) REVERT: C 744 PHE cc_start: 0.7816 (m-80) cc_final: 0.7253 (m-80) REVERT: C 820 LEU cc_start: 0.9065 (tp) cc_final: 0.8811 (tp) REVERT: G 168 LEU cc_start: 0.9364 (tp) cc_final: 0.9089 (pp) REVERT: G 419 LEU cc_start: 0.8748 (mt) cc_final: 0.8449 (mm) outliers start: 26 outliers final: 17 residues processed: 384 average time/residue: 0.2171 time to fit residues: 123.4172 Evaluate side-chains 242 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 224 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 553 ASN Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain G residue 201 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 HIS C 42 ASN ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 746 GLN C 822 HIS G 360 GLN ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.095342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.071863 restraints weight = 72663.007| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.65 r_work: 0.3146 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25212 Z= 0.139 Angle : 0.554 7.341 34054 Z= 0.288 Chirality : 0.040 0.206 3798 Planarity : 0.004 0.040 4344 Dihedral : 7.000 89.364 3426 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.96 % Allowed : 13.62 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.15), residues: 3049 helix: 0.74 (0.13), residues: 1522 sheet: -0.38 (0.33), residues: 293 loop : 0.16 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 220 TYR 0.019 0.001 TYR B 127 PHE 0.024 0.001 PHE G 177 TRP 0.023 0.001 TRP A 787 HIS 0.003 0.001 HIS G 221 Details of bonding type rmsd covalent geometry : bond 0.00310 (25212) covalent geometry : angle 0.55379 (34054) hydrogen bonds : bond 0.05009 ( 1154) hydrogen bonds : angle 4.71751 ( 3300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 252 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8269 (mtt) cc_final: 0.7973 (mtt) REVERT: A 453 ASP cc_start: 0.7934 (t0) cc_final: 0.7716 (t0) REVERT: A 747 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8265 (mtmm) REVERT: B 27 ILE cc_start: 0.7499 (mt) cc_final: 0.7031 (tt) REVERT: B 32 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8440 (mm-30) REVERT: B 810 TRP cc_start: 0.8285 (t60) cc_final: 0.7978 (t60) REVERT: B 845 GLN cc_start: 0.6865 (pp30) cc_final: 0.6519 (pp30) REVERT: C 77 ASP cc_start: 0.8673 (m-30) cc_final: 0.8353 (m-30) REVERT: C 504 ARG cc_start: 0.7180 (mtm180) cc_final: 0.6644 (mpp80) REVERT: C 692 ARG cc_start: 0.7668 (ttt-90) cc_final: 0.7376 (tpp80) REVERT: C 723 LEU cc_start: 0.9488 (tp) cc_final: 0.9205 (tp) REVERT: C 763 MET cc_start: 0.8560 (ppp) cc_final: 0.8163 (ppp) REVERT: G 168 LEU cc_start: 0.9637 (tp) cc_final: 0.9324 (pp) REVERT: G 307 GLU cc_start: 0.9261 (mt-10) cc_final: 0.9040 (mt-10) outliers start: 53 outliers final: 26 residues processed: 292 average time/residue: 0.1903 time to fit residues: 86.4528 Evaluate side-chains 244 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 542 CYS Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 254 ASN Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain G residue 405 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 302 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 294 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.093735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.070270 restraints weight = 73196.453| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.47 r_work: 0.3123 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25212 Z= 0.166 Angle : 0.539 9.173 34054 Z= 0.276 Chirality : 0.041 0.186 3798 Planarity : 0.004 0.041 4344 Dihedral : 6.817 86.985 3410 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.21 % Allowed : 14.54 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.15), residues: 3049 helix: 1.04 (0.13), residues: 1524 sheet: -0.34 (0.33), residues: 288 loop : 0.12 (0.18), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 122 TYR 0.026 0.002 TYR B 127 PHE 0.019 0.002 PHE C 605 TRP 0.015 0.001 TRP G 210 HIS 0.003 0.001 HIS C 486 Details of bonding type rmsd covalent geometry : bond 0.00386 (25212) covalent geometry : angle 0.53863 (34054) hydrogen bonds : bond 0.04149 ( 1154) hydrogen bonds : angle 4.38633 ( 3300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 229 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ARG cc_start: 0.8450 (ptm-80) cc_final: 0.8012 (ptm-80) REVERT: A 453 ASP cc_start: 0.8029 (t0) cc_final: 0.7796 (t0) REVERT: A 491 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: A 747 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8384 (mtmm) REVERT: B 27 ILE cc_start: 0.7530 (mt) cc_final: 0.7063 (tt) REVERT: B 32 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8505 (mm-30) REVERT: B 453 ASP cc_start: 0.8314 (t0) cc_final: 0.8083 (t0) REVERT: B 845 GLN cc_start: 0.7118 (pp30) cc_final: 0.6895 (pp30) REVERT: C 77 ASP cc_start: 0.8754 (m-30) cc_final: 0.8460 (m-30) REVERT: C 504 ARG cc_start: 0.7186 (mtm180) cc_final: 0.6696 (mpp80) REVERT: C 593 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7519 (pp) REVERT: C 692 ARG cc_start: 0.7704 (ttt-90) cc_final: 0.7435 (tpp80) REVERT: C 744 PHE cc_start: 0.8264 (m-80) cc_final: 0.7689 (m-80) REVERT: G 168 LEU cc_start: 0.9602 (tp) cc_final: 0.9319 (pp) REVERT: G 177 PHE cc_start: 0.9116 (t80) cc_final: 0.8902 (t80) REVERT: G 419 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8931 (mp) outliers start: 60 outliers final: 34 residues processed: 276 average time/residue: 0.1905 time to fit residues: 81.8916 Evaluate side-chains 244 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 254 ASN Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain G residue 419 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 227 optimal weight: 4.9990 chunk 225 optimal weight: 1.9990 chunk 194 optimal weight: 0.0060 chunk 14 optimal weight: 3.9990 chunk 266 optimal weight: 0.5980 chunk 68 optimal weight: 0.0970 chunk 127 optimal weight: 0.0980 chunk 85 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 279 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 458 ASN ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 746 GLN ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 488 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.095138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.071801 restraints weight = 72999.686| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.48 r_work: 0.3163 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 25212 Z= 0.102 Angle : 0.498 7.669 34054 Z= 0.255 Chirality : 0.039 0.165 3798 Planarity : 0.003 0.041 4344 Dihedral : 6.652 81.878 3410 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.55 % Allowed : 15.36 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.16), residues: 3049 helix: 1.22 (0.13), residues: 1534 sheet: -0.22 (0.34), residues: 290 loop : 0.16 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 233 TYR 0.015 0.001 TYR G 292 PHE 0.020 0.001 PHE C 605 TRP 0.017 0.001 TRP C 787 HIS 0.003 0.000 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00222 (25212) covalent geometry : angle 0.49752 (34054) hydrogen bonds : bond 0.03520 ( 1154) hydrogen bonds : angle 4.10204 ( 3300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ARG cc_start: 0.8446 (ptm-80) cc_final: 0.8021 (ptm-80) REVERT: A 453 ASP cc_start: 0.8011 (t0) cc_final: 0.7779 (t0) REVERT: A 747 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8383 (mtmm) REVERT: A 821 LYS cc_start: 0.8389 (pttt) cc_final: 0.8066 (pttp) REVERT: B 32 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8452 (mm-30) REVERT: B 74 ASP cc_start: 0.7977 (m-30) cc_final: 0.7573 (m-30) REVERT: B 810 TRP cc_start: 0.8348 (t60) cc_final: 0.8124 (t60) REVERT: C 77 ASP cc_start: 0.8734 (m-30) cc_final: 0.8439 (m-30) REVERT: C 504 ARG cc_start: 0.7144 (mtm180) cc_final: 0.6645 (mpp80) REVERT: C 530 MET cc_start: 0.8837 (ptp) cc_final: 0.8177 (pmm) REVERT: C 593 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7481 (pp) REVERT: C 744 PHE cc_start: 0.8221 (m-80) cc_final: 0.7645 (m-80) REVERT: G 168 LEU cc_start: 0.9597 (tp) cc_final: 0.9330 (pp) REVERT: G 177 PHE cc_start: 0.9146 (t80) cc_final: 0.8945 (t80) outliers start: 42 outliers final: 24 residues processed: 262 average time/residue: 0.1929 time to fit residues: 78.8007 Evaluate side-chains 225 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 254 ASN Chi-restraints excluded: chain G residue 263 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 156 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN C 780 ASN ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.093563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.069970 restraints weight = 73203.848| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.43 r_work: 0.3124 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25212 Z= 0.164 Angle : 0.526 8.424 34054 Z= 0.269 Chirality : 0.041 0.174 3798 Planarity : 0.003 0.041 4344 Dihedral : 6.591 79.516 3409 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.96 % Allowed : 15.95 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.16), residues: 3049 helix: 1.30 (0.13), residues: 1532 sheet: -0.26 (0.33), residues: 290 loop : 0.13 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 384 TYR 0.015 0.002 TYR C 590 PHE 0.023 0.001 PHE C 527 TRP 0.031 0.001 TRP A 787 HIS 0.003 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00383 (25212) covalent geometry : angle 0.52554 (34054) hydrogen bonds : bond 0.03688 ( 1154) hydrogen bonds : angle 4.12643 ( 3300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ARG cc_start: 0.8510 (ptm-80) cc_final: 0.8127 (ptm-80) REVERT: A 453 ASP cc_start: 0.8114 (t0) cc_final: 0.7865 (t0) REVERT: A 546 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8712 (ttpp) REVERT: A 597 LYS cc_start: 0.8835 (tttm) cc_final: 0.8614 (tttm) REVERT: A 694 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7964 (pptt) REVERT: A 747 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8416 (mtmm) REVERT: A 821 LYS cc_start: 0.8383 (pttt) cc_final: 0.8173 (pttp) REVERT: B 27 ILE cc_start: 0.7511 (mt) cc_final: 0.7065 (tt) REVERT: B 32 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8461 (mm-30) REVERT: B 453 ASP cc_start: 0.8285 (t0) cc_final: 0.7941 (t0) REVERT: C 77 ASP cc_start: 0.8771 (m-30) cc_final: 0.8491 (m-30) REVERT: C 526 GLU cc_start: 0.8688 (mp0) cc_final: 0.8413 (mp0) REVERT: C 593 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7331 (pp) REVERT: C 744 PHE cc_start: 0.8181 (m-80) cc_final: 0.7568 (m-80) REVERT: G 168 LEU cc_start: 0.9595 (tp) cc_final: 0.9339 (pp) REVERT: G 452 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8840 (tpt) outliers start: 53 outliers final: 35 residues processed: 255 average time/residue: 0.1840 time to fit residues: 73.9218 Evaluate side-chains 239 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 542 CYS Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 254 ASN Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 417 MET Chi-restraints excluded: chain G residue 452 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 119 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 257 optimal weight: 5.9990 chunk 265 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 281 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.093467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.070201 restraints weight = 72881.469| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.41 r_work: 0.3122 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25212 Z= 0.146 Angle : 0.522 9.326 34054 Z= 0.264 Chirality : 0.041 0.187 3798 Planarity : 0.003 0.041 4344 Dihedral : 6.534 78.526 3408 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.81 % Allowed : 16.61 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.16), residues: 3049 helix: 1.41 (0.14), residues: 1523 sheet: -0.21 (0.33), residues: 288 loop : 0.17 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 384 TYR 0.014 0.001 TYR C 590 PHE 0.027 0.001 PHE C 527 TRP 0.036 0.001 TRP G 178 HIS 0.003 0.000 HIS C 486 Details of bonding type rmsd covalent geometry : bond 0.00340 (25212) covalent geometry : angle 0.52193 (34054) hydrogen bonds : bond 0.03522 ( 1154) hydrogen bonds : angle 4.05206 ( 3300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 215 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ARG cc_start: 0.8532 (ptm-80) cc_final: 0.8134 (ptm-80) REVERT: A 453 ASP cc_start: 0.8152 (t0) cc_final: 0.7900 (t0) REVERT: A 597 LYS cc_start: 0.8825 (tttm) cc_final: 0.8607 (tttm) REVERT: A 694 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7621 (pptt) REVERT: A 747 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8456 (mtmm) REVERT: A 821 LYS cc_start: 0.8375 (pttt) cc_final: 0.8153 (pttp) REVERT: B 27 ILE cc_start: 0.7520 (mt) cc_final: 0.7077 (tt) REVERT: B 32 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8449 (mm-30) REVERT: B 453 ASP cc_start: 0.8267 (t0) cc_final: 0.7934 (t0) REVERT: C 77 ASP cc_start: 0.8758 (m-30) cc_final: 0.8477 (m-30) REVERT: C 526 GLU cc_start: 0.8713 (mp0) cc_final: 0.8465 (mp0) REVERT: C 593 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7386 (pp) REVERT: C 777 LEU cc_start: 0.9555 (mt) cc_final: 0.9218 (pp) REVERT: G 168 LEU cc_start: 0.9600 (tp) cc_final: 0.9352 (pp) REVERT: G 452 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8866 (tpt) REVERT: G 537 MET cc_start: 0.8263 (ttp) cc_final: 0.7589 (tpt) outliers start: 49 outliers final: 35 residues processed: 249 average time/residue: 0.1858 time to fit residues: 72.9499 Evaluate side-chains 244 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 542 CYS Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain G residue 177 PHE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 254 ASN Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain G residue 417 MET Chi-restraints excluded: chain G residue 452 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 238 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 156 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 259 optimal weight: 0.7980 chunk 266 optimal weight: 0.9990 chunk 230 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** A 843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.094127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.070463 restraints weight = 72513.921| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.64 r_work: 0.3120 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25212 Z= 0.116 Angle : 0.512 12.884 34054 Z= 0.256 Chirality : 0.040 0.172 3798 Planarity : 0.003 0.042 4344 Dihedral : 6.449 81.397 3408 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.99 % Allowed : 16.43 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.16), residues: 3049 helix: 1.48 (0.14), residues: 1523 sheet: -0.23 (0.34), residues: 288 loop : 0.20 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 384 TYR 0.016 0.001 TYR B 127 PHE 0.021 0.001 PHE C 527 TRP 0.039 0.001 TRP G 178 HIS 0.002 0.000 HIS C 486 Details of bonding type rmsd covalent geometry : bond 0.00269 (25212) covalent geometry : angle 0.51247 (34054) hydrogen bonds : bond 0.03310 ( 1154) hydrogen bonds : angle 3.94901 ( 3300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ARG cc_start: 0.8599 (ptm-80) cc_final: 0.8176 (ptm-80) REVERT: A 453 ASP cc_start: 0.8218 (t0) cc_final: 0.7939 (t0) REVERT: A 747 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8345 (ptpp) REVERT: B 27 ILE cc_start: 0.7426 (mt) cc_final: 0.7016 (tt) REVERT: B 32 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8449 (mm-30) REVERT: B 453 ASP cc_start: 0.8308 (t0) cc_final: 0.8091 (t0) REVERT: C 77 ASP cc_start: 0.8790 (m-30) cc_final: 0.8499 (m-30) REVERT: C 526 GLU cc_start: 0.8710 (mp0) cc_final: 0.8383 (mp0) REVERT: C 593 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7324 (pp) REVERT: C 763 MET cc_start: 0.8802 (ppp) cc_final: 0.8459 (ppp) REVERT: C 777 LEU cc_start: 0.9511 (mt) cc_final: 0.9203 (pp) REVERT: C 787 TRP cc_start: 0.8575 (t60) cc_final: 0.8310 (t60) REVERT: G 168 LEU cc_start: 0.9602 (tp) cc_final: 0.9359 (pp) REVERT: G 537 MET cc_start: 0.8254 (ttp) cc_final: 0.7564 (tpt) outliers start: 54 outliers final: 37 residues processed: 254 average time/residue: 0.1816 time to fit residues: 72.8816 Evaluate side-chains 242 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 542 CYS Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain G residue 173 ASP Chi-restraints excluded: chain G residue 177 PHE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 254 ASN Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain G residue 414 VAL Chi-restraints excluded: chain G residue 417 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 181 optimal weight: 0.6980 chunk 304 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 203 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 290 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 300 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN ** G 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.093800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.070174 restraints weight = 72841.135| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.54 r_work: 0.3113 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25212 Z= 0.127 Angle : 0.514 10.392 34054 Z= 0.258 Chirality : 0.040 0.166 3798 Planarity : 0.003 0.043 4344 Dihedral : 6.351 84.472 3406 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.99 % Allowed : 16.87 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.16), residues: 3049 helix: 1.52 (0.14), residues: 1527 sheet: -0.19 (0.34), residues: 286 loop : 0.21 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 384 TYR 0.029 0.001 TYR B 127 PHE 0.018 0.001 PHE C 527 TRP 0.027 0.001 TRP G 178 HIS 0.004 0.001 HIS G 221 Details of bonding type rmsd covalent geometry : bond 0.00295 (25212) covalent geometry : angle 0.51427 (34054) hydrogen bonds : bond 0.03323 ( 1154) hydrogen bonds : angle 3.91095 ( 3300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ARG cc_start: 0.8608 (ptm-80) cc_final: 0.8175 (ptm-80) REVERT: A 380 HIS cc_start: 0.8561 (m90) cc_final: 0.8304 (m90) REVERT: A 453 ASP cc_start: 0.8267 (t0) cc_final: 0.7985 (t0) REVERT: A 597 LYS cc_start: 0.8888 (tttm) cc_final: 0.8666 (tttm) REVERT: A 747 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8365 (ptpp) REVERT: B 27 ILE cc_start: 0.7428 (mt) cc_final: 0.7042 (tt) REVERT: B 32 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8446 (mm-30) REVERT: B 453 ASP cc_start: 0.8316 (t0) cc_final: 0.7961 (t0) REVERT: C 77 ASP cc_start: 0.8799 (m-30) cc_final: 0.8504 (m-30) REVERT: C 504 ARG cc_start: 0.7264 (mtm180) cc_final: 0.6474 (mpp80) REVERT: C 526 GLU cc_start: 0.8699 (mp0) cc_final: 0.8385 (mp0) REVERT: C 530 MET cc_start: 0.8908 (ptp) cc_final: 0.8231 (pmm) REVERT: C 593 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7357 (pp) REVERT: C 634 ARG cc_start: 0.7710 (tpp-160) cc_final: 0.7371 (tpp-160) REVERT: C 716 LYS cc_start: 0.9090 (tptp) cc_final: 0.8644 (mttt) REVERT: C 763 MET cc_start: 0.8790 (ppp) cc_final: 0.8555 (ppp) REVERT: C 777 LEU cc_start: 0.9504 (mt) cc_final: 0.9236 (pp) REVERT: C 787 TRP cc_start: 0.8669 (t60) cc_final: 0.8464 (t60) REVERT: G 154 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8725 (tt) REVERT: G 168 LEU cc_start: 0.9640 (tp) cc_final: 0.9390 (pp) REVERT: G 333 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8950 (ttmm) REVERT: G 488 HIS cc_start: 0.8005 (OUTLIER) cc_final: 0.7675 (m90) REVERT: G 537 MET cc_start: 0.8254 (ttp) cc_final: 0.7489 (tpt) outliers start: 54 outliers final: 43 residues processed: 249 average time/residue: 0.1895 time to fit residues: 73.9618 Evaluate side-chains 254 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 490 MET Chi-restraints excluded: chain C residue 542 CYS Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 173 ASP Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 254 ASN Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain G residue 333 LYS Chi-restraints excluded: chain G residue 414 VAL Chi-restraints excluded: chain G residue 417 MET Chi-restraints excluded: chain G residue 488 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 148 optimal weight: 0.0770 chunk 213 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 283 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 264 optimal weight: 0.0370 chunk 243 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 262 optimal weight: 0.6980 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.094535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.070940 restraints weight = 72755.043| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.52 r_work: 0.3134 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25212 Z= 0.102 Angle : 0.510 11.278 34054 Z= 0.255 Chirality : 0.039 0.197 3798 Planarity : 0.003 0.045 4344 Dihedral : 6.254 88.878 3406 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.55 % Allowed : 17.28 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.16), residues: 3049 helix: 1.60 (0.14), residues: 1530 sheet: -0.12 (0.34), residues: 286 loop : 0.27 (0.19), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 384 TYR 0.011 0.001 TYR B 127 PHE 0.016 0.001 PHE C 605 TRP 0.029 0.001 TRP G 178 HIS 0.003 0.000 HIS B 822 Details of bonding type rmsd covalent geometry : bond 0.00232 (25212) covalent geometry : angle 0.50983 (34054) hydrogen bonds : bond 0.03121 ( 1154) hydrogen bonds : angle 3.79792 ( 3300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ARG cc_start: 0.8598 (ptm-80) cc_final: 0.8192 (ptm-80) REVERT: A 453 ASP cc_start: 0.8237 (t0) cc_final: 0.7964 (t0) REVERT: A 747 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8618 (ptmt) REVERT: B 27 ILE cc_start: 0.7404 (mt) cc_final: 0.7015 (tt) REVERT: B 32 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8434 (mm-30) REVERT: B 453 ASP cc_start: 0.8288 (t0) cc_final: 0.7944 (t0) REVERT: B 819 ARG cc_start: 0.8022 (mtp180) cc_final: 0.7765 (ptp-170) REVERT: C 77 ASP cc_start: 0.8764 (m-30) cc_final: 0.8481 (m-30) REVERT: C 427 ARG cc_start: 0.8647 (mtm180) cc_final: 0.8312 (mtt180) REVERT: C 504 ARG cc_start: 0.7213 (mtm180) cc_final: 0.6347 (mpp80) REVERT: C 593 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7387 (pp) REVERT: C 634 ARG cc_start: 0.7691 (tpp-160) cc_final: 0.7400 (tpp80) REVERT: C 645 THR cc_start: 0.8398 (p) cc_final: 0.8126 (t) REVERT: C 777 LEU cc_start: 0.9482 (mt) cc_final: 0.9262 (pp) REVERT: G 154 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8742 (tt) REVERT: G 168 LEU cc_start: 0.9637 (tp) cc_final: 0.9388 (pp) REVERT: G 190 GLU cc_start: 0.8867 (tt0) cc_final: 0.8520 (mt-10) REVERT: G 537 MET cc_start: 0.8233 (ttp) cc_final: 0.7555 (tpt) outliers start: 42 outliers final: 38 residues processed: 249 average time/residue: 0.1919 time to fit residues: 75.0716 Evaluate side-chains 246 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 490 MET Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 173 ASP Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 254 ASN Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 414 VAL Chi-restraints excluded: chain G residue 417 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 155 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 chunk 205 optimal weight: 0.9990 chunk 238 optimal weight: 6.9990 chunk 126 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 292 optimal weight: 0.9980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.094755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071041 restraints weight = 72734.090| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.56 r_work: 0.3140 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25212 Z= 0.101 Angle : 0.514 11.770 34054 Z= 0.257 Chirality : 0.040 0.409 3798 Planarity : 0.003 0.045 4344 Dihedral : 6.140 84.992 3406 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.48 % Allowed : 17.31 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.16), residues: 3049 helix: 1.66 (0.14), residues: 1531 sheet: -0.10 (0.34), residues: 286 loop : 0.29 (0.19), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 384 TYR 0.019 0.001 TYR B 127 PHE 0.016 0.001 PHE C 605 TRP 0.025 0.001 TRP C 787 HIS 0.003 0.000 HIS B 822 Details of bonding type rmsd covalent geometry : bond 0.00230 (25212) covalent geometry : angle 0.51432 (34054) hydrogen bonds : bond 0.03068 ( 1154) hydrogen bonds : angle 3.74722 ( 3300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 ARG cc_start: 0.8527 (tmt-80) cc_final: 0.8296 (tmt-80) REVERT: A 368 ARG cc_start: 0.8594 (ptm-80) cc_final: 0.8189 (ptm-80) REVERT: A 380 HIS cc_start: 0.8582 (m90) cc_final: 0.8381 (m90) REVERT: A 453 ASP cc_start: 0.8250 (t0) cc_final: 0.8005 (t0) REVERT: A 747 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8645 (ptmt) REVERT: B 32 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8413 (mm-30) REVERT: B 453 ASP cc_start: 0.8314 (t0) cc_final: 0.7994 (t0) REVERT: C 77 ASP cc_start: 0.8772 (m-30) cc_final: 0.8487 (m-30) REVERT: C 504 ARG cc_start: 0.7154 (mtm180) cc_final: 0.6486 (mpp80) REVERT: C 530 MET cc_start: 0.8807 (ptp) cc_final: 0.8148 (pmm) REVERT: C 593 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7405 (pp) REVERT: C 597 LYS cc_start: 0.8645 (mttm) cc_final: 0.8256 (tttm) REVERT: C 634 ARG cc_start: 0.7683 (tpp-160) cc_final: 0.7348 (tpp-160) REVERT: C 645 THR cc_start: 0.8378 (p) cc_final: 0.8097 (t) REVERT: G 154 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8778 (tt) REVERT: G 168 LEU cc_start: 0.9639 (tp) cc_final: 0.9385 (pp) REVERT: G 190 GLU cc_start: 0.8893 (tt0) cc_final: 0.8533 (mt-10) REVERT: G 537 MET cc_start: 0.8220 (ttp) cc_final: 0.7527 (tpt) outliers start: 40 outliers final: 34 residues processed: 241 average time/residue: 0.1897 time to fit residues: 71.5112 Evaluate side-chains 244 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 254 ASN Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 414 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 297 optimal weight: 0.0000 chunk 299 optimal weight: 0.7980 chunk 224 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 64 optimal weight: 0.0070 chunk 142 optimal weight: 3.9990 overall best weight: 0.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.095181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.071855 restraints weight = 72526.494| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.68 r_work: 0.3149 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25212 Z= 0.095 Angle : 0.518 12.122 34054 Z= 0.256 Chirality : 0.040 0.340 3798 Planarity : 0.003 0.045 4344 Dihedral : 6.027 79.791 3405 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.48 % Allowed : 17.79 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.16), residues: 3049 helix: 1.67 (0.14), residues: 1538 sheet: -0.06 (0.34), residues: 286 loop : 0.28 (0.19), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 384 TYR 0.014 0.001 TYR B 127 PHE 0.016 0.001 PHE C 817 TRP 0.035 0.001 TRP C 787 HIS 0.004 0.000 HIS C 486 Details of bonding type rmsd covalent geometry : bond 0.00214 (25212) covalent geometry : angle 0.51764 (34054) hydrogen bonds : bond 0.02978 ( 1154) hydrogen bonds : angle 3.70340 ( 3300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6778.27 seconds wall clock time: 117 minutes 6.40 seconds (7026.40 seconds total)