Starting phenix.real_space_refine on Tue Nov 18 13:48:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fa4_50267/11_2025/9fa4_50267.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fa4_50267/11_2025/9fa4_50267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fa4_50267/11_2025/9fa4_50267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fa4_50267/11_2025/9fa4_50267.map" model { file = "/net/cci-nas-00/data/ceres_data/9fa4_50267/11_2025/9fa4_50267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fa4_50267/11_2025/9fa4_50267.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 9317 2.51 5 N 2491 2.21 5 O 2694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14589 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 18, 'TRANS': 341} Chain breaks: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 4573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4573 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 19, 'TRANS': 588} Chain breaks: 6 Unresolved non-hydrogen bonds: 441 Unresolved non-hydrogen angles: 552 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 11, 'ARG:plan': 17, 'PHE:plan': 4, 'HIS:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 284 Chain: "A" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3727 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 26, 'TRANS': 490} Chain breaks: 5 Unresolved non-hydrogen bonds: 406 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 334 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'TYR:plan': 4, 'HIS:plan': 4, 'PHE:plan': 2, 'ASP:plan': 10, 'GLU:plan': 10, 'GLN:plan1': 4, 'ARG:plan': 12, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 221 Chain: "B" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3508 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 451} Chain breaks: 2 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 356 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 12, 'GLU:plan': 11, 'GLN:plan1': 5, 'ARG:plan': 8, 'ASN:plan1': 8, 'PHE:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 190 Time building chain proxies: 3.57, per 1000 atoms: 0.24 Number of scatterers: 14589 At special positions: 0 Unit cell: (176.3, 128.74, 234.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2694 8.00 N 2491 7.00 C 9317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 697.5 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3782 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 58.8% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'C' and resid 1 through 9 Processing helix chain 'C' and resid 12 through 35 Processing helix chain 'C' and resid 41 through 52 removed outlier: 3.948A pdb=" N VAL C 45 " --> pdb=" O ASP C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 85 Processing helix chain 'C' and resid 87 through 100 removed outlier: 3.508A pdb=" N SER C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 125 Processing helix chain 'C' and resid 126 through 139 removed outlier: 3.789A pdb=" N GLN C 138 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 158 removed outlier: 3.779A pdb=" N ARG C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 169 removed outlier: 3.554A pdb=" N LEU C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN C 169 " --> pdb=" O GLN C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 174 through 189 Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 199 through 213 removed outlier: 3.622A pdb=" N ASP C 213 " --> pdb=" O TRP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 217 removed outlier: 3.652A pdb=" N ILE C 217 " --> pdb=" O PRO C 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 214 through 217' Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 239 through 258 Proline residue: C 251 - end of helix Processing helix chain 'C' and resid 277 through 308 Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 321 through 336 removed outlier: 3.843A pdb=" N LEU C 325 " --> pdb=" O HIS C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 362 Processing helix chain 'C' and resid 368 through 376 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'D' and resid 2 through 17 removed outlier: 3.810A pdb=" N ASP D 6 " --> pdb=" O SER D 2 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 36 Processing helix chain 'D' and resid 39 through 53 removed outlier: 3.852A pdb=" N GLN D 43 " --> pdb=" O ASP D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 70 Processing helix chain 'D' and resid 73 through 88 removed outlier: 3.751A pdb=" N TRP D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 106 removed outlier: 3.538A pdb=" N THR D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 122 Processing helix chain 'D' and resid 124 through 139 Processing helix chain 'D' and resid 142 through 160 removed outlier: 4.540A pdb=" N VAL D 148 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY D 149 " --> pdb=" O GLN D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 177 through 185 Processing helix chain 'D' and resid 191 through 210 removed outlier: 3.588A pdb=" N ASN D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 282 through 296 Processing helix chain 'D' and resid 303 through 329 removed outlier: 3.957A pdb=" N THR D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 426 removed outlier: 3.603A pdb=" N LEU D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 441 removed outlier: 3.668A pdb=" N TRP D 440 " --> pdb=" O ILE D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 460 removed outlier: 3.731A pdb=" N MET D 455 " --> pdb=" O PHE D 451 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE D 457 " --> pdb=" O THR D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 476 Processing helix chain 'D' and resid 490 through 505 removed outlier: 3.624A pdb=" N ARG D 494 " --> pdb=" O LEU D 490 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 496 " --> pdb=" O HIS D 492 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA D 505 " --> pdb=" O THR D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 524 removed outlier: 3.522A pdb=" N ASP D 518 " --> pdb=" O GLU D 514 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS D 521 " --> pdb=" O LEU D 517 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR D 522 " --> pdb=" O ASP D 518 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET D 523 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL D 524 " --> pdb=" O MET D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 576 Processing helix chain 'D' and resid 583 through 593 Processing helix chain 'D' and resid 600 through 615 Processing helix chain 'D' and resid 621 through 625 removed outlier: 3.880A pdb=" N ASN D 624 " --> pdb=" O ASN D 621 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR D 625 " --> pdb=" O PHE D 622 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 621 through 625' Processing helix chain 'D' and resid 628 through 641 removed outlier: 3.508A pdb=" N TYR D 637 " --> pdb=" O GLU D 633 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 638 " --> pdb=" O GLU D 634 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG D 639 " --> pdb=" O PHE D 635 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR D 640 " --> pdb=" O ALA D 636 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN D 641 " --> pdb=" O TYR D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 667 through 686 removed outlier: 3.873A pdb=" N PHE D 675 " --> pdb=" O VAL D 671 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG D 676 " --> pdb=" O LYS D 672 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET D 679 " --> pdb=" O PHE D 675 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG D 685 " --> pdb=" O ARG D 681 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS D 686 " --> pdb=" O GLN D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 701 Processing helix chain 'D' and resid 704 through 709 Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 50 through 70 Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 137 through 147 Processing helix chain 'A' and resid 168 through 193 removed outlier: 3.760A pdb=" N ASN A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.579A pdb=" N PHE A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 291 Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 414 through 424 Processing helix chain 'A' and resid 443 through 456 Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 487 through 508 Processing helix chain 'A' and resid 524 through 543 removed outlier: 3.682A pdb=" N HIS A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 547 through 561 removed outlier: 3.554A pdb=" N GLN A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 14 Processing helix chain 'B' and resid 27 through 46 Processing helix chain 'B' and resid 69 through 77 removed outlier: 3.950A pdb=" N LEU B 73 " --> pdb=" O ASP B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 103 removed outlier: 3.674A pdb=" N ALA B 91 " --> pdb=" O CYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 134 removed outlier: 3.746A pdb=" N ASN B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 166 removed outlier: 3.513A pdb=" N THR B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 Processing helix chain 'B' and resid 193 through 209 Processing helix chain 'B' and resid 298 through 302 Processing helix chain 'B' and resid 309 through 321 Processing helix chain 'B' and resid 360 through 364 removed outlier: 4.044A pdb=" N GLY B 364 " --> pdb=" O PRO B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 425 removed outlier: 3.839A pdb=" N LEU B 412 " --> pdb=" O LYS B 408 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 448 Processing helix chain 'B' and resid 449 through 466 Processing helix chain 'B' and resid 472 through 490 Processing sheet with id=AA1, first strand: chain 'D' and resid 345 through 348 Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 87 removed outlier: 3.885A pdb=" N HIS A 86 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR A 10 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE A 79 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE A 12 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER A 81 " --> pdb=" O PHE A 12 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 14 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 203 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 231 " --> pdb=" O CYS A 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 260 removed outlier: 4.353A pdb=" N HIS A 286 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ARG A 336 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY A 333 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ILE A 384 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A 376 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU A 389 " --> pdb=" O SER A 374 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER A 374 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 373 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLN A 364 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N HIS A 375 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 427 through 429 Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 67 removed outlier: 3.888A pdb=" N MET B 63 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU B 53 " --> pdb=" O MET B 63 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N THR B 51 " --> pdb=" O PRO B 65 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL B 4 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL B 114 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL B 6 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 184 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 154 " --> pdb=" O GLN B 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 16 through 17 removed outlier: 3.976A pdb=" N TYR B 25 " --> pdb=" O VAL B 17 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 326 through 327 removed outlier: 3.603A pdb=" N GLU B 252 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N LEU B 251 " --> pdb=" O HIS B 213 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B 215 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE B 253 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LYS B 217 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 274 " --> pdb=" O GLN B 226 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU B 348 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET B 335 " --> pdb=" O SER B 351 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 257 through 258 842 hydrogen bonds defined for protein. 2475 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2966 1.33 - 1.45: 3220 1.45 - 1.57: 8560 1.57 - 1.69: 0 1.69 - 1.81: 129 Bond restraints: 14875 Sorted by residual: bond pdb=" C GLY B 34 " pdb=" N LEU B 35 " ideal model delta sigma weight residual 1.335 1.207 0.128 1.31e-02 5.83e+03 9.57e+01 bond pdb=" C LEU B 35 " pdb=" N THR B 36 " ideal model delta sigma weight residual 1.335 1.444 -0.110 1.25e-02 6.40e+03 7.70e+01 bond pdb=" N TRP D 597 " pdb=" CA TRP D 597 " ideal model delta sigma weight residual 1.461 1.491 -0.029 9.20e-03 1.18e+04 1.02e+01 bond pdb=" C GLY D 460 " pdb=" O GLY D 460 " ideal model delta sigma weight residual 1.235 1.275 -0.040 1.35e-02 5.49e+03 8.98e+00 bond pdb=" N VAL B 5 " pdb=" CA VAL B 5 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.23e-02 6.61e+03 7.20e+00 ... (remaining 14870 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 20032 2.70 - 5.40: 217 5.40 - 8.10: 24 8.10 - 10.80: 6 10.80 - 13.50: 1 Bond angle restraints: 20280 Sorted by residual: angle pdb=" CA GLY B 34 " pdb=" C GLY B 34 " pdb=" N LEU B 35 " ideal model delta sigma weight residual 116.89 124.77 -7.88 1.06e+00 8.90e-01 5.53e+01 angle pdb=" O GLY B 34 " pdb=" C GLY B 34 " pdb=" N LEU B 35 " ideal model delta sigma weight residual 122.19 115.84 6.35 9.60e-01 1.09e+00 4.37e+01 angle pdb=" N ILE D 456 " pdb=" CA ILE D 456 " pdb=" C ILE D 456 " ideal model delta sigma weight residual 110.36 104.65 5.71 1.05e+00 9.07e-01 2.96e+01 angle pdb=" C LEU B 35 " pdb=" N THR B 36 " pdb=" CA THR B 36 " ideal model delta sigma weight residual 120.54 113.95 6.59 1.35e+00 5.49e-01 2.38e+01 angle pdb=" O LEU B 35 " pdb=" C LEU B 35 " pdb=" N THR B 36 " ideal model delta sigma weight residual 122.12 126.97 -4.85 1.06e+00 8.90e-01 2.09e+01 ... (remaining 20275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 7861 17.75 - 35.49: 861 35.49 - 53.24: 202 53.24 - 70.98: 41 70.98 - 88.73: 16 Dihedral angle restraints: 8981 sinusoidal: 3200 harmonic: 5781 Sorted by residual: dihedral pdb=" CA GLN D 273 " pdb=" C GLN D 273 " pdb=" N MET D 274 " pdb=" CA MET D 274 " ideal model delta harmonic sigma weight residual -180.00 -151.07 -28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA VAL D 524 " pdb=" C VAL D 524 " pdb=" N LEU D 525 " pdb=" CA LEU D 525 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA TYR B 83 " pdb=" C TYR B 83 " pdb=" N ASP B 84 " pdb=" CA ASP B 84 " ideal model delta harmonic sigma weight residual -180.00 -159.36 -20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 8978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1950 0.047 - 0.094: 379 0.094 - 0.142: 80 0.142 - 0.189: 11 0.189 - 0.236: 3 Chirality restraints: 2423 Sorted by residual: chirality pdb=" CA LEU B 35 " pdb=" N LEU B 35 " pdb=" C LEU B 35 " pdb=" CB LEU B 35 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA LEU B 274 " pdb=" N LEU B 274 " pdb=" C LEU B 274 " pdb=" CB LEU B 274 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA LEU B 30 " pdb=" N LEU B 30 " pdb=" C LEU B 30 " pdb=" CB LEU B 30 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2420 not shown) Planarity restraints: 2606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET D 455 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" C MET D 455 " -0.039 2.00e-02 2.50e+03 pdb=" O MET D 455 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE D 456 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 27 " 0.200 9.50e-02 1.11e+02 8.95e-02 4.91e+00 pdb=" NE ARG B 27 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 27 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 27 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 27 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 621 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C ASN D 621 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN D 621 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE D 622 " -0.012 2.00e-02 2.50e+03 ... (remaining 2603 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1350 2.74 - 3.28: 15476 3.28 - 3.82: 24770 3.82 - 4.36: 26740 4.36 - 4.90: 45600 Nonbonded interactions: 113936 Sorted by model distance: nonbonded pdb=" O LEU A 354 " pdb=" OG SER A 379 " model vdw 2.201 3.040 nonbonded pdb=" O ILE D 207 " pdb=" OG1 THR D 211 " model vdw 2.257 3.040 nonbonded pdb=" O ARG B 462 " pdb=" OG1 THR B 465 " model vdw 2.270 3.040 nonbonded pdb=" OG SER B 10 " pdb=" OG SER B 12 " model vdw 2.281 3.040 nonbonded pdb=" O THR D 556 " pdb=" N LYS D 558 " model vdw 2.299 3.120 ... (remaining 113931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 16.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.720 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 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 : 0.004 0.128 14875 Z= 0.221 Angle : 0.670 13.501 20280 Z= 0.384 Chirality : 0.041 0.236 2423 Planarity : 0.004 0.089 2606 Dihedral : 16.114 88.726 5199 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.26 % Favored : 93.58 % Rotamer: Outliers : 2.33 % Allowed : 22.14 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.44 (0.20), residues: 1932 helix: 1.79 (0.16), residues: 1037 sheet: -2.57 (0.40), residues: 167 loop : -1.22 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 331 TYR 0.014 0.001 TYR A 62 PHE 0.027 0.001 PHE C 51 TRP 0.020 0.001 TRP D 597 HIS 0.005 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00371 (14875) covalent geometry : angle 0.66977 (20280) hydrogen bonds : bond 0.17858 ( 842) hydrogen bonds : angle 6.38785 ( 2475) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.596 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: C 10 ARG cc_start: 0.3560 (ppt170) cc_final: 0.3207 (ppt170) REVERT: D 288 MET cc_start: 0.8562 (mmp) cc_final: 0.8247 (tpp) REVERT: A 60 MET cc_start: 0.8756 (mmm) cc_final: 0.8302 (mmm) REVERT: B 449 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8452 (t80) REVERT: B 452 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9033 (tt) outliers start: 34 outliers final: 28 residues processed: 168 average time/residue: 0.1314 time to fit residues: 32.2412 Evaluate side-chains 173 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 51 PHE Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.0670 chunk 194 optimal weight: 0.2980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.0040 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 0.3930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.169919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.142172 restraints weight = 46072.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.137719 restraints weight = 71716.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.135565 restraints weight = 54352.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.133516 restraints weight = 60294.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.134176 restraints weight = 54094.645| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14875 Z= 0.133 Angle : 0.595 10.082 20280 Z= 0.298 Chirality : 0.039 0.163 2423 Planarity : 0.004 0.049 2606 Dihedral : 5.700 58.123 2115 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.00 % Favored : 93.84 % Rotamer: Outliers : 2.88 % Allowed : 20.01 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.58 (0.20), residues: 1932 helix: 1.86 (0.16), residues: 1074 sheet: -2.74 (0.41), residues: 142 loop : -1.25 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 139 TYR 0.013 0.001 TYR A 62 PHE 0.016 0.001 PHE B 201 TRP 0.012 0.001 TRP D 420 HIS 0.006 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00282 (14875) covalent geometry : angle 0.59502 (20280) hydrogen bonds : bond 0.04249 ( 842) hydrogen bonds : angle 4.70023 ( 2475) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.610 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: C 110 ARG cc_start: -0.0723 (tmt170) cc_final: -0.1236 (tpt90) REVERT: C 126 ARG cc_start: 0.7026 (mtt180) cc_final: 0.6680 (mtt-85) REVERT: D 114 MET cc_start: 0.0345 (mpp) cc_final: 0.0136 (mpp) REVERT: D 275 ASP cc_start: 0.3620 (OUTLIER) cc_final: 0.2589 (t70) REVERT: B 449 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8338 (t80) REVERT: B 452 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9044 (tt) outliers start: 42 outliers final: 26 residues processed: 173 average time/residue: 0.1312 time to fit residues: 33.2635 Evaluate side-chains 168 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 95 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 185 optimal weight: 0.0270 chunk 94 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 106 optimal weight: 0.0670 chunk 6 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 128 optimal weight: 0.0060 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 HIS A 493 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.170271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.141103 restraints weight = 47037.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.138976 restraints weight = 66694.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.135424 restraints weight = 46888.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.134614 restraints weight = 46259.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.135099 restraints weight = 43020.118| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14875 Z= 0.114 Angle : 0.567 9.921 20280 Z= 0.283 Chirality : 0.039 0.199 2423 Planarity : 0.003 0.049 2606 Dihedral : 5.083 58.730 2089 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.75 % Favored : 94.05 % Rotamer: Outliers : 3.70 % Allowed : 19.40 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.63 (0.20), residues: 1932 helix: 1.92 (0.16), residues: 1082 sheet: -2.68 (0.40), residues: 142 loop : -1.31 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 110 TYR 0.014 0.001 TYR A 62 PHE 0.013 0.001 PHE B 56 TRP 0.008 0.001 TRP D 256 HIS 0.005 0.001 HIS D 503 Details of bonding type rmsd covalent geometry : bond 0.00245 (14875) covalent geometry : angle 0.56712 (20280) hydrogen bonds : bond 0.03563 ( 842) hydrogen bonds : angle 4.32137 ( 2475) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 142 time to evaluate : 0.615 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: C 110 ARG cc_start: -0.0830 (OUTLIER) cc_final: -0.1278 (tpt90) REVERT: D 274 MET cc_start: 0.4948 (mmp) cc_final: 0.4598 (mpp) REVERT: D 275 ASP cc_start: 0.3628 (OUTLIER) cc_final: 0.2657 (t70) REVERT: B 397 ARG cc_start: 0.8448 (mmt-90) cc_final: 0.8007 (mmt-90) REVERT: B 449 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8359 (t80) REVERT: B 452 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9037 (tt) outliers start: 54 outliers final: 27 residues processed: 180 average time/residue: 0.1316 time to fit residues: 34.7791 Evaluate side-chains 168 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 0.0870 chunk 41 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 124 optimal weight: 0.0010 chunk 160 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 overall best weight: 0.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.170787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.149000 restraints weight = 51930.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.144803 restraints weight = 84268.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.143178 restraints weight = 74624.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.143236 restraints weight = 67464.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.142563 restraints weight = 49522.227| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14875 Z= 0.134 Angle : 0.571 10.540 20280 Z= 0.284 Chirality : 0.039 0.185 2423 Planarity : 0.003 0.047 2606 Dihedral : 4.871 59.127 2081 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.64 % Favored : 94.25 % Rotamer: Outliers : 3.43 % Allowed : 20.08 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.74 (0.20), residues: 1932 helix: 2.02 (0.16), residues: 1081 sheet: -2.65 (0.40), residues: 142 loop : -1.28 (0.25), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 110 TYR 0.015 0.001 TYR A 62 PHE 0.020 0.001 PHE D 323 TRP 0.017 0.002 TRP A 533 HIS 0.004 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00300 (14875) covalent geometry : angle 0.57101 (20280) hydrogen bonds : bond 0.03299 ( 842) hydrogen bonds : angle 4.20868 ( 2475) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 139 time to evaluate : 0.547 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: C 110 ARG cc_start: -0.0719 (OUTLIER) cc_final: -0.1313 (tpt90) REVERT: D 695 HIS cc_start: 0.8555 (OUTLIER) cc_final: 0.8092 (t-90) REVERT: B 37 MET cc_start: 0.8196 (ttt) cc_final: 0.7916 (ttm) REVERT: B 397 ARG cc_start: 0.8480 (mmt-90) cc_final: 0.8025 (mmt180) REVERT: B 449 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8265 (t80) REVERT: B 452 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8932 (tt) outliers start: 50 outliers final: 29 residues processed: 173 average time/residue: 0.1343 time to fit residues: 34.1229 Evaluate side-chains 170 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 303 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 182 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 92 optimal weight: 40.0000 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 309 GLN A 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.168044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.139396 restraints weight = 46162.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.137312 restraints weight = 72987.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.134710 restraints weight = 60038.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.133425 restraints weight = 52018.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.133706 restraints weight = 52354.408| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14875 Z= 0.182 Angle : 0.595 10.263 20280 Z= 0.297 Chirality : 0.039 0.178 2423 Planarity : 0.004 0.045 2606 Dihedral : 4.901 54.378 2079 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.16 % Favored : 93.74 % Rotamer: Outliers : 3.43 % Allowed : 20.15 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.74 (0.20), residues: 1932 helix: 2.02 (0.16), residues: 1087 sheet: -2.78 (0.40), residues: 142 loop : -1.27 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 313 TYR 0.017 0.001 TYR A 62 PHE 0.024 0.002 PHE D 323 TRP 0.015 0.002 TRP A 318 HIS 0.009 0.001 HIS D 503 Details of bonding type rmsd covalent geometry : bond 0.00411 (14875) covalent geometry : angle 0.59511 (20280) hydrogen bonds : bond 0.03257 ( 842) hydrogen bonds : angle 4.21334 ( 2475) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 137 time to evaluate : 0.688 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: C 110 ARG cc_start: -0.0514 (OUTLIER) cc_final: -0.2765 (tpt170) REVERT: D 275 ASP cc_start: 0.4248 (OUTLIER) cc_final: 0.3324 (t70) REVERT: D 288 MET cc_start: 0.8412 (tpp) cc_final: 0.8086 (tpp) REVERT: D 695 HIS cc_start: 0.8605 (OUTLIER) cc_final: 0.8054 (t-90) REVERT: B 449 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8330 (t80) REVERT: B 452 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.8992 (tt) outliers start: 50 outliers final: 32 residues processed: 177 average time/residue: 0.1319 time to fit residues: 34.1671 Evaluate side-chains 172 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 303 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 31 optimal weight: 50.0000 chunk 150 optimal weight: 0.5980 chunk 153 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 166 optimal weight: 0.6980 chunk 169 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 64 optimal weight: 0.1980 chunk 146 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 661 HIS A 141 HIS A 500 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.169528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.145977 restraints weight = 50182.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.140793 restraints weight = 79619.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.138450 restraints weight = 66882.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.138165 restraints weight = 65012.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.137504 restraints weight = 54670.875| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14875 Z= 0.136 Angle : 0.575 12.409 20280 Z= 0.283 Chirality : 0.039 0.170 2423 Planarity : 0.003 0.045 2606 Dihedral : 4.837 49.672 2079 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.64 % Favored : 94.25 % Rotamer: Outliers : 3.02 % Allowed : 21.04 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.83 (0.21), residues: 1932 helix: 2.09 (0.16), residues: 1079 sheet: -2.57 (0.40), residues: 152 loop : -1.19 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 313 TYR 0.015 0.001 TYR A 62 PHE 0.019 0.001 PHE C 95 TRP 0.012 0.001 TRP A 318 HIS 0.007 0.001 HIS D 503 Details of bonding type rmsd covalent geometry : bond 0.00307 (14875) covalent geometry : angle 0.57458 (20280) hydrogen bonds : bond 0.03091 ( 842) hydrogen bonds : angle 4.10727 ( 2475) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 0.600 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: D 288 MET cc_start: 0.8515 (tpp) cc_final: 0.8214 (tpp) REVERT: D 423 LEU cc_start: 0.7945 (mt) cc_final: 0.7708 (tt) REVERT: D 695 HIS cc_start: 0.8573 (OUTLIER) cc_final: 0.8089 (t-90) REVERT: A 60 MET cc_start: 0.8701 (mmm) cc_final: 0.8424 (mmm) REVERT: A 452 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8028 (mp) REVERT: B 449 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8291 (t80) REVERT: B 452 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8996 (tt) outliers start: 44 outliers final: 30 residues processed: 173 average time/residue: 0.1278 time to fit residues: 32.6898 Evaluate side-chains 168 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 303 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 36 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 167 optimal weight: 0.1980 chunk 64 optimal weight: 0.3980 chunk 91 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.168054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.140995 restraints weight = 46107.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.131091 restraints weight = 75781.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.130728 restraints weight = 57715.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.127740 restraints weight = 51691.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.127521 restraints weight = 50727.712| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14875 Z= 0.159 Angle : 0.590 12.405 20280 Z= 0.292 Chirality : 0.039 0.176 2423 Planarity : 0.004 0.044 2606 Dihedral : 4.862 50.175 2079 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.63 % Rotamer: Outliers : 3.08 % Allowed : 21.80 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.81 (0.20), residues: 1932 helix: 2.06 (0.16), residues: 1081 sheet: -2.57 (0.40), residues: 152 loop : -1.20 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 126 TYR 0.016 0.001 TYR A 62 PHE 0.033 0.002 PHE D 323 TRP 0.013 0.001 TRP A 318 HIS 0.005 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00363 (14875) covalent geometry : angle 0.58984 (20280) hydrogen bonds : bond 0.03111 ( 842) hydrogen bonds : angle 4.12556 ( 2475) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 0.590 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: D 275 ASP cc_start: 0.4727 (OUTLIER) cc_final: 0.3660 (t70) REVERT: D 288 MET cc_start: 0.8930 (tpp) cc_final: 0.8642 (tpp) REVERT: D 695 HIS cc_start: 0.8620 (OUTLIER) cc_final: 0.8088 (t-90) REVERT: A 452 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7975 (mp) REVERT: B 25 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6556 (t80) REVERT: B 449 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8359 (t80) REVERT: B 452 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9097 (tt) outliers start: 45 outliers final: 34 residues processed: 169 average time/residue: 0.1355 time to fit residues: 33.3911 Evaluate side-chains 171 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 PHE Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 303 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 38 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 92 optimal weight: 50.0000 chunk 14 optimal weight: 9.9990 chunk 131 optimal weight: 0.3980 chunk 184 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 GLN A 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.167615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.146161 restraints weight = 49942.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.142637 restraints weight = 81847.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.140705 restraints weight = 79717.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.140589 restraints weight = 74717.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.139789 restraints weight = 59259.818| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14875 Z= 0.205 Angle : 0.628 12.195 20280 Z= 0.311 Chirality : 0.040 0.189 2423 Planarity : 0.004 0.072 2606 Dihedral : 4.984 51.317 2079 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.11 % Favored : 93.79 % Rotamer: Outliers : 3.50 % Allowed : 21.45 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.71 (0.20), residues: 1932 helix: 1.96 (0.16), residues: 1086 sheet: -2.63 (0.40), residues: 150 loop : -1.23 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 331 TYR 0.018 0.001 TYR A 62 PHE 0.023 0.002 PHE D 323 TRP 0.031 0.002 TRP A 533 HIS 0.005 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00465 (14875) covalent geometry : angle 0.62796 (20280) hydrogen bonds : bond 0.03268 ( 842) hydrogen bonds : angle 4.21425 ( 2475) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 133 time to evaluate : 0.597 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: C 150 LYS cc_start: -0.6788 (mttt) cc_final: -0.7152 (mmtt) REVERT: D 275 ASP cc_start: 0.4811 (OUTLIER) cc_final: 0.3986 (t70) REVERT: A 60 MET cc_start: 0.8788 (mmm) cc_final: 0.8478 (mmm) REVERT: A 452 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8018 (mp) REVERT: B 25 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.6482 (t80) REVERT: B 69 ASP cc_start: 0.7919 (t0) cc_final: 0.7675 (p0) REVERT: B 449 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8338 (t80) REVERT: B 452 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.8976 (tt) outliers start: 51 outliers final: 35 residues processed: 172 average time/residue: 0.1305 time to fit residues: 32.5460 Evaluate side-chains 172 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 303 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 71 optimal weight: 0.0980 chunk 31 optimal weight: 50.0000 chunk 104 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 141 optimal weight: 0.0370 chunk 149 optimal weight: 0.5980 chunk 173 optimal weight: 0.0570 chunk 189 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 chunk 130 optimal weight: 0.1980 overall best weight: 0.1976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.169025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.138905 restraints weight = 46687.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.137369 restraints weight = 70865.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.133470 restraints weight = 51142.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.132305 restraints weight = 57297.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.132885 restraints weight = 45781.229| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14875 Z= 0.108 Angle : 0.598 13.303 20280 Z= 0.291 Chirality : 0.039 0.209 2423 Planarity : 0.003 0.044 2606 Dihedral : 4.816 50.372 2079 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.69 % Favored : 94.20 % Rotamer: Outliers : 2.54 % Allowed : 22.14 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.82 (0.20), residues: 1932 helix: 2.03 (0.16), residues: 1083 sheet: -2.48 (0.41), residues: 147 loop : -1.16 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 144 TYR 0.012 0.001 TYR A 62 PHE 0.014 0.001 PHE C 95 TRP 0.018 0.001 TRP A 533 HIS 0.004 0.001 HIS D 503 Details of bonding type rmsd covalent geometry : bond 0.00236 (14875) covalent geometry : angle 0.59841 (20280) hydrogen bonds : bond 0.03008 ( 842) hydrogen bonds : angle 4.05855 ( 2475) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.599 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: C 150 LYS cc_start: -0.6941 (mttt) cc_final: -0.7223 (mmtt) REVERT: D 275 ASP cc_start: 0.4853 (OUTLIER) cc_final: 0.3957 (t70) REVERT: D 561 MET cc_start: 0.8177 (tpp) cc_final: 0.7851 (tpp) REVERT: D 695 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.8154 (t-90) REVERT: B 25 TYR cc_start: 0.6980 (OUTLIER) cc_final: 0.6487 (t80) REVERT: B 449 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8260 (t80) REVERT: B 452 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.8980 (tt) outliers start: 37 outliers final: 27 residues processed: 172 average time/residue: 0.1335 time to fit residues: 33.4493 Evaluate side-chains 168 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 PHE Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 303 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 79 optimal weight: 6.9990 chunk 186 optimal weight: 0.0040 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 102 optimal weight: 0.0770 chunk 160 optimal weight: 0.1980 chunk 110 optimal weight: 5.9990 chunk 158 optimal weight: 0.0270 chunk 28 optimal weight: 3.9990 overall best weight: 0.2608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.168806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.142460 restraints weight = 47613.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.131073 restraints weight = 70870.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.129453 restraints weight = 58237.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.127231 restraints weight = 58960.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.127629 restraints weight = 48409.451| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14875 Z= 0.110 Angle : 0.599 13.171 20280 Z= 0.292 Chirality : 0.039 0.195 2423 Planarity : 0.003 0.044 2606 Dihedral : 4.739 51.413 2079 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.59 % Favored : 94.31 % Rotamer: Outliers : 2.26 % Allowed : 22.96 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.87 (0.20), residues: 1932 helix: 2.05 (0.16), residues: 1083 sheet: -2.36 (0.41), residues: 147 loop : -1.11 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 126 TYR 0.013 0.001 TYR A 62 PHE 0.014 0.001 PHE B 56 TRP 0.018 0.001 TRP D 597 HIS 0.004 0.001 HIS D 503 Details of bonding type rmsd covalent geometry : bond 0.00243 (14875) covalent geometry : angle 0.59895 (20280) hydrogen bonds : bond 0.03006 ( 842) hydrogen bonds : angle 3.96851 ( 2475) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.563 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: C 150 LYS cc_start: -0.7343 (mttt) cc_final: -0.7566 (mmtt) REVERT: D 275 ASP cc_start: 0.4981 (OUTLIER) cc_final: 0.3929 (t70) REVERT: D 561 MET cc_start: 0.8269 (tpp) cc_final: 0.7908 (tpp) REVERT: D 695 HIS cc_start: 0.8582 (OUTLIER) cc_final: 0.8160 (t-90) REVERT: B 25 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6682 (t80) REVERT: B 449 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8284 (t80) REVERT: B 452 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9075 (tt) outliers start: 33 outliers final: 25 residues processed: 161 average time/residue: 0.1304 time to fit residues: 30.5284 Evaluate side-chains 166 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 PHE Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 303 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 449 PHE Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 10 optimal weight: 0.2980 chunk 180 optimal weight: 0.0870 chunk 122 optimal weight: 0.0870 chunk 126 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 167 optimal weight: 0.0980 chunk 66 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 overall best weight: 0.1736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 GLN C 284 HIS ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.169617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.132164 restraints weight = 47414.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.124430 restraints weight = 45899.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.125121 restraints weight = 44558.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.125379 restraints weight = 37523.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.125775 restraints weight = 32783.284| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14875 Z= 0.103 Angle : 0.592 13.557 20280 Z= 0.288 Chirality : 0.039 0.220 2423 Planarity : 0.004 0.091 2606 Dihedral : 4.670 52.618 2078 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.33 % Favored : 94.57 % Rotamer: Outliers : 2.06 % Allowed : 23.24 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.91 (0.20), residues: 1932 helix: 2.04 (0.16), residues: 1083 sheet: -2.21 (0.41), residues: 147 loop : -1.07 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 126 TYR 0.015 0.001 TYR A 62 PHE 0.014 0.001 PHE B 56 TRP 0.016 0.001 TRP A 533 HIS 0.004 0.001 HIS D 503 Details of bonding type rmsd covalent geometry : bond 0.00225 (14875) covalent geometry : angle 0.59207 (20280) hydrogen bonds : bond 0.02954 ( 842) hydrogen bonds : angle 3.92539 ( 2475) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3288.58 seconds wall clock time: 57 minutes 24.62 seconds (3444.62 seconds total)