Starting phenix.real_space_refine on Wed Jan 14 19:40:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m2y_23637/01_2026/7m2y_23637.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m2y_23637/01_2026/7m2y_23637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m2y_23637/01_2026/7m2y_23637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m2y_23637/01_2026/7m2y_23637.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m2y_23637/01_2026/7m2y_23637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m2y_23637/01_2026/7m2y_23637.map" } resolution = 4.03 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= 0.005 sd= 0.822 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 80 5.16 5 C 11819 2.51 5 N 3115 2.21 5 O 3542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18560 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3447 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 1 Chain: "B" Number of atoms: 3491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3491 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 20, 'TRANS': 426} Chain breaks: 1 Chain: "C" Number of atoms: 5435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5435 Classifications: {'peptide': 656} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 636} Chain breaks: 2 Chain: "D" Number of atoms: 5868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5868 Classifications: {'peptide': 703} Link IDs: {'PTRANS': 25, 'TRANS': 677} Chain breaks: 5 Chain: "U" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 263 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.23, per 1000 atoms: 0.23 Number of scatterers: 18560 At special positions: 0 Unit cell: (136.157, 144.667, 168.778, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 4 15.00 O 3542 8.00 N 3115 7.00 C 11819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 899.0 milliseconds 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4370 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 12 sheets defined 63.5% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 72 through 83 Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 115 through 129 removed outlier: 3.675A pdb=" N SER A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 179 through 198 removed outlier: 5.278A pdb=" N TYR A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 252 through 260 removed outlier: 4.212A pdb=" N SER A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N THR A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 298 through 299 No H-bonds generated for 'chain 'A' and resid 298 through 299' Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 327 through 335 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 399 removed outlier: 3.855A pdb=" N THR A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP A 395 " --> pdb=" O CYS A 391 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.891A pdb=" N ASN A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL A 409 " --> pdb=" O ASN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 415 removed outlier: 4.016A pdb=" N SER A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 440 Processing helix chain 'A' and resid 442 through 452 removed outlier: 4.015A pdb=" N LEU A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N VAL A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 29 removed outlier: 3.508A pdb=" N PHE B 20 " --> pdb=" O HIS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 97 through 102 removed outlier: 4.044A pdb=" N GLY B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.971A pdb=" N THR B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 128 removed outlier: 3.594A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 162 Processing helix chain 'B' and resid 183 through 195 removed outlier: 4.026A pdb=" N ILE B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 removed outlier: 3.577A pdb=" N ASN B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 226 Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 290 through 297 removed outlier: 4.112A pdb=" N MET B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 Proline residue: B 301 - end of helix Processing helix chain 'B' and resid 329 through 340 removed outlier: 3.849A pdb=" N ARG B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 334 " --> pdb=" O GLN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 349 Processing helix chain 'B' and resid 382 through 386 Processing helix chain 'B' and resid 387 through 399 Processing helix chain 'B' and resid 415 through 440 Processing helix chain 'B' and resid 441 through 442 No H-bonds generated for 'chain 'B' and resid 441 through 442' Processing helix chain 'B' and resid 443 through 447 Processing helix chain 'C' and resid 166 through 172 Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 180 through 193 removed outlier: 3.852A pdb=" N SER C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 243 removed outlier: 4.494A pdb=" N ALA C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 274 Processing helix chain 'C' and resid 279 through 301 removed outlier: 4.734A pdb=" N GLU C 289 " --> pdb=" O ARG C 285 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASN C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 320 Processing helix chain 'C' and resid 324 through 353 removed outlier: 3.886A pdb=" N LEU C 341 " --> pdb=" O SER C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 395 through 416 Processing helix chain 'C' and resid 418 through 435 Processing helix chain 'C' and resid 442 through 467 removed outlier: 3.722A pdb=" N ASN C 465 " --> pdb=" O ASN C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 482 Processing helix chain 'C' and resid 485 through 496 removed outlier: 3.636A pdb=" N MET C 489 " --> pdb=" O LYS C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 502 Processing helix chain 'C' and resid 508 through 523 Processing helix chain 'C' and resid 525 through 530 Processing helix chain 'C' and resid 535 through 539 Processing helix chain 'C' and resid 554 through 556 No H-bonds generated for 'chain 'C' and resid 554 through 556' Processing helix chain 'C' and resid 568 through 573 removed outlier: 3.797A pdb=" N ASN C 573 " --> pdb=" O SER C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 615 Processing helix chain 'C' and resid 621 through 627 removed outlier: 4.157A pdb=" N ARG C 625 " --> pdb=" O ASN C 621 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 627 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 655 removed outlier: 3.501A pdb=" N ARG C 633 " --> pdb=" O ASN C 629 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE C 634 " --> pdb=" O LYS C 630 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 635 " --> pdb=" O LEU C 631 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN C 640 " --> pdb=" O ILE C 636 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 removed outlier: 3.723A pdb=" N GLN C 669 " --> pdb=" O THR C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 737 Processing helix chain 'C' and resid 758 through 790 removed outlier: 4.309A pdb=" N LEU C 762 " --> pdb=" O TYR C 758 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 763 " --> pdb=" O PRO C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 832 removed outlier: 3.971A pdb=" N LYS C 804 " --> pdb=" O GLY C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 845 Processing helix chain 'D' and resid 43 through 47 Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 99 through 126 removed outlier: 4.441A pdb=" N TYR D 112 " --> pdb=" O ARG D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 149 Processing helix chain 'D' and resid 149 through 157 Processing helix chain 'D' and resid 157 through 165 Processing helix chain 'D' and resid 169 through 180 Processing helix chain 'D' and resid 181 through 206 Processing helix chain 'D' and resid 225 through 229 Processing helix chain 'D' and resid 244 through 258 removed outlier: 3.551A pdb=" N ILE D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 290 removed outlier: 3.925A pdb=" N GLN D 277 " --> pdb=" O ASN D 273 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASP D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 337 through 362 Processing helix chain 'D' and resid 380 through 386 Processing helix chain 'D' and resid 388 through 412 Processing helix chain 'D' and resid 414 through 427 Processing helix chain 'D' and resid 431 through 447 removed outlier: 5.319A pdb=" N LYS D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN D 442 " --> pdb=" O PHE D 438 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY D 444 " --> pdb=" O THR D 440 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 452 removed outlier: 3.751A pdb=" N ASN D 452 " --> pdb=" O HIS D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 471 removed outlier: 4.291A pdb=" N LEU D 461 " --> pdb=" O ASN D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 481 Processing helix chain 'D' and resid 490 through 495 Processing helix chain 'D' and resid 496 through 498 No H-bonds generated for 'chain 'D' and resid 496 through 498' Processing helix chain 'D' and resid 567 through 572 Processing helix chain 'D' and resid 575 through 607 Processing helix chain 'D' and resid 609 through 614 removed outlier: 4.017A pdb=" N TYR D 614 " --> pdb=" O SER D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 625 through 651 Processing helix chain 'D' and resid 651 through 663 Processing helix chain 'D' and resid 668 through 685 Processing helix chain 'D' and resid 686 through 691 Processing helix chain 'D' and resid 692 through 717 removed outlier: 5.038A pdb=" N GLN D 698 " --> pdb=" O PRO D 694 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG D 714 " --> pdb=" O ILE D 710 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ALA D 715 " --> pdb=" O LYS D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 725 Proline residue: D 722 - end of helix Processing helix chain 'D' and resid 753 through 786 Processing helix chain 'D' and resid 802 through 810 Processing helix chain 'U' and resid 118 through 140 Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 68 removed outlier: 6.351A pdb=" N THR A 7 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE A 136 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N TYR A 170 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 138 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL A 172 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N HIS A 140 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 202 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N PHE A 267 " --> pdb=" O MET A 380 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N MET A 380 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N SER A 373 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE A 322 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET A 375 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASN A 320 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU A 377 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL A 318 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN A 379 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 56 Processing sheet with id=AA3, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.464A pdb=" N TRP B 93 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N MET B 68 " --> pdb=" O TRP B 93 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ILE B 67 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR B 7 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N MET B 69 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLN B 9 " --> pdb=" O MET B 69 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU B 4 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLN B 137 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 6 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU B 139 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU B 8 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU B 134 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N THR B 168 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE B 136 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N TYR B 170 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 138 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL B 172 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N HIS B 140 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N VAL B 202 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR B 169 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N PHE B 204 " --> pdb=" O THR B 169 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER B 171 " --> pdb=" O PHE B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 54 through 56 Processing sheet with id=AA5, first strand: chain 'B' and resid 269 through 272 removed outlier: 6.711A pdb=" N SER B 373 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE B 322 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N MET B 375 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN B 320 " --> pdb=" O MET B 375 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU B 377 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL B 318 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN B 379 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N HIS B 353 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 318 " --> pdb=" O HIS B 353 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ASN B 355 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN B 320 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 207 through 209 Processing sheet with id=AA7, first strand: chain 'C' and resid 364 through 366 Processing sheet with id=AA8, first strand: chain 'C' and resid 541 through 545 Processing sheet with id=AA9, first strand: chain 'C' and resid 681 through 683 Processing sheet with id=AB1, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AB2, first strand: chain 'D' and resid 232 through 235 removed outlier: 7.023A pdb=" N ALA D 233 " --> pdb=" O ILE D 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 482 through 486 1015 hydrogen bonds defined for protein. 2946 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: 3.39 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 3170 1.30 - 1.44: 5553 1.44 - 1.57: 10016 1.57 - 1.71: 65 1.71 - 1.85: 138 Bond restraints: 18942 Sorted by residual: bond pdb=" CB HIS A 29 " pdb=" CG HIS A 29 " ideal model delta sigma weight residual 1.497 1.372 0.125 1.40e-02 5.10e+03 7.99e+01 bond pdb=" CB TYR D 190 " pdb=" CG TYR D 190 " ideal model delta sigma weight residual 1.512 1.338 0.174 2.20e-02 2.07e+03 6.28e+01 bond pdb=" CB TYR C 288 " pdb=" CG TYR C 288 " ideal model delta sigma weight residual 1.512 1.348 0.164 2.20e-02 2.07e+03 5.56e+01 bond pdb=" CB PHE D 78 " pdb=" CG PHE D 78 " ideal model delta sigma weight residual 1.502 1.339 0.163 2.30e-02 1.89e+03 5.03e+01 bond pdb=" CB PHE C 267 " pdb=" CG PHE C 267 " ideal model delta sigma weight residual 1.502 1.352 0.150 2.30e-02 1.89e+03 4.24e+01 ... (remaining 18937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 24221 3.66 - 7.32: 1337 7.32 - 10.99: 73 10.99 - 14.65: 7 14.65 - 18.31: 1 Bond angle restraints: 25639 Sorted by residual: angle pdb=" N THR B 201 " pdb=" CA THR B 201 " pdb=" C THR B 201 " ideal model delta sigma weight residual 108.79 127.10 -18.31 1.53e+00 4.27e-01 1.43e+02 angle pdb=" N ASP A 70 " pdb=" CA ASP A 70 " pdb=" C ASP A 70 " ideal model delta sigma weight residual 111.71 124.32 -12.61 1.15e+00 7.56e-01 1.20e+02 angle pdb=" N GLN D 51 " pdb=" CA GLN D 51 " pdb=" C GLN D 51 " ideal model delta sigma weight residual 113.88 101.33 12.55 1.23e+00 6.61e-01 1.04e+02 angle pdb=" N LEU C 792 " pdb=" CA LEU C 792 " pdb=" C LEU C 792 " ideal model delta sigma weight residual 113.41 101.32 12.09 1.22e+00 6.72e-01 9.82e+01 angle pdb=" N ILE D 804 " pdb=" CA ILE D 804 " pdb=" C ILE D 804 " ideal model delta sigma weight residual 111.00 101.30 9.70 1.09e+00 8.42e-01 7.93e+01 ... (remaining 25634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 11015 17.98 - 35.96: 314 35.96 - 53.94: 78 53.94 - 71.92: 47 71.92 - 89.90: 8 Dihedral angle restraints: 11462 sinusoidal: 4722 harmonic: 6740 Sorted by residual: dihedral pdb=" C5' GDP B 501 " pdb=" O5' GDP B 501 " pdb=" PA GDP B 501 " pdb=" O3A GDP B 501 " ideal model delta sinusoidal sigma weight residual 179.98 -102.97 -77.05 1 2.00e+01 2.50e-03 1.86e+01 dihedral pdb=" C5' GDP A 501 " pdb=" O5' GDP A 501 " pdb=" PA GDP A 501 " pdb=" O3A GDP A 501 " ideal model delta sinusoidal sigma weight residual 179.98 -103.00 -77.02 1 2.00e+01 2.50e-03 1.86e+01 dihedral pdb=" C ASP B 97 " pdb=" N ASP B 97 " pdb=" CA ASP B 97 " pdb=" CB ASP B 97 " ideal model delta harmonic sigma weight residual -122.60 -112.18 -10.42 0 2.50e+00 1.60e-01 1.74e+01 ... (remaining 11459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1619 0.082 - 0.164: 895 0.164 - 0.246: 266 0.246 - 0.328: 67 0.328 - 0.410: 9 Chirality restraints: 2856 Sorted by residual: chirality pdb=" CA THR B 201 " pdb=" N THR B 201 " pdb=" C THR B 201 " pdb=" CB THR B 201 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CG LEU B 150 " pdb=" CB LEU B 150 " pdb=" CD1 LEU B 150 " pdb=" CD2 LEU B 150 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CB VAL B 419 " pdb=" CA VAL B 419 " pdb=" CG1 VAL B 419 " pdb=" CG2 VAL B 419 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 2853 not shown) Planarity restraints: 3297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 185 " 0.103 2.00e-02 2.50e+03 5.34e-02 5.70e+01 pdb=" CG TYR A 185 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 185 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR A 185 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR A 185 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 185 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 185 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 185 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 297 " -0.084 2.00e-02 2.50e+03 4.67e-02 4.37e+01 pdb=" CG TYR C 297 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR C 297 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR C 297 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR C 297 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR C 297 " 0.025 2.00e-02 2.50e+03 pdb=" CZ TYR C 297 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR C 297 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 93 " 0.066 2.00e-02 2.50e+03 3.49e-02 3.05e+01 pdb=" CG TRP A 93 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP A 93 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 93 " -0.030 2.00e-02 2.50e+03 pdb=" NE1 TRP A 93 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP A 93 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 93 " -0.053 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 93 " 0.033 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 93 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP A 93 " 0.045 2.00e-02 2.50e+03 ... (remaining 3294 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 119 2.55 - 3.14: 16614 3.14 - 3.72: 31226 3.72 - 4.31: 45711 4.31 - 4.90: 69835 Nonbonded interactions: 163505 Sorted by model distance: nonbonded pdb=" OG1 THR A 146 " pdb=" O1B GDP A 501 " model vdw 1.961 3.040 nonbonded pdb=" CB ASN C 621 " pdb=" CD PRO C 622 " model vdw 2.086 3.840 nonbonded pdb=" OG SER A 141 " pdb=" C4' GDP A 501 " model vdw 2.242 3.470 nonbonded pdb=" CA GLY B 144 " pdb=" O5' GDP B 501 " model vdw 2.246 3.440 nonbonded pdb=" OH TYR C 288 " pdb=" OH TYR D 123 " model vdw 2.256 3.040 ... (remaining 163500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 3 through 277 or resid 288 through 501)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.590 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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 : 0.023 0.660 18944 Z= 1.310 Angle : 1.803 18.309 25639 Z= 1.236 Chirality : 0.107 0.410 2856 Planarity : 0.010 0.053 3297 Dihedral : 10.989 89.903 7092 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.18 % Favored : 97.56 % Rotamer: Outliers : 0.05 % Allowed : 0.53 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 (0.17), residues: 2250 helix: -0.11 (0.13), residues: 1248 sheet: -0.07 (0.46), residues: 137 loop : 0.56 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 243 TYR 0.103 0.011 TYR A 185 PHE 0.052 0.007 PHE A 86 TRP 0.066 0.011 TRP A 93 HIS 0.014 0.003 HIS D 633 Details of bonding type rmsd covalent geometry : bond 0.02207 (18942) covalent geometry : angle 1.80257 (25639) hydrogen bonds : bond 0.17354 ( 1015) hydrogen bonds : angle 7.62814 ( 2946) Misc. bond : bond 0.50086 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 803 time to evaluate : 0.771 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 53 PHE cc_start: 0.8480 (m-80) cc_final: 0.8280 (m-10) REVERT: A 75 VAL cc_start: 0.6825 (t) cc_final: 0.5635 (t) REVERT: A 187 THR cc_start: 0.9030 (m) cc_final: 0.8818 (p) REVERT: A 310 MET cc_start: 0.8647 (mmm) cc_final: 0.8362 (tpp) REVERT: A 322 ILE cc_start: 0.9248 (mm) cc_final: 0.8633 (tp) REVERT: A 376 MET cc_start: 0.8394 (ttm) cc_final: 0.7836 (tpp) REVERT: A 377 LEU cc_start: 0.8964 (mp) cc_final: 0.8481 (mt) REVERT: A 407 TYR cc_start: 0.7446 (m-80) cc_final: 0.7199 (m-10) REVERT: B 7 THR cc_start: 0.8318 (p) cc_final: 0.7461 (t) REVERT: B 8 LEU cc_start: 0.8149 (tp) cc_final: 0.7644 (mt) REVERT: B 9 GLN cc_start: 0.5898 (mp10) cc_final: 0.5596 (mt0) REVERT: B 17 VAL cc_start: 0.9271 (t) cc_final: 0.8864 (p) REVERT: B 22 TRP cc_start: 0.7971 (m100) cc_final: 0.7644 (m100) REVERT: B 51 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7964 (tmmt) REVERT: B 128 ASP cc_start: 0.8650 (m-30) cc_final: 0.8357 (m-30) REVERT: B 158 LEU cc_start: 0.9068 (mt) cc_final: 0.8802 (mt) REVERT: B 249 TYR cc_start: 0.5820 (m-80) cc_final: 0.5493 (m-80) REVERT: B 293 ASP cc_start: 0.7735 (m-30) cc_final: 0.5748 (m-30) REVERT: C 186 LYS cc_start: 0.9121 (mttt) cc_final: 0.8884 (mmmm) REVERT: C 304 LEU cc_start: 0.9051 (tt) cc_final: 0.8756 (tp) REVERT: C 347 MET cc_start: 0.8241 (mtp) cc_final: 0.7952 (mtm) REVERT: C 379 TYR cc_start: 0.7613 (m-10) cc_final: 0.7186 (m-10) REVERT: C 495 LYS cc_start: 0.9343 (mmmt) cc_final: 0.8801 (mmtm) REVERT: C 604 MET cc_start: 0.8014 (ptp) cc_final: 0.7318 (ptp) REVERT: C 653 LEU cc_start: 0.9167 (mt) cc_final: 0.8944 (mp) REVERT: C 781 ASP cc_start: 0.7787 (m-30) cc_final: 0.7586 (p0) REVERT: D 58 LEU cc_start: 0.8985 (mt) cc_final: 0.8571 (mt) REVERT: D 68 ILE cc_start: 0.9021 (pt) cc_final: 0.8766 (pt) REVERT: D 180 THR cc_start: 0.8926 (p) cc_final: 0.8566 (t) REVERT: D 264 SER cc_start: 0.8485 (t) cc_final: 0.7557 (p) REVERT: D 343 LEU cc_start: 0.9012 (tp) cc_final: 0.8649 (tp) REVERT: D 352 ILE cc_start: 0.9085 (mt) cc_final: 0.8849 (tt) REVERT: D 425 ILE cc_start: 0.9077 (mt) cc_final: 0.8791 (mt) REVERT: D 461 LEU cc_start: 0.8579 (mt) cc_final: 0.8020 (pp) REVERT: D 633 HIS cc_start: 0.8141 (t-90) cc_final: 0.7692 (t-90) REVERT: D 709 PHE cc_start: 0.6654 (t80) cc_final: 0.6307 (t80) REVERT: U 121 GLU cc_start: 0.8471 (tp30) cc_final: 0.8019 (tp30) outliers start: 1 outliers final: 0 residues processed: 804 average time/residue: 0.1627 time to fit residues: 190.9310 Evaluate side-chains 466 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 466 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.0470 chunk 212 optimal weight: 8.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN B 385 ASN C 222 HIS C 232 GLN C 290 ASN C 380 HIS C 423 ASN C 642 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN D 434 ASN D 442 ASN D 464 ASN D 565 ASN ** D 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 HIS D 637 ASN D 649 GLN ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 122 GLN U 127 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.111499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.085759 restraints weight = 69280.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.088916 restraints weight = 33865.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.090899 restraints weight = 19881.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.092171 restraints weight = 13196.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.092913 restraints weight = 9720.693| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 18944 Z= 0.231 Angle : 0.841 13.744 25639 Z= 0.454 Chirality : 0.048 0.228 2856 Planarity : 0.006 0.070 3297 Dihedral : 6.539 84.167 2505 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.93 % Favored : 96.84 % Rotamer: Outliers : 0.24 % Allowed : 2.58 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.20 (0.17), residues: 2250 helix: 0.37 (0.14), residues: 1261 sheet: -0.13 (0.42), residues: 132 loop : 0.06 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 193 TYR 0.031 0.003 TYR A 247 PHE 0.040 0.003 PHE B 394 TRP 0.024 0.003 TRP B 347 HIS 0.014 0.002 HIS D 638 Details of bonding type rmsd covalent geometry : bond 0.00481 (18942) covalent geometry : angle 0.84095 (25639) hydrogen bonds : bond 0.07214 ( 1015) hydrogen bonds : angle 5.99650 ( 2946) Misc. bond : bond 0.00236 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 611 time to evaluate : 0.732 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: A 22 TRP cc_start: 0.7455 (m100) cc_final: 0.6145 (m100) REVERT: A 68 MET cc_start: 0.7296 (mpp) cc_final: 0.6995 (mpp) REVERT: A 86 PHE cc_start: 0.6589 (t80) cc_final: 0.6132 (t80) REVERT: A 161 ARG cc_start: 0.7035 (ttm-80) cc_final: 0.6760 (tpp80) REVERT: A 265 LEU cc_start: 0.8129 (mp) cc_final: 0.7480 (pp) REVERT: A 310 MET cc_start: 0.8743 (mmm) cc_final: 0.8165 (tpp) REVERT: A 322 ILE cc_start: 0.9474 (mm) cc_final: 0.8940 (tp) REVERT: A 356 ILE cc_start: 0.8200 (pt) cc_final: 0.7808 (pt) REVERT: A 376 MET cc_start: 0.8637 (ttm) cc_final: 0.8145 (tpp) REVERT: A 377 LEU cc_start: 0.8943 (mp) cc_final: 0.8549 (mm) REVERT: A 407 TYR cc_start: 0.7664 (m-80) cc_final: 0.7276 (m-80) REVERT: B 8 LEU cc_start: 0.8244 (tp) cc_final: 0.7767 (mt) REVERT: B 22 TRP cc_start: 0.8506 (m100) cc_final: 0.7989 (m100) REVERT: B 27 LYS cc_start: 0.7886 (mttt) cc_final: 0.7655 (mttt) REVERT: B 28 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8550 (mt-10) REVERT: B 51 LYS cc_start: 0.7620 (ttmt) cc_final: 0.7368 (tmmt) REVERT: B 128 ASP cc_start: 0.8753 (m-30) cc_final: 0.8413 (m-30) REVERT: B 132 ASN cc_start: 0.8026 (t0) cc_final: 0.7333 (t0) REVERT: B 134 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7778 (mm-30) REVERT: B 150 LEU cc_start: 0.8921 (pp) cc_final: 0.8340 (pp) REVERT: B 240 ASN cc_start: 0.8900 (p0) cc_final: 0.8338 (t0) REVERT: B 267 PHE cc_start: 0.8581 (m-80) cc_final: 0.7804 (m-80) REVERT: B 293 ASP cc_start: 0.8089 (m-30) cc_final: 0.7523 (m-30) REVERT: C 169 GLN cc_start: 0.9033 (mt0) cc_final: 0.8554 (mt0) REVERT: C 211 SER cc_start: 0.8765 (p) cc_final: 0.7987 (m) REVERT: C 241 PHE cc_start: 0.9253 (m-80) cc_final: 0.8893 (m-10) REVERT: C 259 GLU cc_start: 0.9084 (tp30) cc_final: 0.8369 (tp30) REVERT: C 346 LEU cc_start: 0.9720 (mt) cc_final: 0.9506 (mt) REVERT: C 354 LEU cc_start: 0.8882 (tp) cc_final: 0.8606 (mt) REVERT: C 393 PHE cc_start: 0.8108 (p90) cc_final: 0.7840 (p90) REVERT: C 397 GLU cc_start: 0.8829 (mp0) cc_final: 0.8323 (pm20) REVERT: C 404 MET cc_start: 0.8998 (mmm) cc_final: 0.8794 (mmm) REVERT: C 409 TYR cc_start: 0.8980 (t80) cc_final: 0.8571 (t80) REVERT: C 410 ILE cc_start: 0.9502 (mm) cc_final: 0.9177 (mm) REVERT: C 441 ILE cc_start: 0.8243 (mt) cc_final: 0.7921 (mt) REVERT: C 475 PHE cc_start: 0.9405 (m-80) cc_final: 0.9177 (m-80) REVERT: C 495 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8319 (mmtm) REVERT: C 521 GLN cc_start: 0.8844 (pm20) cc_final: 0.8579 (mp10) REVERT: C 529 MET cc_start: 0.8344 (tmm) cc_final: 0.7752 (tmm) REVERT: C 604 MET cc_start: 0.7997 (ptp) cc_final: 0.7288 (ptt) REVERT: C 733 THR cc_start: 0.9042 (m) cc_final: 0.8828 (p) REVERT: C 781 ASP cc_start: 0.8027 (m-30) cc_final: 0.7629 (p0) REVERT: D 32 TRP cc_start: 0.8077 (t60) cc_final: 0.7320 (t60) REVERT: D 39 LYS cc_start: 0.9103 (tttt) cc_final: 0.8867 (ptmm) REVERT: D 173 LEU cc_start: 0.9762 (tp) cc_final: 0.9558 (tp) REVERT: D 239 TYR cc_start: 0.8541 (m-80) cc_final: 0.8176 (m-10) REVERT: D 249 LYS cc_start: 0.9456 (mttt) cc_final: 0.8980 (mttp) REVERT: D 253 GLN cc_start: 0.9452 (mm-40) cc_final: 0.9079 (mt0) REVERT: D 261 ASP cc_start: 0.8106 (t0) cc_final: 0.7260 (t0) REVERT: D 264 SER cc_start: 0.9577 (t) cc_final: 0.7742 (p) REVERT: D 350 THR cc_start: 0.9638 (m) cc_final: 0.9147 (p) REVERT: D 354 LEU cc_start: 0.9428 (mt) cc_final: 0.9200 (mt) REVERT: D 383 ASP cc_start: 0.9173 (t0) cc_final: 0.7748 (t0) REVERT: D 386 GLU cc_start: 0.8788 (pt0) cc_final: 0.8501 (pp20) REVERT: D 422 LEU cc_start: 0.9339 (tp) cc_final: 0.9128 (tp) REVERT: D 426 PHE cc_start: 0.9133 (m-80) cc_final: 0.8904 (m-80) REVERT: D 431 SER cc_start: 0.9134 (m) cc_final: 0.8565 (m) REVERT: D 461 LEU cc_start: 0.8748 (mt) cc_final: 0.8182 (pp) REVERT: D 486 PHE cc_start: 0.7473 (m-10) cc_final: 0.7193 (m-10) REVERT: D 489 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8508 (mm-30) REVERT: D 498 TYR cc_start: 0.8263 (m-80) cc_final: 0.7825 (m-80) REVERT: D 646 TYR cc_start: 0.8463 (t80) cc_final: 0.8221 (t80) REVERT: U 122 GLN cc_start: 0.9189 (mm110) cc_final: 0.8874 (mm-40) REVERT: U 138 LEU cc_start: 0.8686 (tt) cc_final: 0.8393 (pp) outliers start: 5 outliers final: 0 residues processed: 615 average time/residue: 0.1510 time to fit residues: 139.1003 Evaluate side-chains 454 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 74 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 212 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 186 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 HIS A 317 ASN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN C 269 ASN C 380 HIS C 601 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 485 GLN D 565 ASN ** D 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 117 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.110572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.085068 restraints weight = 69443.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.088154 restraints weight = 33981.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.090102 restraints weight = 19968.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.091362 restraints weight = 13251.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.092136 restraints weight = 9726.166| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 18944 Z= 0.200 Angle : 0.734 13.380 25639 Z= 0.393 Chirality : 0.046 0.200 2856 Planarity : 0.005 0.069 3297 Dihedral : 6.346 77.085 2505 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.51 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 (0.17), residues: 2250 helix: 0.40 (0.14), residues: 1271 sheet: -0.52 (0.40), residues: 144 loop : -0.32 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 114 TYR 0.030 0.002 TYR A 247 PHE 0.052 0.003 PHE D 700 TRP 0.019 0.003 TRP B 347 HIS 0.017 0.002 HIS U 127 Details of bonding type rmsd covalent geometry : bond 0.00418 (18942) covalent geometry : angle 0.73392 (25639) hydrogen bonds : bond 0.06164 ( 1015) hydrogen bonds : angle 5.67592 ( 2946) Misc. bond : bond 0.00193 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 559 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.7717 (mpp) cc_final: 0.7092 (mpp) REVERT: A 86 PHE cc_start: 0.6717 (t80) cc_final: 0.6375 (t80) REVERT: A 140 HIS cc_start: 0.7804 (p-80) cc_final: 0.7520 (p-80) REVERT: A 167 LEU cc_start: 0.8857 (mt) cc_final: 0.8571 (mt) REVERT: A 189 LEU cc_start: 0.8160 (mt) cc_final: 0.7747 (mt) REVERT: A 265 LEU cc_start: 0.8136 (mp) cc_final: 0.7191 (pp) REVERT: A 266 HIS cc_start: 0.7822 (p-80) cc_final: 0.7449 (p90) REVERT: A 310 MET cc_start: 0.8731 (mmm) cc_final: 0.8170 (tpp) REVERT: A 320 ASN cc_start: 0.8755 (t0) cc_final: 0.8449 (t0) REVERT: A 322 ILE cc_start: 0.9512 (mm) cc_final: 0.8927 (tp) REVERT: A 355 ASN cc_start: 0.8862 (t0) cc_final: 0.8611 (t0) REVERT: A 356 ILE cc_start: 0.8498 (pt) cc_final: 0.7836 (pt) REVERT: A 375 MET cc_start: 0.8951 (mmm) cc_final: 0.8631 (mmt) REVERT: A 376 MET cc_start: 0.8554 (ttm) cc_final: 0.7841 (tpp) REVERT: A 377 LEU cc_start: 0.8945 (mp) cc_final: 0.8661 (mm) REVERT: A 407 TYR cc_start: 0.7886 (m-80) cc_final: 0.7463 (m-80) REVERT: B 8 LEU cc_start: 0.8100 (tp) cc_final: 0.7696 (mt) REVERT: B 51 LYS cc_start: 0.7727 (ttmt) cc_final: 0.7465 (tmmt) REVERT: B 69 MET cc_start: 0.5425 (tpp) cc_final: 0.5091 (tpp) REVERT: B 128 ASP cc_start: 0.8490 (m-30) cc_final: 0.8202 (m-30) REVERT: B 132 ASN cc_start: 0.8321 (t0) cc_final: 0.7546 (t0) REVERT: B 134 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7582 (mm-30) REVERT: B 137 GLN cc_start: 0.6851 (pp30) cc_final: 0.6619 (pp30) REVERT: B 240 ASN cc_start: 0.8820 (p0) cc_final: 0.8270 (t0) REVERT: B 293 ASP cc_start: 0.8305 (m-30) cc_final: 0.7884 (m-30) REVERT: B 296 LEU cc_start: 0.8719 (mt) cc_final: 0.8385 (mt) REVERT: B 335 MET cc_start: 0.7625 (ptt) cc_final: 0.7286 (ppp) REVERT: B 434 MET cc_start: 0.2901 (tpt) cc_final: 0.1908 (ptp) REVERT: C 169 GLN cc_start: 0.9027 (mt0) cc_final: 0.8549 (mt0) REVERT: C 183 ASP cc_start: 0.9092 (m-30) cc_final: 0.8818 (m-30) REVERT: C 211 SER cc_start: 0.8661 (p) cc_final: 0.7882 (m) REVERT: C 249 MET cc_start: 0.8974 (mpp) cc_final: 0.8609 (mmt) REVERT: C 364 ILE cc_start: 0.9358 (mm) cc_final: 0.9022 (mm) REVERT: C 393 PHE cc_start: 0.8417 (p90) cc_final: 0.8116 (p90) REVERT: C 397 GLU cc_start: 0.8892 (mp0) cc_final: 0.8676 (mp0) REVERT: C 409 TYR cc_start: 0.9042 (t80) cc_final: 0.8473 (t80) REVERT: C 441 ILE cc_start: 0.8193 (mt) cc_final: 0.7853 (mt) REVERT: C 452 GLN cc_start: 0.9566 (tt0) cc_final: 0.9208 (tt0) REVERT: C 475 PHE cc_start: 0.9538 (m-80) cc_final: 0.9229 (m-80) REVERT: C 478 LYS cc_start: 0.9162 (tmmt) cc_final: 0.8887 (ttpp) REVERT: C 495 LYS cc_start: 0.9203 (mmmt) cc_final: 0.8653 (mmtm) REVERT: C 517 GLN cc_start: 0.9076 (tp40) cc_final: 0.8412 (tm-30) REVERT: C 521 GLN cc_start: 0.8554 (pm20) cc_final: 0.7805 (mp10) REVERT: C 529 MET cc_start: 0.8465 (tmm) cc_final: 0.8047 (tmm) REVERT: C 550 HIS cc_start: 0.7625 (t-90) cc_final: 0.7331 (t-90) REVERT: C 604 MET cc_start: 0.7980 (ptp) cc_final: 0.7564 (ptt) REVERT: C 664 MET cc_start: 0.8571 (mmp) cc_final: 0.8368 (mmm) REVERT: C 781 ASP cc_start: 0.8053 (m-30) cc_final: 0.7777 (m-30) REVERT: D 4 LYS cc_start: 0.9025 (mmtp) cc_final: 0.8781 (mmmm) REVERT: D 32 TRP cc_start: 0.8198 (t60) cc_final: 0.7350 (t60) REVERT: D 173 LEU cc_start: 0.9751 (tp) cc_final: 0.9527 (tp) REVERT: D 249 LYS cc_start: 0.9524 (mttt) cc_final: 0.8703 (mttm) REVERT: D 253 GLN cc_start: 0.9473 (mm-40) cc_final: 0.9038 (mp10) REVERT: D 261 ASP cc_start: 0.8231 (t0) cc_final: 0.7523 (t0) REVERT: D 264 SER cc_start: 0.9551 (t) cc_final: 0.7842 (p) REVERT: D 266 MET cc_start: 0.9134 (mtm) cc_final: 0.8648 (mtp) REVERT: D 271 LEU cc_start: 0.9833 (mt) cc_final: 0.9538 (mt) REVERT: D 343 LEU cc_start: 0.9532 (tp) cc_final: 0.9261 (tp) REVERT: D 383 ASP cc_start: 0.9156 (t0) cc_final: 0.8508 (t0) REVERT: D 400 ARG cc_start: 0.9091 (ttp80) cc_final: 0.8832 (ttt90) REVERT: D 431 SER cc_start: 0.9102 (m) cc_final: 0.8571 (m) REVERT: D 461 LEU cc_start: 0.8698 (mt) cc_final: 0.8131 (pp) REVERT: D 486 PHE cc_start: 0.7381 (m-10) cc_final: 0.6980 (m-10) REVERT: D 498 TYR cc_start: 0.8361 (m-80) cc_final: 0.7913 (m-80) REVERT: D 603 TRP cc_start: 0.7736 (t60) cc_final: 0.7455 (t60) REVERT: D 652 ILE cc_start: 0.9564 (mp) cc_final: 0.9166 (mp) REVERT: D 685 THR cc_start: 0.8189 (p) cc_final: 0.6882 (p) outliers start: 0 outliers final: 0 residues processed: 559 average time/residue: 0.1347 time to fit residues: 115.5578 Evaluate side-chains 438 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 35 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 126 optimal weight: 8.9990 chunk 168 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 217 optimal weight: 0.3980 chunk 132 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN C 380 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 GLN ** C 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 464 ASN ** D 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.112357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.086429 restraints weight = 69260.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.089576 restraints weight = 34025.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.091551 restraints weight = 20059.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.092832 restraints weight = 13387.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.093648 restraints weight = 9843.599| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18944 Z= 0.160 Angle : 0.695 10.120 25639 Z= 0.369 Chirality : 0.045 0.185 2856 Planarity : 0.005 0.058 3297 Dihedral : 6.205 74.887 2505 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.47 % Favored : 96.36 % Rotamer: Outliers : 0.24 % Allowed : 2.34 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.02 (0.17), residues: 2250 helix: 0.45 (0.14), residues: 1278 sheet: -0.61 (0.40), residues: 151 loop : -0.44 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 133 TYR 0.037 0.002 TYR D 413 PHE 0.048 0.002 PHE D 700 TRP 0.026 0.002 TRP A 105 HIS 0.014 0.002 HIS D 638 Details of bonding type rmsd covalent geometry : bond 0.00334 (18942) covalent geometry : angle 0.69488 (25639) hydrogen bonds : bond 0.05619 ( 1015) hydrogen bonds : angle 5.48356 ( 2946) Misc. bond : bond 0.00143 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 552 time to evaluate : 0.813 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: A 8 LEU cc_start: 0.8993 (mm) cc_final: 0.8659 (mp) REVERT: A 86 PHE cc_start: 0.6856 (t80) cc_final: 0.6404 (t80) REVERT: A 123 ILE cc_start: 0.8461 (pt) cc_final: 0.8070 (pt) REVERT: A 137 GLN cc_start: 0.5691 (tm-30) cc_final: 0.5437 (tm-30) REVERT: A 140 HIS cc_start: 0.7787 (p-80) cc_final: 0.7526 (p-80) REVERT: A 161 ARG cc_start: 0.6819 (ttm-80) cc_final: 0.6579 (ttm-80) REVERT: A 162 TYR cc_start: 0.7446 (m-80) cc_final: 0.6920 (m-80) REVERT: A 189 LEU cc_start: 0.8040 (mt) cc_final: 0.7659 (mt) REVERT: A 265 LEU cc_start: 0.8064 (mp) cc_final: 0.7214 (pp) REVERT: A 266 HIS cc_start: 0.7986 (p-80) cc_final: 0.7560 (p90) REVERT: A 310 MET cc_start: 0.8733 (mmm) cc_final: 0.8145 (tpp) REVERT: A 315 TYR cc_start: 0.6903 (m-80) cc_final: 0.6692 (m-80) REVERT: A 320 ASN cc_start: 0.8723 (t0) cc_final: 0.8484 (t0) REVERT: A 322 ILE cc_start: 0.9471 (mm) cc_final: 0.8893 (tp) REVERT: A 333 ARG cc_start: 0.7745 (mmp80) cc_final: 0.7440 (mmp80) REVERT: A 355 ASN cc_start: 0.8875 (t0) cc_final: 0.8506 (m-40) REVERT: A 356 ILE cc_start: 0.8448 (pt) cc_final: 0.7619 (pt) REVERT: A 375 MET cc_start: 0.8970 (mmm) cc_final: 0.8746 (tpp) REVERT: A 376 MET cc_start: 0.8495 (ttm) cc_final: 0.7823 (tpp) REVERT: A 377 LEU cc_start: 0.8994 (mp) cc_final: 0.8730 (mt) REVERT: A 407 TYR cc_start: 0.8072 (m-80) cc_final: 0.7497 (m-80) REVERT: B 8 LEU cc_start: 0.8087 (tp) cc_final: 0.7689 (mt) REVERT: B 51 LYS cc_start: 0.7721 (ttmt) cc_final: 0.7456 (tmmt) REVERT: B 55 ARG cc_start: 0.9256 (mtp85) cc_final: 0.8985 (mmm-85) REVERT: B 128 ASP cc_start: 0.8490 (m-30) cc_final: 0.8228 (m-30) REVERT: B 132 ASN cc_start: 0.8196 (t0) cc_final: 0.7204 (t0) REVERT: B 134 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7393 (mm-30) REVERT: B 240 ASN cc_start: 0.8779 (p0) cc_final: 0.8155 (t0) REVERT: B 243 ARG cc_start: 0.9197 (mtm110) cc_final: 0.8843 (mtm110) REVERT: B 293 ASP cc_start: 0.8527 (m-30) cc_final: 0.8078 (m-30) REVERT: B 296 LEU cc_start: 0.8476 (mt) cc_final: 0.8272 (mt) REVERT: B 327 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6687 (tm-30) REVERT: B 335 MET cc_start: 0.7533 (ptt) cc_final: 0.7215 (ppp) REVERT: B 375 MET cc_start: 0.7347 (ppp) cc_final: 0.7143 (ppp) REVERT: B 434 MET cc_start: 0.2948 (tpt) cc_final: 0.2349 (ptp) REVERT: C 169 GLN cc_start: 0.9072 (mt0) cc_final: 0.8533 (mt0) REVERT: C 183 ASP cc_start: 0.9113 (m-30) cc_final: 0.8606 (m-30) REVERT: C 187 TYR cc_start: 0.8930 (m-80) cc_final: 0.8642 (m-80) REVERT: C 211 SER cc_start: 0.8492 (p) cc_final: 0.7692 (m) REVERT: C 249 MET cc_start: 0.8982 (mpp) cc_final: 0.8639 (mmt) REVERT: C 393 PHE cc_start: 0.8471 (p90) cc_final: 0.8154 (p90) REVERT: C 409 TYR cc_start: 0.8896 (t80) cc_final: 0.8514 (t80) REVERT: C 410 ILE cc_start: 0.9766 (tt) cc_final: 0.9440 (tt) REVERT: C 441 ILE cc_start: 0.8160 (mt) cc_final: 0.7796 (mt) REVERT: C 452 GLN cc_start: 0.9517 (tt0) cc_final: 0.9236 (tt0) REVERT: C 475 PHE cc_start: 0.9568 (m-80) cc_final: 0.9106 (m-80) REVERT: C 478 LYS cc_start: 0.9210 (tmmt) cc_final: 0.8943 (ttpp) REVERT: C 483 MET cc_start: 0.8675 (mpp) cc_final: 0.8292 (mmm) REVERT: C 495 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8563 (mmtm) REVERT: C 529 MET cc_start: 0.8466 (tmm) cc_final: 0.8139 (tmm) REVERT: C 550 HIS cc_start: 0.7665 (t-90) cc_final: 0.7345 (t-90) REVERT: C 596 ASN cc_start: 0.8050 (t0) cc_final: 0.7535 (t0) REVERT: C 604 MET cc_start: 0.7974 (ptp) cc_final: 0.7431 (ptp) REVERT: C 781 ASP cc_start: 0.8015 (m-30) cc_final: 0.7765 (m-30) REVERT: D 32 TRP cc_start: 0.8164 (t60) cc_final: 0.7310 (t60) REVERT: D 46 ILE cc_start: 0.9507 (pt) cc_final: 0.9299 (mm) REVERT: D 249 LYS cc_start: 0.9545 (mttt) cc_final: 0.8746 (mttm) REVERT: D 261 ASP cc_start: 0.8236 (t0) cc_final: 0.7488 (t0) REVERT: D 264 SER cc_start: 0.9542 (t) cc_final: 0.7898 (p) REVERT: D 266 MET cc_start: 0.9166 (mtm) cc_final: 0.8667 (mtp) REVERT: D 271 LEU cc_start: 0.9811 (mt) cc_final: 0.9504 (mt) REVERT: D 383 ASP cc_start: 0.8904 (t0) cc_final: 0.8526 (t0) REVERT: D 399 SER cc_start: 0.9335 (t) cc_final: 0.8953 (p) REVERT: D 400 ARG cc_start: 0.8998 (ttp80) cc_final: 0.8760 (ttt90) REVERT: D 414 ASP cc_start: 0.9175 (t0) cc_final: 0.8681 (t0) REVERT: D 418 VAL cc_start: 0.9685 (m) cc_final: 0.9445 (p) REVERT: D 431 SER cc_start: 0.9085 (m) cc_final: 0.8754 (m) REVERT: D 461 LEU cc_start: 0.8580 (mt) cc_final: 0.8021 (pp) REVERT: D 486 PHE cc_start: 0.7202 (m-10) cc_final: 0.6621 (m-10) REVERT: D 495 LEU cc_start: 0.9371 (mm) cc_final: 0.9171 (mm) REVERT: D 498 TYR cc_start: 0.8559 (m-80) cc_final: 0.8160 (m-80) REVERT: D 582 TYR cc_start: 0.9126 (m-80) cc_final: 0.8883 (m-10) REVERT: D 652 ILE cc_start: 0.9483 (mp) cc_final: 0.9060 (mp) REVERT: D 685 THR cc_start: 0.8152 (p) cc_final: 0.7683 (p) REVERT: D 709 PHE cc_start: 0.6900 (t80) cc_final: 0.6584 (t80) REVERT: U 122 GLN cc_start: 0.9288 (mm110) cc_final: 0.8910 (mm-40) REVERT: U 128 GLN cc_start: 0.8713 (pt0) cc_final: 0.8293 (pp30) REVERT: U 138 LEU cc_start: 0.8554 (tt) cc_final: 0.8092 (mm) REVERT: U 139 GLU cc_start: 0.7088 (pt0) cc_final: 0.6806 (pt0) outliers start: 5 outliers final: 1 residues processed: 556 average time/residue: 0.1418 time to fit residues: 121.3788 Evaluate side-chains 457 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 456 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 130 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 161 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 chunk 192 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 174 optimal weight: 0.2980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN C 348 ASN C 380 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 480 GLN D 559 HIS D 589 GLN D 682 ASN D 784 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.112458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.086671 restraints weight = 70127.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.089852 restraints weight = 34414.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.091860 restraints weight = 20308.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.093130 restraints weight = 13521.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.093971 restraints weight = 9959.196| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18944 Z= 0.149 Angle : 0.671 9.288 25639 Z= 0.359 Chirality : 0.045 0.224 2856 Planarity : 0.005 0.061 3297 Dihedral : 6.099 69.888 2505 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.60 % Favored : 96.22 % Rotamer: Outliers : 0.05 % Allowed : 1.77 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 (0.17), residues: 2250 helix: 0.49 (0.14), residues: 1280 sheet: -0.60 (0.41), residues: 147 loop : -0.48 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 133 TYR 0.029 0.002 TYR A 247 PHE 0.049 0.002 PHE D 700 TRP 0.042 0.002 TRP A 105 HIS 0.015 0.001 HIS D 638 Details of bonding type rmsd covalent geometry : bond 0.00309 (18942) covalent geometry : angle 0.67113 (25639) hydrogen bonds : bond 0.05328 ( 1015) hydrogen bonds : angle 5.40915 ( 2946) Misc. bond : bond 0.00117 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 549 time to evaluate : 1.210 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 8 LEU cc_start: 0.9008 (mm) cc_final: 0.8672 (mp) REVERT: A 86 PHE cc_start: 0.6945 (t80) cc_final: 0.6460 (t80) REVERT: A 123 ILE cc_start: 0.8432 (pt) cc_final: 0.8135 (pt) REVERT: A 137 GLN cc_start: 0.5708 (tm-30) cc_final: 0.5269 (tm-30) REVERT: A 140 HIS cc_start: 0.7788 (p-80) cc_final: 0.7342 (p-80) REVERT: A 161 ARG cc_start: 0.6878 (ttm-80) cc_final: 0.6650 (ttm-80) REVERT: A 162 TYR cc_start: 0.7561 (m-80) cc_final: 0.7078 (m-80) REVERT: A 170 TYR cc_start: 0.8227 (m-80) cc_final: 0.7928 (m-80) REVERT: A 176 ARG cc_start: 0.1651 (mtt90) cc_final: 0.0122 (tpt170) REVERT: A 189 LEU cc_start: 0.8141 (mt) cc_final: 0.7788 (mt) REVERT: A 265 LEU cc_start: 0.8045 (mp) cc_final: 0.7211 (pp) REVERT: A 266 HIS cc_start: 0.8127 (p-80) cc_final: 0.7655 (p90) REVERT: A 310 MET cc_start: 0.8747 (mmm) cc_final: 0.8147 (tpp) REVERT: A 315 TYR cc_start: 0.6878 (m-80) cc_final: 0.6555 (m-80) REVERT: A 320 ASN cc_start: 0.8698 (t0) cc_final: 0.8427 (t0) REVERT: A 322 ILE cc_start: 0.9493 (mm) cc_final: 0.8995 (tp) REVERT: A 333 ARG cc_start: 0.7587 (mmp80) cc_final: 0.7254 (mmp80) REVERT: A 355 ASN cc_start: 0.8891 (t0) cc_final: 0.8547 (m-40) REVERT: A 356 ILE cc_start: 0.8410 (pt) cc_final: 0.7497 (pt) REVERT: A 375 MET cc_start: 0.8985 (mmm) cc_final: 0.8779 (tpt) REVERT: A 407 TYR cc_start: 0.7710 (m-80) cc_final: 0.7162 (m-80) REVERT: B 1 MET cc_start: 0.3270 (mmt) cc_final: 0.2879 (mmt) REVERT: B 6 ILE cc_start: 0.8535 (mm) cc_final: 0.8233 (mt) REVERT: B 7 THR cc_start: 0.8334 (p) cc_final: 0.7964 (t) REVERT: B 8 LEU cc_start: 0.8096 (tp) cc_final: 0.7729 (mt) REVERT: B 22 TRP cc_start: 0.8739 (m100) cc_final: 0.8230 (m100) REVERT: B 51 LYS cc_start: 0.7708 (ttmt) cc_final: 0.7428 (tmmt) REVERT: B 55 ARG cc_start: 0.9302 (mtp85) cc_final: 0.9068 (mmm-85) REVERT: B 69 MET cc_start: 0.4953 (tpp) cc_final: 0.4705 (tpt) REVERT: B 128 ASP cc_start: 0.8511 (m-30) cc_final: 0.8246 (m-30) REVERT: B 132 ASN cc_start: 0.8175 (t0) cc_final: 0.7142 (t0) REVERT: B 134 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7372 (mm-30) REVERT: B 137 GLN cc_start: 0.6645 (OUTLIER) cc_final: 0.6420 (pp30) REVERT: B 138 LEU cc_start: 0.6853 (tp) cc_final: 0.6563 (tp) REVERT: B 240 ASN cc_start: 0.8790 (p0) cc_final: 0.8029 (t0) REVERT: B 243 ARG cc_start: 0.9174 (mtm110) cc_final: 0.8787 (mtm110) REVERT: B 267 PHE cc_start: 0.7852 (m-80) cc_final: 0.7608 (m-80) REVERT: B 293 ASP cc_start: 0.8735 (m-30) cc_final: 0.8213 (m-30) REVERT: B 310 MET cc_start: 0.3962 (mmt) cc_final: 0.2901 (mmt) REVERT: B 327 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6967 (tm-30) REVERT: B 376 MET cc_start: 0.8296 (tmm) cc_final: 0.8047 (tmm) REVERT: B 434 MET cc_start: 0.2936 (tpt) cc_final: 0.2425 (ptp) REVERT: C 169 GLN cc_start: 0.9078 (mt0) cc_final: 0.8503 (mt0) REVERT: C 172 ASN cc_start: 0.9065 (m-40) cc_final: 0.8789 (m110) REVERT: C 183 ASP cc_start: 0.8991 (m-30) cc_final: 0.8654 (m-30) REVERT: C 211 SER cc_start: 0.8455 (p) cc_final: 0.7683 (m) REVERT: C 232 GLN cc_start: 0.9105 (tt0) cc_final: 0.8897 (tt0) REVERT: C 236 TYR cc_start: 0.8270 (m-10) cc_final: 0.8032 (m-10) REVERT: C 241 PHE cc_start: 0.9148 (m-80) cc_final: 0.8827 (m-10) REVERT: C 249 MET cc_start: 0.8936 (mpp) cc_final: 0.8717 (mmt) REVERT: C 393 PHE cc_start: 0.8552 (p90) cc_final: 0.8224 (p90) REVERT: C 409 TYR cc_start: 0.9109 (t80) cc_final: 0.8687 (t80) REVERT: C 410 ILE cc_start: 0.9707 (tt) cc_final: 0.9288 (tt) REVERT: C 441 ILE cc_start: 0.8248 (mt) cc_final: 0.7918 (mt) REVERT: C 475 PHE cc_start: 0.9628 (m-80) cc_final: 0.9012 (m-80) REVERT: C 478 LYS cc_start: 0.9224 (tmmt) cc_final: 0.8978 (ttpp) REVERT: C 483 MET cc_start: 0.8508 (mpp) cc_final: 0.8098 (mpp) REVERT: C 489 MET cc_start: 0.9355 (tpt) cc_final: 0.9027 (tpt) REVERT: C 495 LYS cc_start: 0.9120 (mmmt) cc_final: 0.8638 (mmtt) REVERT: C 500 LEU cc_start: 0.9286 (mt) cc_final: 0.9011 (mt) REVERT: C 511 LYS cc_start: 0.9188 (tptm) cc_final: 0.8926 (ttpp) REVERT: C 596 ASN cc_start: 0.8089 (t0) cc_final: 0.7771 (t0) REVERT: C 604 MET cc_start: 0.7904 (ptp) cc_final: 0.7468 (ppp) REVERT: C 731 PHE cc_start: 0.7118 (m-80) cc_final: 0.6627 (m-80) REVERT: C 781 ASP cc_start: 0.8017 (m-30) cc_final: 0.7802 (m-30) REVERT: D 1 MET cc_start: 0.6320 (mtp) cc_final: 0.5831 (mtp) REVERT: D 4 LYS cc_start: 0.8995 (mmtp) cc_final: 0.8701 (mmmm) REVERT: D 32 TRP cc_start: 0.8123 (t60) cc_final: 0.7247 (t60) REVERT: D 112 TYR cc_start: 0.8294 (m-10) cc_final: 0.8000 (m-10) REVERT: D 168 PHE cc_start: 0.7811 (t80) cc_final: 0.7091 (t80) REVERT: D 172 GLU cc_start: 0.8778 (tt0) cc_final: 0.8416 (tt0) REVERT: D 179 GLU cc_start: 0.8127 (pt0) cc_final: 0.7861 (pt0) REVERT: D 198 ARG cc_start: 0.9277 (ptm-80) cc_final: 0.8852 (ttp80) REVERT: D 261 ASP cc_start: 0.8260 (t0) cc_final: 0.7490 (t0) REVERT: D 264 SER cc_start: 0.9542 (t) cc_final: 0.7935 (p) REVERT: D 271 LEU cc_start: 0.9797 (mt) cc_final: 0.9477 (mt) REVERT: D 383 ASP cc_start: 0.9023 (t0) cc_final: 0.8732 (t0) REVERT: D 395 ASP cc_start: 0.8493 (t0) cc_final: 0.8240 (t0) REVERT: D 414 ASP cc_start: 0.9148 (t0) cc_final: 0.8678 (t0) REVERT: D 418 VAL cc_start: 0.9722 (m) cc_final: 0.9521 (p) REVERT: D 423 GLN cc_start: 0.9538 (mt0) cc_final: 0.9250 (mp10) REVERT: D 461 LEU cc_start: 0.8648 (mt) cc_final: 0.8100 (pp) REVERT: D 486 PHE cc_start: 0.7147 (m-10) cc_final: 0.6376 (m-10) REVERT: D 495 LEU cc_start: 0.9476 (mm) cc_final: 0.9270 (mm) REVERT: D 498 TYR cc_start: 0.8546 (m-80) cc_final: 0.8115 (m-80) REVERT: D 646 TYR cc_start: 0.8614 (t80) cc_final: 0.8284 (t80) REVERT: D 652 ILE cc_start: 0.9448 (mp) cc_final: 0.9039 (mp) REVERT: D 684 MET cc_start: 0.6900 (tmm) cc_final: 0.6622 (tmm) REVERT: D 709 PHE cc_start: 0.6929 (t80) cc_final: 0.6625 (t80) REVERT: U 132 GLU cc_start: 0.9444 (mp0) cc_final: 0.9228 (mp0) REVERT: U 138 LEU cc_start: 0.8495 (tt) cc_final: 0.8023 (mm) REVERT: U 139 GLU cc_start: 0.7301 (pt0) cc_final: 0.7081 (pt0) outliers start: 1 outliers final: 0 residues processed: 549 average time/residue: 0.1437 time to fit residues: 121.2081 Evaluate side-chains 443 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 442 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 164 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 147 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 HIS ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS D 65 ASN D 442 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.113946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.088662 restraints weight = 68384.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.091809 restraints weight = 33708.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.093798 restraints weight = 19949.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.095058 restraints weight = 13296.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.095919 restraints weight = 9825.316| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18944 Z= 0.143 Angle : 0.650 10.048 25639 Z= 0.344 Chirality : 0.044 0.182 2856 Planarity : 0.005 0.064 3297 Dihedral : 5.977 61.909 2505 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.20 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.17), residues: 2250 helix: 0.49 (0.14), residues: 1292 sheet: -0.58 (0.42), residues: 135 loop : -0.55 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 329 TYR 0.035 0.002 TYR D 582 PHE 0.064 0.002 PHE A 136 TRP 0.057 0.002 TRP A 105 HIS 0.014 0.001 HIS D 638 Details of bonding type rmsd covalent geometry : bond 0.00301 (18942) covalent geometry : angle 0.65046 (25639) hydrogen bonds : bond 0.05001 ( 1015) hydrogen bonds : angle 5.31316 ( 2946) Misc. bond : bond 0.00098 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 0.732 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 68 MET cc_start: 0.7629 (mpp) cc_final: 0.7393 (mmt) REVERT: A 86 PHE cc_start: 0.6917 (t80) cc_final: 0.6418 (t80) REVERT: A 120 LEU cc_start: 0.6053 (mt) cc_final: 0.5591 (mt) REVERT: A 123 ILE cc_start: 0.8317 (pt) cc_final: 0.7700 (pt) REVERT: A 140 HIS cc_start: 0.7771 (p-80) cc_final: 0.7275 (p-80) REVERT: A 161 ARG cc_start: 0.6860 (ttm-80) cc_final: 0.6514 (mtp-110) REVERT: A 162 TYR cc_start: 0.7665 (m-80) cc_final: 0.6622 (m-80) REVERT: A 170 TYR cc_start: 0.8303 (m-80) cc_final: 0.7468 (m-80) REVERT: A 202 VAL cc_start: 0.8872 (p) cc_final: 0.8649 (p) REVERT: A 234 ILE cc_start: 0.9237 (mt) cc_final: 0.8918 (mt) REVERT: A 265 LEU cc_start: 0.7820 (mp) cc_final: 0.7093 (pp) REVERT: A 266 HIS cc_start: 0.8151 (p-80) cc_final: 0.7673 (p90) REVERT: A 310 MET cc_start: 0.8716 (mmm) cc_final: 0.8175 (tpp) REVERT: A 322 ILE cc_start: 0.9509 (mm) cc_final: 0.9008 (tp) REVERT: A 333 ARG cc_start: 0.7609 (mmp80) cc_final: 0.7260 (mmp80) REVERT: A 355 ASN cc_start: 0.8898 (t0) cc_final: 0.8600 (m-40) REVERT: A 356 ILE cc_start: 0.8513 (pt) cc_final: 0.7621 (pt) REVERT: A 376 MET cc_start: 0.8550 (ttm) cc_final: 0.8223 (tpt) REVERT: A 407 TYR cc_start: 0.7697 (m-80) cc_final: 0.7126 (m-10) REVERT: B 1 MET cc_start: 0.2819 (mmt) cc_final: 0.2586 (mmt) REVERT: B 6 ILE cc_start: 0.8533 (mm) cc_final: 0.8282 (mt) REVERT: B 7 THR cc_start: 0.8205 (p) cc_final: 0.7942 (t) REVERT: B 8 LEU cc_start: 0.8102 (tp) cc_final: 0.7854 (mt) REVERT: B 22 TRP cc_start: 0.8679 (m100) cc_final: 0.8173 (m100) REVERT: B 51 LYS cc_start: 0.7718 (ttmt) cc_final: 0.7442 (tmmt) REVERT: B 55 ARG cc_start: 0.9298 (mtp85) cc_final: 0.9051 (mmm-85) REVERT: B 69 MET cc_start: 0.5063 (tpp) cc_final: 0.4248 (tpp) REVERT: B 128 ASP cc_start: 0.8534 (m-30) cc_final: 0.8281 (m-30) REVERT: B 132 ASN cc_start: 0.8208 (t0) cc_final: 0.7247 (t0) REVERT: B 134 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7206 (mm-30) REVERT: B 150 LEU cc_start: 0.8779 (pp) cc_final: 0.8537 (pp) REVERT: B 240 ASN cc_start: 0.8696 (p0) cc_final: 0.8139 (t0) REVERT: B 243 ARG cc_start: 0.9142 (mtm110) cc_final: 0.8804 (mtm110) REVERT: B 267 PHE cc_start: 0.8165 (m-80) cc_final: 0.7858 (m-80) REVERT: B 293 ASP cc_start: 0.8810 (m-30) cc_final: 0.8330 (m-30) REVERT: B 310 MET cc_start: 0.3719 (mmt) cc_final: 0.3080 (mmt) REVERT: B 327 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7086 (tm-30) REVERT: B 376 MET cc_start: 0.8417 (tmm) cc_final: 0.8207 (tmm) REVERT: B 434 MET cc_start: 0.2836 (tpt) cc_final: 0.2441 (ptp) REVERT: C 169 GLN cc_start: 0.9103 (mt0) cc_final: 0.8541 (mt0) REVERT: C 172 ASN cc_start: 0.8990 (m-40) cc_final: 0.8676 (m110) REVERT: C 183 ASP cc_start: 0.9008 (m-30) cc_final: 0.8647 (m-30) REVERT: C 211 SER cc_start: 0.8629 (p) cc_final: 0.7864 (m) REVERT: C 241 PHE cc_start: 0.9127 (m-80) cc_final: 0.8874 (m-10) REVERT: C 259 GLU cc_start: 0.8904 (tp30) cc_final: 0.8278 (tp30) REVERT: C 393 PHE cc_start: 0.8551 (p90) cc_final: 0.8228 (p90) REVERT: C 409 TYR cc_start: 0.9197 (t80) cc_final: 0.8802 (t80) REVERT: C 410 ILE cc_start: 0.9704 (tt) cc_final: 0.9272 (tt) REVERT: C 413 GLU cc_start: 0.8911 (pp20) cc_final: 0.8709 (pp20) REVERT: C 441 ILE cc_start: 0.8242 (mt) cc_final: 0.7881 (mt) REVERT: C 452 GLN cc_start: 0.9418 (tt0) cc_final: 0.9050 (tt0) REVERT: C 475 PHE cc_start: 0.9597 (m-80) cc_final: 0.9162 (m-80) REVERT: C 478 LYS cc_start: 0.9193 (tmmt) cc_final: 0.8917 (ttpp) REVERT: C 495 LYS cc_start: 0.9184 (mmmt) cc_final: 0.8615 (mmtm) REVERT: C 511 LYS cc_start: 0.9257 (tptm) cc_final: 0.9011 (tttt) REVERT: C 604 MET cc_start: 0.7927 (ptp) cc_final: 0.7442 (ppp) REVERT: C 659 GLU cc_start: 0.9205 (tp30) cc_final: 0.8894 (tp30) REVERT: C 663 GLU cc_start: 0.9603 (pt0) cc_final: 0.9099 (pt0) REVERT: C 781 ASP cc_start: 0.8011 (m-30) cc_final: 0.7791 (m-30) REVERT: D 1 MET cc_start: 0.6596 (mtp) cc_final: 0.6258 (mtp) REVERT: D 4 LYS cc_start: 0.8634 (mmtp) cc_final: 0.8374 (mmmm) REVERT: D 32 TRP cc_start: 0.8100 (t60) cc_final: 0.7196 (t60) REVERT: D 112 TYR cc_start: 0.8306 (m-10) cc_final: 0.7955 (m-10) REVERT: D 168 PHE cc_start: 0.7926 (t80) cc_final: 0.7233 (t80) REVERT: D 172 GLU cc_start: 0.8775 (tt0) cc_final: 0.8434 (tt0) REVERT: D 198 ARG cc_start: 0.9289 (ptm-80) cc_final: 0.8941 (ttp80) REVERT: D 266 MET cc_start: 0.9156 (mtm) cc_final: 0.8743 (mtp) REVERT: D 271 LEU cc_start: 0.9793 (mt) cc_final: 0.9501 (mt) REVERT: D 285 GLU cc_start: 0.8873 (mp0) cc_final: 0.8597 (mp0) REVERT: D 343 LEU cc_start: 0.9515 (tp) cc_final: 0.9240 (tp) REVERT: D 383 ASP cc_start: 0.9000 (t0) cc_final: 0.8708 (t0) REVERT: D 414 ASP cc_start: 0.9128 (t0) cc_final: 0.8717 (t0) REVERT: D 418 VAL cc_start: 0.9745 (m) cc_final: 0.9521 (p) REVERT: D 419 LEU cc_start: 0.9789 (mt) cc_final: 0.9432 (pp) REVERT: D 461 LEU cc_start: 0.8562 (mt) cc_final: 0.7983 (pp) REVERT: D 486 PHE cc_start: 0.7200 (m-10) cc_final: 0.6416 (m-10) REVERT: D 495 LEU cc_start: 0.9472 (mm) cc_final: 0.9270 (mm) REVERT: D 498 TYR cc_start: 0.8489 (m-80) cc_final: 0.8033 (m-80) REVERT: D 573 ILE cc_start: 0.9077 (mp) cc_final: 0.8499 (tp) REVERT: D 579 MET cc_start: 0.8780 (mmp) cc_final: 0.8517 (mmp) REVERT: D 646 TYR cc_start: 0.8637 (t80) cc_final: 0.8171 (t80) REVERT: D 652 ILE cc_start: 0.9346 (mp) cc_final: 0.8856 (mp) REVERT: D 686 ASN cc_start: 0.8385 (t0) cc_final: 0.8121 (t0) REVERT: D 689 LEU cc_start: 0.8434 (mt) cc_final: 0.8208 (mt) REVERT: D 709 PHE cc_start: 0.6931 (t80) cc_final: 0.6670 (t80) REVERT: U 128 GLN cc_start: 0.8801 (pt0) cc_final: 0.8486 (pp30) REVERT: U 138 LEU cc_start: 0.8435 (tt) cc_final: 0.7986 (mm) REVERT: U 139 GLU cc_start: 0.7210 (pt0) cc_final: 0.7001 (pt0) outliers start: 0 outliers final: 0 residues processed: 540 average time/residue: 0.1387 time to fit residues: 115.3502 Evaluate side-chains 438 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 113 optimal weight: 6.9990 chunk 221 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 199 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 HIS B 81 ASN ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS B 353 HIS C 380 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS C 596 ASN D 442 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.110617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.085191 restraints weight = 70191.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.088240 restraints weight = 34560.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.090179 restraints weight = 20491.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.091407 restraints weight = 13727.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.092240 restraints weight = 10176.320| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.6151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18944 Z= 0.168 Angle : 0.677 9.269 25639 Z= 0.360 Chirality : 0.045 0.181 2856 Planarity : 0.005 0.067 3297 Dihedral : 5.891 54.805 2505 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.96 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.02 (0.17), residues: 2250 helix: 0.51 (0.14), residues: 1293 sheet: -0.96 (0.41), residues: 151 loop : -0.49 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 133 TYR 0.023 0.002 TYR D 582 PHE 0.049 0.003 PHE D 700 TRP 0.051 0.002 TRP A 105 HIS 0.014 0.002 HIS D 638 Details of bonding type rmsd covalent geometry : bond 0.00353 (18942) covalent geometry : angle 0.67746 (25639) hydrogen bonds : bond 0.04963 ( 1015) hydrogen bonds : angle 5.37142 ( 2946) Misc. bond : bond 0.00080 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 531 time to evaluate : 0.713 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 120 LEU cc_start: 0.6178 (mt) cc_final: 0.5613 (mt) REVERT: A 123 ILE cc_start: 0.8090 (pt) cc_final: 0.7449 (pt) REVERT: A 140 HIS cc_start: 0.7837 (p-80) cc_final: 0.7328 (p-80) REVERT: A 161 ARG cc_start: 0.6908 (ttm-80) cc_final: 0.6615 (mtp-110) REVERT: A 162 TYR cc_start: 0.7712 (m-80) cc_final: 0.6722 (m-80) REVERT: A 176 ARG cc_start: 0.1659 (mtt90) cc_final: -0.0008 (tpt170) REVERT: A 266 HIS cc_start: 0.8536 (p-80) cc_final: 0.8009 (p90) REVERT: A 310 MET cc_start: 0.8713 (mmm) cc_final: 0.8165 (tpp) REVERT: A 322 ILE cc_start: 0.9556 (mm) cc_final: 0.9141 (tp) REVERT: A 355 ASN cc_start: 0.8895 (t0) cc_final: 0.8657 (t0) REVERT: A 356 ILE cc_start: 0.8564 (pt) cc_final: 0.7815 (pt) REVERT: A 376 MET cc_start: 0.8772 (ttm) cc_final: 0.8136 (tpp) REVERT: A 407 TYR cc_start: 0.7733 (m-80) cc_final: 0.7175 (m-10) REVERT: B 1 MET cc_start: 0.3056 (mmt) cc_final: 0.1760 (mmt) REVERT: B 6 ILE cc_start: 0.8560 (mm) cc_final: 0.8310 (mt) REVERT: B 7 THR cc_start: 0.8463 (p) cc_final: 0.8206 (t) REVERT: B 8 LEU cc_start: 0.8039 (tp) cc_final: 0.7818 (mt) REVERT: B 22 TRP cc_start: 0.8679 (m100) cc_final: 0.8081 (m100) REVERT: B 51 LYS cc_start: 0.7693 (ttmt) cc_final: 0.7417 (tmmt) REVERT: B 55 ARG cc_start: 0.9312 (mtp85) cc_final: 0.8920 (mmm-85) REVERT: B 69 MET cc_start: 0.4817 (tpp) cc_final: 0.4134 (tpp) REVERT: B 128 ASP cc_start: 0.8500 (m-30) cc_final: 0.8231 (m-30) REVERT: B 132 ASN cc_start: 0.8260 (t0) cc_final: 0.7158 (t0) REVERT: B 138 LEU cc_start: 0.6503 (tp) cc_final: 0.6270 (mm) REVERT: B 240 ASN cc_start: 0.8776 (p0) cc_final: 0.8088 (t0) REVERT: B 243 ARG cc_start: 0.9114 (mtm110) cc_final: 0.8785 (mtm110) REVERT: B 293 ASP cc_start: 0.8890 (m-30) cc_final: 0.8436 (m-30) REVERT: B 310 MET cc_start: 0.3269 (mmt) cc_final: 0.2194 (mmt) REVERT: B 327 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7147 (tm-30) REVERT: B 335 MET cc_start: 0.7682 (ptt) cc_final: 0.7376 (ppp) REVERT: B 380 MET cc_start: 0.3939 (ppp) cc_final: 0.3641 (tmm) REVERT: B 434 MET cc_start: 0.2832 (tpt) cc_final: 0.2423 (ptp) REVERT: C 172 ASN cc_start: 0.8967 (m-40) cc_final: 0.8707 (m110) REVERT: C 183 ASP cc_start: 0.8991 (m-30) cc_final: 0.8648 (m-30) REVERT: C 211 SER cc_start: 0.8517 (p) cc_final: 0.7776 (m) REVERT: C 225 PHE cc_start: 0.9287 (m-80) cc_final: 0.8794 (m-80) REVERT: C 241 PHE cc_start: 0.9119 (m-80) cc_final: 0.8911 (m-10) REVERT: C 249 MET cc_start: 0.9007 (mmt) cc_final: 0.8169 (mmp) REVERT: C 259 GLU cc_start: 0.8969 (tp30) cc_final: 0.8299 (tp30) REVERT: C 347 MET cc_start: 0.9146 (mmt) cc_final: 0.8930 (mmt) REVERT: C 380 HIS cc_start: 0.8590 (t70) cc_final: 0.8375 (t-90) REVERT: C 394 ILE cc_start: 0.9177 (mm) cc_final: 0.8952 (tp) REVERT: C 409 TYR cc_start: 0.9279 (t80) cc_final: 0.8762 (t80) REVERT: C 441 ILE cc_start: 0.8227 (mt) cc_final: 0.7735 (mt) REVERT: C 447 GLU cc_start: 0.8717 (pm20) cc_final: 0.8499 (pm20) REVERT: C 452 GLN cc_start: 0.9480 (tt0) cc_final: 0.9027 (tt0) REVERT: C 475 PHE cc_start: 0.9612 (m-80) cc_final: 0.9098 (m-80) REVERT: C 478 LYS cc_start: 0.9187 (tmmt) cc_final: 0.8862 (ttpp) REVERT: C 495 LYS cc_start: 0.9161 (mmmt) cc_final: 0.8295 (mmtm) REVERT: C 511 LYS cc_start: 0.9340 (tptm) cc_final: 0.9084 (tttt) REVERT: C 518 GLU cc_start: 0.9240 (tm-30) cc_final: 0.8838 (tm-30) REVERT: C 604 MET cc_start: 0.8041 (ptp) cc_final: 0.7552 (ppp) REVERT: C 659 GLU cc_start: 0.9220 (tp30) cc_final: 0.8915 (tp30) REVERT: C 663 GLU cc_start: 0.9662 (pt0) cc_final: 0.9187 (pt0) REVERT: C 781 ASP cc_start: 0.8019 (m-30) cc_final: 0.7793 (m-30) REVERT: D 1 MET cc_start: 0.6721 (mtp) cc_final: 0.6454 (mtp) REVERT: D 4 LYS cc_start: 0.8680 (mmtp) cc_final: 0.8408 (mmmm) REVERT: D 32 TRP cc_start: 0.8052 (t60) cc_final: 0.7233 (t60) REVERT: D 103 LYS cc_start: 0.9347 (mtmt) cc_final: 0.9108 (mtpp) REVERT: D 168 PHE cc_start: 0.8017 (t80) cc_final: 0.7262 (t80) REVERT: D 172 GLU cc_start: 0.8740 (tt0) cc_final: 0.8499 (tt0) REVERT: D 179 GLU cc_start: 0.8133 (pt0) cc_final: 0.7701 (pt0) REVERT: D 189 LEU cc_start: 0.9849 (mt) cc_final: 0.9617 (mm) REVERT: D 198 ARG cc_start: 0.9225 (ptm-80) cc_final: 0.8938 (ptm-80) REVERT: D 266 MET cc_start: 0.9226 (mtm) cc_final: 0.8803 (mtp) REVERT: D 271 LEU cc_start: 0.9797 (mt) cc_final: 0.9492 (mt) REVERT: D 343 LEU cc_start: 0.9549 (tp) cc_final: 0.9260 (tp) REVERT: D 383 ASP cc_start: 0.9183 (t0) cc_final: 0.8981 (t0) REVERT: D 414 ASP cc_start: 0.9048 (t0) cc_final: 0.8643 (t0) REVERT: D 418 VAL cc_start: 0.9785 (m) cc_final: 0.9563 (p) REVERT: D 419 LEU cc_start: 0.9767 (mt) cc_final: 0.9442 (pp) REVERT: D 434 ASN cc_start: 0.9025 (m110) cc_final: 0.8804 (m110) REVERT: D 461 LEU cc_start: 0.8574 (mt) cc_final: 0.8101 (pp) REVERT: D 486 PHE cc_start: 0.7311 (m-10) cc_final: 0.6585 (m-10) REVERT: D 495 LEU cc_start: 0.9446 (mm) cc_final: 0.9197 (mm) REVERT: D 498 TYR cc_start: 0.8473 (m-80) cc_final: 0.7938 (m-80) REVERT: D 579 MET cc_start: 0.8920 (mmp) cc_final: 0.8637 (mmp) REVERT: D 652 ILE cc_start: 0.9421 (mp) cc_final: 0.9011 (mp) REVERT: D 686 ASN cc_start: 0.8406 (t0) cc_final: 0.7999 (t0) REVERT: D 689 LEU cc_start: 0.8369 (mt) cc_final: 0.8096 (mt) REVERT: D 709 PHE cc_start: 0.6961 (t80) cc_final: 0.6709 (t80) REVERT: U 121 GLU cc_start: 0.8908 (tp30) cc_final: 0.8559 (pt0) outliers start: 0 outliers final: 0 residues processed: 531 average time/residue: 0.1389 time to fit residues: 113.3163 Evaluate side-chains 422 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 40 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 213 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 217 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS C 654 ASN D 442 ASN D 480 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.106798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.081564 restraints weight = 71799.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.084489 restraints weight = 35530.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.086339 restraints weight = 21095.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.087516 restraints weight = 14140.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.088322 restraints weight = 10501.256| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.6495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18944 Z= 0.259 Angle : 0.762 12.099 25639 Z= 0.410 Chirality : 0.047 0.219 2856 Planarity : 0.006 0.072 3297 Dihedral : 6.040 54.260 2505 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.62 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.25 (0.17), residues: 2250 helix: 0.33 (0.14), residues: 1301 sheet: -1.18 (0.40), residues: 151 loop : -0.58 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 133 TYR 0.031 0.002 TYR C 343 PHE 0.049 0.003 PHE D 700 TRP 0.065 0.003 TRP A 105 HIS 0.014 0.002 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00538 (18942) covalent geometry : angle 0.76227 (25639) hydrogen bonds : bond 0.05216 ( 1015) hydrogen bonds : angle 5.61628 ( 2946) Misc. bond : bond 0.00071 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 0.742 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: A 140 HIS cc_start: 0.7784 (p-80) cc_final: 0.7383 (p-80) REVERT: A 176 ARG cc_start: 0.1535 (mtt90) cc_final: -0.0075 (tpt170) REVERT: A 234 ILE cc_start: 0.9203 (mt) cc_final: 0.9002 (mt) REVERT: A 310 MET cc_start: 0.8836 (mmm) cc_final: 0.8214 (tpp) REVERT: A 322 ILE cc_start: 0.9595 (mm) cc_final: 0.9080 (tp) REVERT: A 356 ILE cc_start: 0.8667 (pt) cc_final: 0.8224 (pt) REVERT: A 376 MET cc_start: 0.8798 (ttm) cc_final: 0.8078 (tmm) REVERT: A 377 LEU cc_start: 0.8935 (mm) cc_final: 0.8592 (mt) REVERT: A 407 TYR cc_start: 0.7844 (m-80) cc_final: 0.7371 (m-10) REVERT: A 416 MET cc_start: 0.2753 (mmp) cc_final: 0.2503 (tpp) REVERT: B 8 LEU cc_start: 0.8015 (tp) cc_final: 0.7769 (mt) REVERT: B 22 TRP cc_start: 0.8780 (m100) cc_final: 0.8172 (m100) REVERT: B 51 LYS cc_start: 0.7757 (ttmt) cc_final: 0.7478 (tmmt) REVERT: B 55 ARG cc_start: 0.9391 (mtp85) cc_final: 0.8870 (mmm-85) REVERT: B 69 MET cc_start: 0.5683 (tpp) cc_final: 0.5330 (tpp) REVERT: B 128 ASP cc_start: 0.8374 (m-30) cc_final: 0.8142 (m-30) REVERT: B 132 ASN cc_start: 0.7170 (t0) cc_final: 0.6844 (t0) REVERT: B 138 LEU cc_start: 0.6418 (tp) cc_final: 0.6207 (tp) REVERT: B 240 ASN cc_start: 0.8872 (p0) cc_final: 0.8208 (t0) REVERT: B 243 ARG cc_start: 0.9091 (mtm110) cc_final: 0.8832 (mtm110) REVERT: B 293 ASP cc_start: 0.8885 (m-30) cc_final: 0.8454 (m-30) REVERT: B 310 MET cc_start: 0.3428 (mmt) cc_final: 0.2489 (mmt) REVERT: B 327 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7134 (tm-30) REVERT: B 335 MET cc_start: 0.7731 (ptt) cc_final: 0.7426 (ppp) REVERT: B 375 MET cc_start: 0.7205 (ppp) cc_final: 0.6928 (ppp) REVERT: B 380 MET cc_start: 0.5036 (ppp) cc_final: 0.4290 (tmm) REVERT: B 383 VAL cc_start: 0.8947 (m) cc_final: 0.8608 (m) REVERT: B 434 MET cc_start: 0.2926 (tpt) cc_final: 0.2398 (ptp) REVERT: C 166 THR cc_start: 0.9025 (p) cc_final: 0.8640 (t) REVERT: C 169 GLN cc_start: 0.9385 (tt0) cc_final: 0.8839 (tt0) REVERT: C 172 ASN cc_start: 0.8874 (m-40) cc_final: 0.8671 (m110) REVERT: C 183 ASP cc_start: 0.9104 (m-30) cc_final: 0.8804 (m-30) REVERT: C 211 SER cc_start: 0.8834 (p) cc_final: 0.8102 (m) REVERT: C 220 LEU cc_start: 0.9692 (tp) cc_final: 0.9480 (tp) REVERT: C 243 MET cc_start: 0.8936 (tpt) cc_final: 0.8621 (tpp) REVERT: C 249 MET cc_start: 0.9139 (mmt) cc_final: 0.8456 (mmt) REVERT: C 262 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8587 (tm-30) REVERT: C 271 LEU cc_start: 0.9535 (mm) cc_final: 0.9292 (mm) REVERT: C 329 LYS cc_start: 0.9529 (tppt) cc_final: 0.9296 (tppp) REVERT: C 344 GLU cc_start: 0.9140 (tp30) cc_final: 0.8875 (tp30) REVERT: C 347 MET cc_start: 0.9272 (mmt) cc_final: 0.8977 (mmt) REVERT: C 352 LYS cc_start: 0.9301 (mmmm) cc_final: 0.8853 (mtmm) REVERT: C 380 HIS cc_start: 0.8527 (t70) cc_final: 0.8120 (t-90) REVERT: C 394 ILE cc_start: 0.9161 (mm) cc_final: 0.8864 (tp) REVERT: C 409 TYR cc_start: 0.9508 (t80) cc_final: 0.9223 (t80) REVERT: C 410 ILE cc_start: 0.9686 (tt) cc_final: 0.9296 (tt) REVERT: C 452 GLN cc_start: 0.9574 (tt0) cc_final: 0.8979 (tt0) REVERT: C 475 PHE cc_start: 0.9626 (m-80) cc_final: 0.9113 (m-80) REVERT: C 478 LYS cc_start: 0.9213 (tmmt) cc_final: 0.8868 (ttpp) REVERT: C 495 LYS cc_start: 0.9091 (mmmt) cc_final: 0.8302 (mmtm) REVERT: C 511 LYS cc_start: 0.9342 (tptm) cc_final: 0.9060 (tttt) REVERT: C 518 GLU cc_start: 0.9311 (tm-30) cc_final: 0.8784 (tm-30) REVERT: C 562 TYR cc_start: 0.9000 (t80) cc_final: 0.8709 (t80) REVERT: C 604 MET cc_start: 0.8204 (ptp) cc_final: 0.7493 (ptp) REVERT: C 659 GLU cc_start: 0.9202 (tp30) cc_final: 0.8877 (tp30) REVERT: C 661 PHE cc_start: 0.8887 (t80) cc_final: 0.8288 (t80) REVERT: C 663 GLU cc_start: 0.9621 (pt0) cc_final: 0.9369 (pt0) REVERT: C 781 ASP cc_start: 0.8130 (m-30) cc_final: 0.7926 (m-30) REVERT: D 4 LYS cc_start: 0.8776 (mmtp) cc_final: 0.8412 (mmmm) REVERT: D 103 LYS cc_start: 0.9415 (mtmt) cc_final: 0.9175 (mtpp) REVERT: D 189 LEU cc_start: 0.9883 (mt) cc_final: 0.9657 (mm) REVERT: D 248 LEU cc_start: 0.9765 (mt) cc_final: 0.9560 (mt) REVERT: D 266 MET cc_start: 0.9251 (mtm) cc_final: 0.8813 (mtp) REVERT: D 271 LEU cc_start: 0.9797 (mt) cc_final: 0.9510 (mt) REVERT: D 275 ILE cc_start: 0.9533 (pt) cc_final: 0.9331 (pt) REVERT: D 282 MET cc_start: 0.9543 (ttp) cc_final: 0.9288 (ttm) REVERT: D 285 GLU cc_start: 0.8992 (mp0) cc_final: 0.8576 (mp0) REVERT: D 343 LEU cc_start: 0.9580 (tp) cc_final: 0.9283 (tp) REVERT: D 383 ASP cc_start: 0.9246 (t0) cc_final: 0.9008 (t0) REVERT: D 395 ASP cc_start: 0.8367 (t0) cc_final: 0.8155 (t0) REVERT: D 414 ASP cc_start: 0.9161 (t0) cc_final: 0.8719 (t0) REVERT: D 419 LEU cc_start: 0.9791 (mt) cc_final: 0.9363 (pp) REVERT: D 434 ASN cc_start: 0.8979 (m110) cc_final: 0.8757 (m110) REVERT: D 461 LEU cc_start: 0.8612 (mt) cc_final: 0.8151 (pp) REVERT: D 486 PHE cc_start: 0.7273 (m-10) cc_final: 0.6704 (m-10) REVERT: D 495 LEU cc_start: 0.9382 (mm) cc_final: 0.9165 (mm) REVERT: D 498 TYR cc_start: 0.8630 (m-80) cc_final: 0.8006 (m-80) REVERT: D 646 TYR cc_start: 0.8712 (t80) cc_final: 0.8316 (t80) REVERT: D 652 ILE cc_start: 0.9484 (mp) cc_final: 0.9254 (mp) REVERT: D 664 ARG cc_start: 0.8028 (mtm180) cc_final: 0.7707 (mtm180) REVERT: D 686 ASN cc_start: 0.8291 (t0) cc_final: 0.7970 (t0) REVERT: D 709 PHE cc_start: 0.7043 (t80) cc_final: 0.6716 (t80) outliers start: 0 outliers final: 0 residues processed: 497 average time/residue: 0.1373 time to fit residues: 105.1029 Evaluate side-chains 400 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 143 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS C 269 ASN ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS C 654 ASN D 178 ASN D 673 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.109207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.083520 restraints weight = 70570.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.086527 restraints weight = 34929.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.088446 restraints weight = 20771.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.089715 restraints weight = 13923.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.090523 restraints weight = 10260.073| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.6740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18944 Z= 0.165 Angle : 0.708 9.902 25639 Z= 0.380 Chirality : 0.046 0.206 2856 Planarity : 0.005 0.075 3297 Dihedral : 5.986 54.190 2505 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.53 % Favored : 95.24 % Rotamer: Outliers : 0.05 % Allowed : 0.43 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.15 (0.17), residues: 2250 helix: 0.43 (0.14), residues: 1292 sheet: -0.99 (0.40), residues: 144 loop : -0.61 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 618 TYR 0.024 0.002 TYR C 343 PHE 0.053 0.002 PHE D 700 TRP 0.054 0.003 TRP D 32 HIS 0.014 0.001 HIS D 638 Details of bonding type rmsd covalent geometry : bond 0.00355 (18942) covalent geometry : angle 0.70758 (25639) hydrogen bonds : bond 0.04999 ( 1015) hydrogen bonds : angle 5.43768 ( 2946) Misc. bond : bond 0.00084 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 502 time to evaluate : 0.787 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: A 140 HIS cc_start: 0.7751 (p-80) cc_final: 0.7340 (p-80) REVERT: A 155 LEU cc_start: 0.9573 (mt) cc_final: 0.9207 (tp) REVERT: A 167 LEU cc_start: 0.9002 (mt) cc_final: 0.8633 (mt) REVERT: A 176 ARG cc_start: 0.1450 (mtt90) cc_final: -0.0112 (tpt170) REVERT: A 310 MET cc_start: 0.8838 (mmm) cc_final: 0.8184 (tpp) REVERT: A 318 VAL cc_start: 0.8503 (t) cc_final: 0.8060 (p) REVERT: A 356 ILE cc_start: 0.8383 (pt) cc_final: 0.8124 (pt) REVERT: A 416 MET cc_start: 0.3013 (mmp) cc_final: 0.2737 (tpp) REVERT: B 1 MET cc_start: 0.2702 (mmt) cc_final: 0.2449 (mmt) REVERT: B 28 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8657 (mm-30) REVERT: B 81 ASN cc_start: 0.8612 (m-40) cc_final: 0.8056 (t0) REVERT: B 132 ASN cc_start: 0.7410 (t0) cc_final: 0.7148 (t0) REVERT: B 240 ASN cc_start: 0.8829 (p0) cc_final: 0.8118 (t0) REVERT: B 293 ASP cc_start: 0.8908 (m-30) cc_final: 0.8457 (m-30) REVERT: B 310 MET cc_start: 0.3334 (mmt) cc_final: 0.2248 (mmt) REVERT: B 312 ASN cc_start: 0.7003 (t0) cc_final: 0.6503 (p0) REVERT: B 327 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7145 (tm-30) REVERT: B 335 MET cc_start: 0.7529 (ptt) cc_final: 0.7276 (ppp) REVERT: B 380 MET cc_start: 0.4618 (ppp) cc_final: 0.4210 (tmm) REVERT: B 434 MET cc_start: 0.2842 (tpt) cc_final: 0.2436 (ptp) REVERT: C 166 THR cc_start: 0.8942 (p) cc_final: 0.8599 (t) REVERT: C 169 GLN cc_start: 0.9419 (tt0) cc_final: 0.8936 (tt0) REVERT: C 172 ASN cc_start: 0.8962 (m-40) cc_final: 0.8704 (m110) REVERT: C 183 ASP cc_start: 0.9116 (m-30) cc_final: 0.8803 (m-30) REVERT: C 211 SER cc_start: 0.8621 (p) cc_final: 0.7875 (m) REVERT: C 243 MET cc_start: 0.8968 (tpt) cc_final: 0.8563 (tpp) REVERT: C 249 MET cc_start: 0.9142 (mmt) cc_final: 0.8753 (mmm) REVERT: C 329 LYS cc_start: 0.9535 (tppt) cc_final: 0.9315 (tppp) REVERT: C 344 GLU cc_start: 0.9159 (tp30) cc_final: 0.8857 (tp30) REVERT: C 380 HIS cc_start: 0.8542 (t70) cc_final: 0.8149 (t-90) REVERT: C 394 ILE cc_start: 0.9123 (mm) cc_final: 0.8845 (tp) REVERT: C 409 TYR cc_start: 0.9339 (t80) cc_final: 0.8782 (t80) REVERT: C 410 ILE cc_start: 0.9681 (tt) cc_final: 0.9272 (tt) REVERT: C 452 GLN cc_start: 0.9509 (tt0) cc_final: 0.8890 (tt0) REVERT: C 475 PHE cc_start: 0.9637 (m-80) cc_final: 0.9157 (m-80) REVERT: C 478 LYS cc_start: 0.9243 (tmmt) cc_final: 0.8859 (ttpp) REVERT: C 495 LYS cc_start: 0.9084 (mmmt) cc_final: 0.8318 (mmtt) REVERT: C 511 LYS cc_start: 0.9293 (tptm) cc_final: 0.9006 (tttt) REVERT: C 518 GLU cc_start: 0.9277 (tm-30) cc_final: 0.8876 (tm-30) REVERT: C 604 MET cc_start: 0.8133 (ptp) cc_final: 0.7442 (tmm) REVERT: C 659 GLU cc_start: 0.9218 (tp30) cc_final: 0.8917 (tp30) REVERT: C 663 GLU cc_start: 0.9649 (pt0) cc_final: 0.9301 (pt0) REVERT: C 781 ASP cc_start: 0.8094 (m-30) cc_final: 0.7874 (m-30) REVERT: D 4 LYS cc_start: 0.8740 (mmtp) cc_final: 0.8298 (mmmm) REVERT: D 32 TRP cc_start: 0.8154 (t60) cc_final: 0.7912 (t60) REVERT: D 103 LYS cc_start: 0.9387 (mtmt) cc_final: 0.9131 (mtpp) REVERT: D 189 LEU cc_start: 0.9857 (mt) cc_final: 0.9630 (mm) REVERT: D 266 MET cc_start: 0.9297 (mtm) cc_final: 0.8800 (mtp) REVERT: D 271 LEU cc_start: 0.9780 (mt) cc_final: 0.9496 (mt) REVERT: D 282 MET cc_start: 0.9520 (ttp) cc_final: 0.9269 (ttm) REVERT: D 285 GLU cc_start: 0.8968 (mp0) cc_final: 0.8537 (mp0) REVERT: D 343 LEU cc_start: 0.9571 (tp) cc_final: 0.9286 (tp) REVERT: D 414 ASP cc_start: 0.9177 (t0) cc_final: 0.8715 (t0) REVERT: D 419 LEU cc_start: 0.9786 (mt) cc_final: 0.9385 (pp) REVERT: D 434 ASN cc_start: 0.8974 (m110) cc_final: 0.8757 (m110) REVERT: D 441 LYS cc_start: 0.9079 (pttm) cc_final: 0.8571 (tptt) REVERT: D 461 LEU cc_start: 0.8432 (mt) cc_final: 0.8188 (pp) REVERT: D 476 ASN cc_start: 0.8585 (t0) cc_final: 0.8369 (t0) REVERT: D 486 PHE cc_start: 0.7217 (m-10) cc_final: 0.6533 (m-10) REVERT: D 495 LEU cc_start: 0.9394 (mm) cc_final: 0.9173 (mm) REVERT: D 498 TYR cc_start: 0.8595 (m-80) cc_final: 0.7973 (m-80) REVERT: D 573 ILE cc_start: 0.9188 (mp) cc_final: 0.8912 (tp) REVERT: D 612 TRP cc_start: 0.4206 (m100) cc_final: 0.3994 (m100) REVERT: D 646 TYR cc_start: 0.8677 (t80) cc_final: 0.8277 (t80) REVERT: D 652 ILE cc_start: 0.9464 (mp) cc_final: 0.9092 (mp) REVERT: D 664 ARG cc_start: 0.7945 (mtm180) cc_final: 0.7619 (mtm180) REVERT: D 686 ASN cc_start: 0.8440 (t0) cc_final: 0.8102 (t0) outliers start: 1 outliers final: 0 residues processed: 502 average time/residue: 0.1420 time to fit residues: 109.6927 Evaluate side-chains 408 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 185 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS C 654 ASN D 442 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.110426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.084728 restraints weight = 69960.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.087748 restraints weight = 34760.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.089660 restraints weight = 20733.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.090914 restraints weight = 13921.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.091699 restraints weight = 10277.785| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.6925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18944 Z= 0.154 Angle : 0.719 11.190 25639 Z= 0.383 Chirality : 0.046 0.246 2856 Planarity : 0.005 0.073 3297 Dihedral : 5.906 55.197 2505 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.31 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.04 (0.18), residues: 2250 helix: 0.49 (0.14), residues: 1289 sheet: -0.80 (0.41), residues: 139 loop : -0.54 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 243 TYR 0.034 0.002 TYR D 582 PHE 0.050 0.002 PHE D 700 TRP 0.064 0.003 TRP A 105 HIS 0.014 0.001 HIS D 638 Details of bonding type rmsd covalent geometry : bond 0.00330 (18942) covalent geometry : angle 0.71907 (25639) hydrogen bonds : bond 0.04882 ( 1015) hydrogen bonds : angle 5.39989 ( 2946) Misc. bond : bond 0.00085 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 0.808 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: A 140 HIS cc_start: 0.7723 (p-80) cc_final: 0.7205 (p-80) REVERT: A 176 ARG cc_start: 0.1202 (mtt90) cc_final: -0.0224 (tpt170) REVERT: A 310 MET cc_start: 0.8835 (mmm) cc_final: 0.8150 (tpp) REVERT: A 318 VAL cc_start: 0.8436 (t) cc_final: 0.7962 (p) REVERT: A 375 MET cc_start: 0.8651 (tpt) cc_final: 0.8325 (tpt) REVERT: A 416 MET cc_start: 0.2962 (mmp) cc_final: 0.2689 (tpp) REVERT: B 6 ILE cc_start: 0.8046 (mm) cc_final: 0.7843 (mt) REVERT: B 28 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8384 (mt-10) REVERT: B 81 ASN cc_start: 0.8631 (m-40) cc_final: 0.8139 (t0) REVERT: B 119 ILE cc_start: 0.8698 (mm) cc_final: 0.8460 (mm) REVERT: B 136 PHE cc_start: 0.8207 (m-80) cc_final: 0.7288 (m-80) REVERT: B 240 ASN cc_start: 0.8867 (p0) cc_final: 0.8449 (t0) REVERT: B 293 ASP cc_start: 0.8855 (m-30) cc_final: 0.8429 (m-30) REVERT: B 310 MET cc_start: 0.3357 (mmt) cc_final: 0.2269 (mmt) REVERT: B 312 ASN cc_start: 0.7137 (t0) cc_final: 0.6710 (p0) REVERT: B 327 GLU cc_start: 0.7502 (tm-30) cc_final: 0.6858 (mp0) REVERT: B 335 MET cc_start: 0.7622 (ptt) cc_final: 0.7371 (ppp) REVERT: B 380 MET cc_start: 0.4380 (ppp) cc_final: 0.3892 (tmm) REVERT: B 434 MET cc_start: 0.2835 (tpt) cc_final: 0.2412 (ptp) REVERT: C 166 THR cc_start: 0.8897 (p) cc_final: 0.8565 (t) REVERT: C 169 GLN cc_start: 0.9392 (tt0) cc_final: 0.8893 (tt0) REVERT: C 172 ASN cc_start: 0.8955 (m-40) cc_final: 0.8658 (m110) REVERT: C 183 ASP cc_start: 0.9112 (m-30) cc_final: 0.8786 (m-30) REVERT: C 211 SER cc_start: 0.8517 (p) cc_final: 0.7797 (m) REVERT: C 221 LEU cc_start: 0.9869 (mt) cc_final: 0.9582 (mt) REVERT: C 225 PHE cc_start: 0.9236 (m-80) cc_final: 0.8679 (m-80) REVERT: C 243 MET cc_start: 0.8907 (tpt) cc_final: 0.8462 (tpp) REVERT: C 249 MET cc_start: 0.9120 (mmt) cc_final: 0.8771 (mmm) REVERT: C 259 GLU cc_start: 0.8965 (tp30) cc_final: 0.8305 (tp30) REVERT: C 344 GLU cc_start: 0.9180 (tp30) cc_final: 0.8909 (tp30) REVERT: C 354 LEU cc_start: 0.9135 (tp) cc_final: 0.8900 (tt) REVERT: C 380 HIS cc_start: 0.8539 (t70) cc_final: 0.8138 (t-90) REVERT: C 452 GLN cc_start: 0.9465 (tt0) cc_final: 0.8897 (tt0) REVERT: C 461 ASN cc_start: 0.9236 (m-40) cc_final: 0.8973 (m-40) REVERT: C 475 PHE cc_start: 0.9613 (m-80) cc_final: 0.9334 (m-80) REVERT: C 478 LYS cc_start: 0.9278 (tmmt) cc_final: 0.9038 (ttpp) REVERT: C 495 LYS cc_start: 0.9087 (mmmt) cc_final: 0.8315 (mmtt) REVERT: C 511 LYS cc_start: 0.9290 (tptm) cc_final: 0.9017 (tttt) REVERT: C 518 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8895 (tm-30) REVERT: C 604 MET cc_start: 0.8074 (ptp) cc_final: 0.7462 (tmm) REVERT: C 659 GLU cc_start: 0.9176 (tp30) cc_final: 0.8758 (tp30) REVERT: C 663 GLU cc_start: 0.9657 (pt0) cc_final: 0.9123 (pt0) REVERT: C 781 ASP cc_start: 0.8076 (m-30) cc_final: 0.7871 (m-30) REVERT: D 4 LYS cc_start: 0.8737 (mmtp) cc_final: 0.8333 (mmmm) REVERT: D 68 ILE cc_start: 0.9434 (pt) cc_final: 0.9215 (pt) REVERT: D 103 LYS cc_start: 0.9362 (mtmt) cc_final: 0.9104 (mtpp) REVERT: D 112 TYR cc_start: 0.8531 (m-10) cc_final: 0.8079 (m-10) REVERT: D 179 GLU cc_start: 0.8182 (pt0) cc_final: 0.7971 (pt0) REVERT: D 266 MET cc_start: 0.9261 (mtm) cc_final: 0.8876 (mtp) REVERT: D 271 LEU cc_start: 0.9770 (mt) cc_final: 0.9495 (mt) REVERT: D 282 MET cc_start: 0.9550 (ttp) cc_final: 0.9192 (ttt) REVERT: D 285 GLU cc_start: 0.8945 (mp0) cc_final: 0.8486 (mp0) REVERT: D 301 THR cc_start: 0.9254 (p) cc_final: 0.8886 (t) REVERT: D 343 LEU cc_start: 0.9553 (tp) cc_final: 0.9275 (tp) REVERT: D 383 ASP cc_start: 0.9118 (t0) cc_final: 0.8882 (t0) REVERT: D 414 ASP cc_start: 0.9086 (t0) cc_final: 0.8658 (t0) REVERT: D 417 ASN cc_start: 0.9580 (t0) cc_final: 0.9174 (t0) REVERT: D 419 LEU cc_start: 0.9748 (mt) cc_final: 0.9536 (pp) REVERT: D 434 ASN cc_start: 0.8999 (m110) cc_final: 0.8754 (m110) REVERT: D 441 LYS cc_start: 0.9069 (pttm) cc_final: 0.8650 (tptt) REVERT: D 461 LEU cc_start: 0.8446 (mt) cc_final: 0.8124 (pp) REVERT: D 476 ASN cc_start: 0.8465 (t0) cc_final: 0.8170 (t0) REVERT: D 486 PHE cc_start: 0.7225 (m-10) cc_final: 0.6533 (m-10) REVERT: D 495 LEU cc_start: 0.9384 (mm) cc_final: 0.9176 (mm) REVERT: D 498 TYR cc_start: 0.8589 (m-80) cc_final: 0.7960 (m-80) REVERT: D 573 ILE cc_start: 0.9323 (mp) cc_final: 0.8985 (tp) REVERT: D 579 MET cc_start: 0.8781 (mmp) cc_final: 0.8381 (mmp) REVERT: D 582 TYR cc_start: 0.8633 (m-80) cc_final: 0.8037 (m-80) REVERT: D 586 LEU cc_start: 0.9251 (tt) cc_final: 0.8824 (tt) REVERT: D 646 TYR cc_start: 0.8682 (t80) cc_final: 0.8279 (t80) REVERT: D 652 ILE cc_start: 0.9478 (mp) cc_final: 0.9166 (mp) REVERT: D 686 ASN cc_start: 0.8531 (t0) cc_final: 0.8272 (t0) REVERT: U 126 GLU cc_start: 0.9158 (pm20) cc_final: 0.8921 (pm20) outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.1320 time to fit residues: 102.7596 Evaluate side-chains 405 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 104 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 HIS C 654 ASN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.109837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.084440 restraints weight = 72266.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.087441 restraints weight = 35587.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.089343 restraints weight = 21172.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.090582 restraints weight = 14209.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.091347 restraints weight = 10514.184| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.7047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 18944 Z= 0.172 Angle : 0.710 11.498 25639 Z= 0.379 Chirality : 0.046 0.288 2856 Planarity : 0.005 0.076 3297 Dihedral : 5.884 57.252 2505 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.80 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.08 (0.18), residues: 2250 helix: 0.49 (0.14), residues: 1295 sheet: -0.90 (0.40), residues: 146 loop : -0.58 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 243 TYR 0.032 0.002 TYR A 109 PHE 0.049 0.002 PHE D 700 TRP 0.078 0.003 TRP D 32 HIS 0.014 0.001 HIS D 638 Details of bonding type rmsd covalent geometry : bond 0.00374 (18942) covalent geometry : angle 0.71024 (25639) hydrogen bonds : bond 0.04826 ( 1015) hydrogen bonds : angle 5.43624 ( 2946) Misc. bond : bond 0.00087 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4032.22 seconds wall clock time: 70 minutes 29.17 seconds (4229.17 seconds total)