Starting phenix.real_space_refine on Fri Mar 6 22:50:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y0c_10667/03_2026/6y0c_10667.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y0c_10667/03_2026/6y0c_10667.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/6y0c_10667/03_2026/6y0c_10667.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y0c_10667/03_2026/6y0c_10667.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y0c_10667/03_2026/6y0c_10667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y0c_10667/03_2026/6y0c_10667.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= 0.002 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: 6 Type Number sf(0) Gaussians P 19 5.49 5 S 132 5.16 5 C 11063 2.51 5 N 3001 2.21 5 O 3322 1.98 5 H 17430 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34967 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 11153 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 31, 'TRANS': 656} Chain breaks: 2 Chain: "B" Number of atoms: 10982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 10982 Classifications: {'peptide': 686} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 660} Chain breaks: 5 Chain: "C" Number of atoms: 12190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 12190 Classifications: {'peptide': 761} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 732} Chain breaks: 1 Chain: "IN1" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 642 Inner-chain residues flagged as termini: ['pdbres=" GIN1 14 "'] Classifications: {'RNA': 20} Modifications used: {'3*END': 2, '5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 6} Link IDs: {'rna2p': 5, 'rna3p': 14} Chain breaks: 2 Time building chain proxies: 5.64, per 1000 atoms: 0.16 Number of scatterers: 34967 At special positions: 0 Unit cell: (124.775, 133.455, 109.585, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 132 16.00 P 19 15.00 O 3322 8.00 N 3001 7.00 C 11063 6.00 H 17430 1.00 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: 3.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4038 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 22 sheets defined 50.7% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 3.553A pdb=" N ILE A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE A 12 " --> pdb=" O ILE A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 68 through 83 removed outlier: 3.582A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 146 through 167 removed outlier: 3.849A pdb=" N GLU A 167 " --> pdb=" O PHE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.707A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 233 Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.772A pdb=" N LYS A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 4.055A pdb=" N ILE A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 327 removed outlier: 3.839A pdb=" N TYR A 313 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 381 through 390 Processing helix chain 'A' and resid 409 through 427 Processing helix chain 'A' and resid 430 through 452 removed outlier: 3.791A pdb=" N LEU A 451 " --> pdb=" O THR A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 569 through 588 removed outlier: 3.566A pdb=" N THR A 573 " --> pdb=" O ARG A 569 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 601 Processing helix chain 'A' and resid 617 through 634 removed outlier: 5.163A pdb=" N ARG A 622 " --> pdb=" O ARG A 618 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL A 623 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'A' and resid 646 through 658 Processing helix chain 'A' and resid 666 through 677 removed outlier: 3.634A pdb=" N LEU A 670 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 700 removed outlier: 3.720A pdb=" N LYS A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 10 removed outlier: 3.791A pdb=" N MET B 8 " --> pdb=" O PRO B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 19 removed outlier: 4.501A pdb=" N SER B 19 " --> pdb=" O THR B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 86 through 102 Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.930A pdb=" N HIS B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS B 109 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 141 through 157 Processing helix chain 'B' and resid 164 through 178 removed outlier: 3.718A pdb=" N ASP B 177 " --> pdb=" O ILE B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 225 removed outlier: 3.785A pdb=" N LEU B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 268 removed outlier: 4.129A pdb=" N LYS B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 268 " --> pdb=" O ILE B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 295 removed outlier: 3.626A pdb=" N LYS B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.672A pdb=" N TYR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 347 removed outlier: 4.253A pdb=" N ALA B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 413 through 427 removed outlier: 4.038A pdb=" N THR B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU B 425 " --> pdb=" O GLY B 421 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR B 427 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 456 through 473 removed outlier: 3.627A pdb=" N TRP B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 Processing helix chain 'B' and resid 519 through 538 removed outlier: 4.044A pdb=" N PHE B 524 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 560 Processing helix chain 'B' and resid 571 through 584 removed outlier: 3.560A pdb=" N LYS B 582 " --> pdb=" O ASN B 578 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR B 583 " --> pdb=" O GLU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.881A pdb=" N LEU B 605 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 613 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 676 through 696 removed outlier: 3.529A pdb=" N GLU B 681 " --> pdb=" O ALA B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 728 Processing helix chain 'B' and resid 732 through 754 removed outlier: 3.725A pdb=" N ARG B 754 " --> pdb=" O ARG B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 17 Processing helix chain 'C' and resid 18 through 26 Processing helix chain 'C' and resid 30 through 39 removed outlier: 3.685A pdb=" N THR C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 57 removed outlier: 3.537A pdb=" N SER C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER C 57 " --> pdb=" O TRP C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 99 through 108 removed outlier: 3.955A pdb=" N ASN C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 162 through 174 Processing helix chain 'C' and resid 183 through 189 Processing helix chain 'C' and resid 189 through 200 removed outlier: 3.794A pdb=" N VAL C 193 " --> pdb=" O ASN C 189 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 259 through 277 removed outlier: 3.701A pdb=" N LYS C 263 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 294 Processing helix chain 'C' and resid 306 through 313 Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 402 through 417 Processing helix chain 'C' and resid 420 through 425 removed outlier: 3.978A pdb=" N LYS C 424 " --> pdb=" O GLY C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 436 removed outlier: 4.148A pdb=" N SER C 436 " --> pdb=" O MET C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 456 removed outlier: 3.613A pdb=" N SER C 456 " --> pdb=" O TRP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 467 removed outlier: 3.638A pdb=" N LEU C 460 " --> pdb=" O SER C 456 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 467 " --> pdb=" O LEU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 removed outlier: 3.889A pdb=" N ASP C 535 " --> pdb=" O THR C 532 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU C 536 " --> pdb=" O ILE C 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 532 through 536' Processing helix chain 'C' and resid 558 through 573 Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 590 through 595 removed outlier: 4.018A pdb=" N LEU C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR C 595 " --> pdb=" O TYR C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 590 through 595' Processing helix chain 'C' and resid 597 through 604 Processing helix chain 'C' and resid 605 through 607 No H-bonds generated for 'chain 'C' and resid 605 through 607' Processing helix chain 'C' and resid 608 through 610 No H-bonds generated for 'chain 'C' and resid 608 through 610' Processing helix chain 'C' and resid 611 through 630 removed outlier: 3.771A pdb=" N SER C 624 " --> pdb=" O ARG C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 641 Processing helix chain 'C' and resid 642 through 644 No H-bonds generated for 'chain 'C' and resid 642 through 644' Processing helix chain 'C' and resid 705 through 709 removed outlier: 3.923A pdb=" N LEU C 708 " --> pdb=" O SER C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 732 Processing helix chain 'C' and resid 758 through 771 removed outlier: 3.878A pdb=" N ASP C 762 " --> pdb=" O ALA C 758 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS C 771 " --> pdb=" O VAL C 767 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63 removed outlier: 3.522A pdb=" N VAL A 62 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.745A pdb=" N ALA B 454 " --> pdb=" O PHE B 300 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 274 removed outlier: 3.643A pdb=" N PHE A 271 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N PHE A 485 " --> pdb=" O PHE A 509 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 509 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 506 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS A 551 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 330 through 331 removed outlier: 4.478A pdb=" N ILE A 456 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 457 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 490 " --> pdb=" O LYS A 457 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ALA A 463 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU A 484 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N SER A 465 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASP A 482 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N PHE A 485 " --> pdb=" O PHE A 509 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 509 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 556 " --> pdb=" O TYR A 502 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 350 removed outlier: 3.504A pdb=" N GLU B 367 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE B 369 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 529 through 530 Processing sheet with id=AA7, first strand: chain 'A' and resid 611 through 616 removed outlier: 3.679A pdb=" N GLY A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN A 615 " --> pdb=" O TRP A 604 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP A 604 " --> pdb=" O GLN A 615 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 133 removed outlier: 3.692A pdb=" N ARG B 138 " --> pdb=" O ASP B 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 180 through 182 removed outlier: 3.634A pdb=" N ILE B 214 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 227 through 229 Processing sheet with id=AB3, first strand: chain 'B' and resid 350 through 352 Processing sheet with id=AB4, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 142 removed outlier: 6.547A pdb=" N TRP C 137 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN C 252 " --> pdb=" O TRP C 137 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU C 139 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 148 through 153 Processing sheet with id=AB7, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AB8, first strand: chain 'C' and resid 335 through 336 removed outlier: 3.545A pdb=" N LEU C 335 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 342 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU C 374 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C 397 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP C 395 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR C 497 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE C 396 " --> pdb=" O THR C 497 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 352 through 357 Processing sheet with id=AC1, first strand: chain 'C' and resid 469 through 471 Processing sheet with id=AC2, first strand: chain 'C' and resid 657 through 658 Processing sheet with id=AC3, first strand: chain 'C' and resid 684 through 685 Processing sheet with id=AC4, first strand: chain 'C' and resid 713 through 714 795 hydrogen bonds defined for protein. 2244 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: 8.89 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 17369 1.00 - 1.20: 61 1.20 - 1.40: 7105 1.40 - 1.61: 10566 1.61 - 1.81: 234 Bond restraints: 35335 Sorted by residual: bond pdb=" N3 UIN1 44 " pdb=" H3 UIN1 44 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.16e+01 bond pdb=" N3 UIN1 43 " pdb=" H3 UIN1 43 " ideal model delta sigma weight residual 0.860 1.039 -0.179 2.00e-02 2.50e+03 7.98e+01 bond pdb=" C6 UIN1 43 " pdb=" H6 UIN1 43 " ideal model delta sigma weight residual 0.930 1.085 -0.155 2.00e-02 2.50e+03 6.00e+01 bond pdb=" C5 UIN1 44 " pdb=" H5 UIN1 44 " ideal model delta sigma weight residual 0.930 1.084 -0.154 2.00e-02 2.50e+03 5.92e+01 bond pdb=" C5 UIN1 43 " pdb=" H5 UIN1 43 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.87e+01 ... (remaining 35330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.20: 63949 5.20 - 10.40: 18 10.40 - 15.59: 4 15.59 - 20.79: 4 20.79 - 25.99: 5 Bond angle restraints: 63980 Sorted by residual: angle pdb=" CD GLN A 43 " pdb=" NE2 GLN A 43 " pdb="HE22 GLN A 43 " ideal model delta sigma weight residual 120.00 145.99 -25.99 3.00e+00 1.11e-01 7.51e+01 angle pdb="HE21 GLN A 43 " pdb=" NE2 GLN A 43 " pdb="HE22 GLN A 43 " ideal model delta sigma weight residual 120.00 95.45 24.55 3.00e+00 1.11e-01 6.70e+01 angle pdb="HE21 GLN B 130 " pdb=" NE2 GLN B 130 " pdb="HE22 GLN B 130 " ideal model delta sigma weight residual 120.00 95.94 24.06 3.00e+00 1.11e-01 6.43e+01 angle pdb=" CD GLN B 130 " pdb=" NE2 GLN B 130 " pdb="HE22 GLN B 130 " ideal model delta sigma weight residual 120.00 143.98 -23.98 3.00e+00 1.11e-01 6.39e+01 angle pdb=" CD GLN A 43 " pdb=" NE2 GLN A 43 " pdb="HE21 GLN A 43 " ideal model delta sigma weight residual 120.00 97.77 22.23 3.00e+00 1.11e-01 5.49e+01 ... (remaining 63975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 15709 35.98 - 71.96: 771 71.96 - 107.94: 49 107.94 - 143.93: 2 143.93 - 179.91: 4 Dihedral angle restraints: 16535 sinusoidal: 9298 harmonic: 7237 Sorted by residual: dihedral pdb=" O4' UIN1 44 " pdb=" C1' UIN1 44 " pdb=" N1 UIN1 44 " pdb=" C2 UIN1 44 " ideal model delta sinusoidal sigma weight residual -160.00 14.88 -174.88 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' UIN1 42 " pdb=" C1' UIN1 42 " pdb=" N1 UIN1 42 " pdb=" C2 UIN1 42 " ideal model delta sinusoidal sigma weight residual -128.00 12.79 -140.79 1 1.70e+01 3.46e-03 5.90e+01 dihedral pdb=" C3' GIN1 14 " pdb=" C4' GIN1 14 " pdb=" O4' GIN1 14 " pdb=" C1' GIN1 14 " ideal model delta sinusoidal sigma weight residual 20.00 -10.28 30.28 1 8.00e+00 1.56e-02 2.05e+01 ... (remaining 16532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1909 0.042 - 0.084: 592 0.084 - 0.127: 153 0.127 - 0.169: 13 0.169 - 0.211: 4 Chirality restraints: 2671 Sorted by residual: chirality pdb=" C2' UIN1 44 " pdb=" C3' UIN1 44 " pdb=" O2' UIN1 44 " pdb=" C1' UIN1 44 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB THR A 553 " pdb=" CA THR A 553 " pdb=" OG1 THR A 553 " pdb=" CG2 THR A 553 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ARG B 573 " pdb=" N ARG B 573 " pdb=" C ARG B 573 " pdb=" CB ARG B 573 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.63e-01 ... (remaining 2668 not shown) Planarity restraints: 5072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 318 " 0.064 2.00e-02 2.50e+03 9.67e-02 1.40e+02 pdb=" CG ASN A 318 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 318 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 318 " -0.162 2.00e-02 2.50e+03 pdb="HD21 ASN A 318 " -0.031 2.00e-02 2.50e+03 pdb="HD22 ASN A 318 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 672 " 0.068 2.00e-02 2.50e+03 9.50e-02 1.35e+02 pdb=" CG ASN C 672 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN C 672 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 672 " -0.155 2.00e-02 2.50e+03 pdb="HD21 ASN C 672 " -0.024 2.00e-02 2.50e+03 pdb="HD22 ASN C 672 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 130 " -0.052 2.00e-02 2.50e+03 9.32e-02 1.30e+02 pdb=" CD GLN B 130 " 0.000 2.00e-02 2.50e+03 pdb=" OE1 GLN B 130 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN B 130 " 0.158 2.00e-02 2.50e+03 pdb="HE21 GLN B 130 " 0.041 2.00e-02 2.50e+03 pdb="HE22 GLN B 130 " -0.151 2.00e-02 2.50e+03 ... (remaining 5069 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 3416 2.21 - 2.81: 72862 2.81 - 3.40: 91606 3.40 - 4.00: 121263 4.00 - 4.60: 190528 Nonbonded interactions: 479675 Sorted by model distance: nonbonded pdb=" O CYS A 80 " pdb=" H LEU A 85 " model vdw 1.612 2.450 nonbonded pdb=" O PHE A 48 " pdb="HE21 GLN A 149 " model vdw 1.612 2.450 nonbonded pdb=" HZ3 LYS C 75 " pdb=" OD1 ASP C 85 " model vdw 1.620 2.450 nonbonded pdb=" OE1 GLU A 86 " pdb=" H GLU A 86 " model vdw 1.626 2.450 nonbonded pdb="HD21 ASN A 383 " pdb=" O MET B 1 " model vdw 1.650 2.450 ... (remaining 479670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.090 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: 0.180 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.050 Process input model: 33.340 Find NCS groups from input model: 0.210 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 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 : 0.006 0.059 17905 Z= 0.263 Angle : 0.683 6.061 24163 Z= 0.393 Chirality : 0.043 0.211 2671 Planarity : 0.006 0.056 3016 Dihedral : 16.933 174.881 6999 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.17 % Allowed : 14.41 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.17), residues: 2113 helix: 0.37 (0.16), residues: 963 sheet: -3.22 (0.32), residues: 210 loop : -2.58 (0.17), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 624 TYR 0.023 0.002 TYR B 6 PHE 0.030 0.003 PHE B 632 TRP 0.031 0.002 TRP C 53 HIS 0.011 0.002 HIS B 660 Details of bonding type rmsd covalent geometry : bond 0.00627 (17905) covalent geometry : angle 0.68339 (24163) hydrogen bonds : bond 0.15899 ( 791) hydrogen bonds : angle 6.25627 ( 2244) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 451 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 410 time to evaluate : 0.945 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.7037 (m-10) cc_final: 0.6334 (m-10) REVERT: A 96 ASP cc_start: 0.7431 (t0) cc_final: 0.6915 (t0) REVERT: A 411 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7493 (tp) REVERT: B 24 TYR cc_start: 0.7941 (m-10) cc_final: 0.7464 (m-10) REVERT: B 133 ASP cc_start: 0.7439 (t0) cc_final: 0.7206 (t0) REVERT: B 519 ASN cc_start: 0.7030 (p0) cc_final: 0.6692 (p0) REVERT: C 58 LYS cc_start: 0.4764 (OUTLIER) cc_final: 0.4428 (mppt) REVERT: C 383 THR cc_start: 0.7316 (OUTLIER) cc_final: 0.7080 (p) REVERT: C 481 MET cc_start: 0.7211 (ttt) cc_final: 0.6540 (ttm) REVERT: C 677 SER cc_start: 0.7550 (OUTLIER) cc_final: 0.6869 (t) REVERT: C 718 ASP cc_start: 0.7479 (t0) cc_final: 0.6467 (p0) outliers start: 41 outliers final: 14 residues processed: 441 average time/residue: 0.3776 time to fit residues: 233.6225 Evaluate side-chains 253 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 235 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 570 LYS Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 677 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.119450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.101186 restraints weight = 104102.920| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.04 r_work: 0.3476 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17905 Z= 0.169 Angle : 0.583 7.083 24163 Z= 0.316 Chirality : 0.039 0.155 2671 Planarity : 0.004 0.054 3016 Dihedral : 10.917 175.434 2626 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.48 % Allowed : 16.84 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.18), residues: 2113 helix: 0.95 (0.17), residues: 981 sheet: -2.08 (0.34), residues: 218 loop : -2.08 (0.18), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 466 TYR 0.013 0.001 TYR B 6 PHE 0.017 0.002 PHE A 48 TRP 0.010 0.001 TRP B 457 HIS 0.010 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00378 (17905) covalent geometry : angle 0.58274 (24163) hydrogen bonds : bond 0.04989 ( 791) hydrogen bonds : angle 4.83620 ( 2244) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 247 time to evaluate : 1.007 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7630 (tp30) cc_final: 0.7425 (tp30) REVERT: A 329 MET cc_start: 0.7011 (mtm) cc_final: 0.6622 (mtp) REVERT: B 41 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7966 (tt0) REVERT: B 96 MET cc_start: 0.8739 (mtt) cc_final: 0.8456 (mtt) REVERT: B 151 ASP cc_start: 0.8396 (m-30) cc_final: 0.8184 (m-30) REVERT: B 449 VAL cc_start: 0.8702 (t) cc_final: 0.8485 (p) REVERT: B 585 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7166 (mm-30) REVERT: B 678 MET cc_start: 0.5699 (mpp) cc_final: 0.5285 (mmm) REVERT: C 62 ILE cc_start: 0.6192 (mt) cc_final: 0.5881 (mt) REVERT: C 481 MET cc_start: 0.7680 (ttt) cc_final: 0.6977 (ttm) outliers start: 28 outliers final: 16 residues processed: 271 average time/residue: 0.3508 time to fit residues: 137.7813 Evaluate side-chains 228 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 675 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 13 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 158 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.116666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.098967 restraints weight = 105107.415| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.93 r_work: 0.3449 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17905 Z= 0.175 Angle : 0.544 5.984 24163 Z= 0.294 Chirality : 0.038 0.157 2671 Planarity : 0.004 0.048 3016 Dihedral : 10.640 172.493 2610 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.75 % Allowed : 16.84 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.18), residues: 2113 helix: 1.12 (0.17), residues: 987 sheet: -1.82 (0.34), residues: 230 loop : -1.90 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 466 TYR 0.013 0.001 TYR B 6 PHE 0.014 0.001 PHE B 106 TRP 0.009 0.001 TRP C 83 HIS 0.008 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00395 (17905) covalent geometry : angle 0.54392 (24163) hydrogen bonds : bond 0.04690 ( 791) hydrogen bonds : angle 4.54629 ( 2244) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 0.860 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: 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 7 GLU cc_start: 0.7780 (tp30) cc_final: 0.7524 (tp30) REVERT: A 329 MET cc_start: 0.7123 (mtm) cc_final: 0.6772 (mtp) REVERT: A 529 HIS cc_start: 0.7518 (p-80) cc_final: 0.7165 (p90) REVERT: B 41 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8257 (tt0) REVERT: B 96 MET cc_start: 0.8739 (mtt) cc_final: 0.8470 (mtt) REVERT: B 307 ASP cc_start: 0.7493 (m-30) cc_final: 0.7208 (p0) REVERT: B 585 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7417 (mm-30) REVERT: B 678 MET cc_start: 0.5944 (mpp) cc_final: 0.5668 (mmm) REVERT: C 62 ILE cc_start: 0.6718 (OUTLIER) cc_final: 0.6351 (mt) REVERT: C 481 MET cc_start: 0.7580 (ttt) cc_final: 0.6849 (ttm) outliers start: 33 outliers final: 25 residues processed: 241 average time/residue: 0.3382 time to fit residues: 119.8012 Evaluate side-chains 223 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 675 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 130 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 198 optimal weight: 0.9980 chunk 200 optimal weight: 0.0570 chunk 157 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.0370 chunk 172 optimal weight: 1.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.117004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.099370 restraints weight = 104452.090| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.91 r_work: 0.3455 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17905 Z= 0.122 Angle : 0.490 5.849 24163 Z= 0.262 Chirality : 0.037 0.157 2671 Planarity : 0.003 0.045 3016 Dihedral : 10.446 165.168 2610 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.11 % Allowed : 17.43 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.18), residues: 2113 helix: 1.38 (0.17), residues: 985 sheet: -1.55 (0.36), residues: 220 loop : -1.77 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 299 TYR 0.008 0.001 TYR B 6 PHE 0.011 0.001 PHE B 556 TRP 0.009 0.001 TRP C 53 HIS 0.008 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00276 (17905) covalent geometry : angle 0.49041 (24163) hydrogen bonds : bond 0.03988 ( 791) hydrogen bonds : angle 4.30194 ( 2244) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 0.964 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: 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 7 GLU cc_start: 0.7850 (tp30) cc_final: 0.7596 (tp30) REVERT: A 329 MET cc_start: 0.7004 (mtm) cc_final: 0.6646 (mtp) REVERT: B 307 ASP cc_start: 0.7332 (m-30) cc_final: 0.7090 (p0) REVERT: B 583 THR cc_start: 0.6498 (m) cc_final: 0.6282 (p) REVERT: B 678 MET cc_start: 0.5856 (mpp) cc_final: 0.5522 (mmm) REVERT: B 691 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7931 (ttm) REVERT: C 62 ILE cc_start: 0.6647 (mt) cc_final: 0.6427 (mt) REVERT: C 481 MET cc_start: 0.7554 (ttt) cc_final: 0.6844 (ttm) outliers start: 21 outliers final: 16 residues processed: 218 average time/residue: 0.2988 time to fit residues: 98.7987 Evaluate side-chains 207 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 675 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 49 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.115001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.097364 restraints weight = 105697.954| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.91 r_work: 0.3417 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17905 Z= 0.151 Angle : 0.504 5.892 24163 Z= 0.270 Chirality : 0.037 0.187 2671 Planarity : 0.003 0.043 3016 Dihedral : 10.351 158.698 2608 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.85 % Allowed : 17.06 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.18), residues: 2113 helix: 1.45 (0.17), residues: 983 sheet: -1.34 (0.37), residues: 213 loop : -1.75 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 418 TYR 0.012 0.001 TYR C 447 PHE 0.025 0.001 PHE C 658 TRP 0.007 0.001 TRP C 53 HIS 0.008 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00344 (17905) covalent geometry : angle 0.50396 (24163) hydrogen bonds : bond 0.04108 ( 791) hydrogen bonds : angle 4.31111 ( 2244) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.850 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: 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 7 GLU cc_start: 0.7891 (tp30) cc_final: 0.7637 (tp30) REVERT: A 329 MET cc_start: 0.7005 (mtm) cc_final: 0.6627 (mtp) REVERT: A 572 ILE cc_start: 0.8747 (mt) cc_final: 0.8524 (mp) REVERT: B 678 MET cc_start: 0.6016 (mpp) cc_final: 0.5686 (mmm) REVERT: C 62 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6511 (mt) REVERT: C 718 ASP cc_start: 0.7663 (t0) cc_final: 0.6499 (p0) outliers start: 35 outliers final: 26 residues processed: 235 average time/residue: 0.3080 time to fit residues: 108.8913 Evaluate side-chains 223 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 767 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 116 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.113423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.095703 restraints weight = 106100.549| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.92 r_work: 0.3389 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17905 Z= 0.185 Angle : 0.526 5.051 24163 Z= 0.284 Chirality : 0.038 0.160 2671 Planarity : 0.004 0.043 3016 Dihedral : 10.315 156.957 2606 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.85 % Allowed : 17.43 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.18), residues: 2113 helix: 1.36 (0.17), residues: 975 sheet: -1.33 (0.37), residues: 213 loop : -1.71 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 141 TYR 0.014 0.001 TYR C 447 PHE 0.026 0.002 PHE A 706 TRP 0.007 0.001 TRP B 457 HIS 0.010 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00421 (17905) covalent geometry : angle 0.52600 (24163) hydrogen bonds : bond 0.04317 ( 791) hydrogen bonds : angle 4.41016 ( 2244) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.973 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7965 (tp30) cc_final: 0.7719 (tp30) REVERT: A 329 MET cc_start: 0.7004 (mtm) cc_final: 0.6692 (mtp) REVERT: A 572 ILE cc_start: 0.8761 (mt) cc_final: 0.8524 (mp) REVERT: A 575 MET cc_start: 0.8532 (tpp) cc_final: 0.8288 (tpt) REVERT: B 678 MET cc_start: 0.6507 (mpp) cc_final: 0.6146 (mmm) REVERT: C 62 ILE cc_start: 0.6823 (OUTLIER) cc_final: 0.6563 (mt) REVERT: C 378 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7268 (tm-30) REVERT: C 481 MET cc_start: 0.7611 (ttt) cc_final: 0.6847 (ttm) REVERT: C 656 ARG cc_start: 0.8672 (mtm-85) cc_final: 0.8230 (mtm110) REVERT: C 718 ASP cc_start: 0.7683 (t0) cc_final: 0.6605 (p0) outliers start: 35 outliers final: 31 residues processed: 222 average time/residue: 0.3184 time to fit residues: 105.7842 Evaluate side-chains 222 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 570 LYS Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 767 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 97 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.113125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.095304 restraints weight = 106996.147| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.93 r_work: 0.3389 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17905 Z= 0.166 Angle : 0.509 5.427 24163 Z= 0.274 Chirality : 0.038 0.162 2671 Planarity : 0.003 0.045 3016 Dihedral : 10.280 156.060 2606 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.28 % Allowed : 16.84 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.18), residues: 2113 helix: 1.38 (0.17), residues: 975 sheet: -1.31 (0.37), residues: 213 loop : -1.69 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 150 TYR 0.011 0.001 TYR C 447 PHE 0.020 0.001 PHE A 90 TRP 0.007 0.001 TRP C 53 HIS 0.008 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00378 (17905) covalent geometry : angle 0.50939 (24163) hydrogen bonds : bond 0.04196 ( 791) hydrogen bonds : angle 4.36005 ( 2244) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 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: 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 7 GLU cc_start: 0.7977 (tp30) cc_final: 0.7727 (tp30) REVERT: A 329 MET cc_start: 0.7014 (mtm) cc_final: 0.6726 (mtp) REVERT: A 572 ILE cc_start: 0.8720 (mt) cc_final: 0.8516 (mp) REVERT: B 678 MET cc_start: 0.6430 (mpp) cc_final: 0.6189 (mmm) REVERT: B 679 MET cc_start: 0.6312 (tmm) cc_final: 0.5910 (tmm) REVERT: B 724 MET cc_start: 0.7792 (ttt) cc_final: 0.7483 (tpp) REVERT: C 51 MET cc_start: 0.8110 (tpp) cc_final: 0.7876 (tpp) REVERT: C 62 ILE cc_start: 0.6850 (OUTLIER) cc_final: 0.6623 (mt) REVERT: C 378 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7281 (tm-30) REVERT: C 481 MET cc_start: 0.7672 (ttt) cc_final: 0.6852 (ttm) REVERT: C 718 ASP cc_start: 0.7704 (t0) cc_final: 0.6626 (p0) outliers start: 43 outliers final: 37 residues processed: 230 average time/residue: 0.3203 time to fit residues: 108.9384 Evaluate side-chains 226 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 570 LYS Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 767 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 198 optimal weight: 0.8980 chunk 84 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.113212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.095432 restraints weight = 106649.680| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.92 r_work: 0.3392 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17905 Z= 0.138 Angle : 0.490 6.231 24163 Z= 0.262 Chirality : 0.037 0.159 2671 Planarity : 0.003 0.046 3016 Dihedral : 10.205 155.774 2606 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.01 % Allowed : 17.21 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.18), residues: 2113 helix: 1.53 (0.17), residues: 974 sheet: -1.30 (0.37), residues: 214 loop : -1.66 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 150 TYR 0.010 0.001 TYR C 447 PHE 0.024 0.001 PHE A 706 TRP 0.008 0.001 TRP C 53 HIS 0.007 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00313 (17905) covalent geometry : angle 0.49023 (24163) hydrogen bonds : bond 0.03941 ( 791) hydrogen bonds : angle 4.26751 ( 2244) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.962 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: 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 7 GLU cc_start: 0.7979 (tp30) cc_final: 0.7721 (tp30) REVERT: A 184 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: A 329 MET cc_start: 0.6988 (mtm) cc_final: 0.6719 (mtp) REVERT: B 175 MET cc_start: 0.8871 (mtp) cc_final: 0.8650 (mtp) REVERT: B 679 MET cc_start: 0.6396 (tmm) cc_final: 0.6028 (tmm) REVERT: B 724 MET cc_start: 0.7807 (ttt) cc_final: 0.7505 (tpp) REVERT: C 62 ILE cc_start: 0.6834 (OUTLIER) cc_final: 0.6517 (mt) REVERT: C 378 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7243 (tm-30) REVERT: C 380 LYS cc_start: 0.8145 (mtmt) cc_final: 0.7918 (mttm) REVERT: C 481 MET cc_start: 0.7582 (ttt) cc_final: 0.6775 (ttm) REVERT: C 718 ASP cc_start: 0.7676 (t0) cc_final: 0.6625 (p0) outliers start: 38 outliers final: 31 residues processed: 227 average time/residue: 0.3316 time to fit residues: 110.8558 Evaluate side-chains 221 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 767 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 87 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 210 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 209 optimal weight: 0.5980 chunk 163 optimal weight: 0.0770 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.113850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.096228 restraints weight = 105856.347| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.91 r_work: 0.3401 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 17905 Z= 0.110 Angle : 0.472 6.525 24163 Z= 0.250 Chirality : 0.036 0.159 2671 Planarity : 0.003 0.047 3016 Dihedral : 9.980 156.188 2601 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.43 % Allowed : 18.01 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.19), residues: 2113 helix: 1.70 (0.17), residues: 974 sheet: -1.24 (0.37), residues: 214 loop : -1.61 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 150 TYR 0.008 0.001 TYR C 447 PHE 0.012 0.001 PHE C 658 TRP 0.009 0.001 TRP C 53 HIS 0.007 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00249 (17905) covalent geometry : angle 0.47181 (24163) hydrogen bonds : bond 0.03651 ( 791) hydrogen bonds : angle 4.12331 ( 2244) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 0.947 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: 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 7 GLU cc_start: 0.8028 (tp30) cc_final: 0.7752 (tp30) REVERT: A 184 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: A 329 MET cc_start: 0.6962 (mtm) cc_final: 0.6692 (mtp) REVERT: B 151 ASP cc_start: 0.8413 (m-30) cc_final: 0.8010 (m-30) REVERT: B 175 MET cc_start: 0.8814 (mtp) cc_final: 0.8562 (mtp) REVERT: B 679 MET cc_start: 0.6426 (tmm) cc_final: 0.6114 (tmm) REVERT: B 724 MET cc_start: 0.7803 (ttt) cc_final: 0.7505 (tpp) REVERT: C 62 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6524 (mt) REVERT: C 378 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7217 (tm-30) REVERT: C 380 LYS cc_start: 0.8166 (mtmt) cc_final: 0.7939 (mttm) REVERT: C 481 MET cc_start: 0.7584 (ttt) cc_final: 0.6714 (ttm) REVERT: C 718 ASP cc_start: 0.7627 (t0) cc_final: 0.6558 (p0) outliers start: 27 outliers final: 22 residues processed: 219 average time/residue: 0.3248 time to fit residues: 104.9753 Evaluate side-chains 213 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 767 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 208 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 30 optimal weight: 0.0670 chunk 187 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.113190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.095566 restraints weight = 106218.997| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.91 r_work: 0.3394 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17905 Z= 0.137 Angle : 0.491 7.278 24163 Z= 0.261 Chirality : 0.037 0.157 2671 Planarity : 0.003 0.050 3016 Dihedral : 9.966 155.929 2601 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.75 % Allowed : 17.80 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.18), residues: 2113 helix: 1.64 (0.17), residues: 977 sheet: -1.27 (0.37), residues: 214 loop : -1.59 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 558 TYR 0.010 0.001 TYR C 447 PHE 0.014 0.001 PHE A 706 TRP 0.007 0.001 TRP C 53 HIS 0.007 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00315 (17905) covalent geometry : angle 0.49132 (24163) hydrogen bonds : bond 0.03806 ( 791) hydrogen bonds : angle 4.16107 ( 2244) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 62 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.949 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: 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 7 GLU cc_start: 0.7882 (tp30) cc_final: 0.7658 (tp30) REVERT: A 184 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: A 329 MET cc_start: 0.7004 (mtm) cc_final: 0.6743 (mtp) REVERT: B 151 ASP cc_start: 0.8410 (m-30) cc_final: 0.7996 (m-30) REVERT: B 175 MET cc_start: 0.8921 (mtp) cc_final: 0.8683 (mtp) REVERT: B 679 MET cc_start: 0.6435 (tmm) cc_final: 0.6116 (tmm) REVERT: B 724 MET cc_start: 0.7768 (ttt) cc_final: 0.7553 (tpp) REVERT: C 62 ILE cc_start: 0.6694 (OUTLIER) cc_final: 0.6386 (mt) REVERT: C 378 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7152 (tm-30) REVERT: C 380 LYS cc_start: 0.8176 (mtmt) cc_final: 0.7949 (mttm) REVERT: C 481 MET cc_start: 0.7587 (ttt) cc_final: 0.6728 (ttm) REVERT: C 664 PHE cc_start: 0.8930 (p90) cc_final: 0.8607 (p90) REVERT: C 718 ASP cc_start: 0.7633 (t0) cc_final: 0.6565 (p0) outliers start: 33 outliers final: 27 residues processed: 217 average time/residue: 0.3276 time to fit residues: 105.6796 Evaluate side-chains 217 residues out of total 1888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 585 GLU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 502 PHE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 111 CYS Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 767 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 195 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 124 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.112576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.094554 restraints weight = 106186.621| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.96 r_work: 0.3363 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17905 Z= 0.138 Angle : 0.492 7.162 24163 Z= 0.262 Chirality : 0.037 0.158 2671 Planarity : 0.003 0.052 3016 Dihedral : 9.938 155.566 2601 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.69 % Allowed : 17.80 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.18), residues: 2113 helix: 1.65 (0.17), residues: 982 sheet: -1.27 (0.37), residues: 214 loop : -1.56 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 558 TYR 0.010 0.001 TYR C 447 PHE 0.013 0.001 PHE C 658 TRP 0.007 0.001 TRP C 53 HIS 0.009 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00317 (17905) covalent geometry : angle 0.49220 (24163) hydrogen bonds : bond 0.03849 ( 791) hydrogen bonds : angle 4.16644 ( 2244) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 6127.28 seconds wall clock time: 104 minutes 21.81 seconds (6261.81 seconds total)