Starting phenix.real_space_refine on Fri May 16 14:58:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fa4_50267/05_2025/9fa4_50267.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fa4_50267/05_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_50267/05_2025/9fa4_50267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fa4_50267/05_2025/9fa4_50267.map" model { file = "/net/cci-nas-00/data/ceres_data/9fa4_50267/05_2025/9fa4_50267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fa4_50267/05_2025/9fa4_50267.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3} 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, 'ASP:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 17} 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: {'GLN:plan1': 4, 'ARG:plan': 12, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 10, 'HIS:plan': 4} 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: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 190 Time building chain proxies: 12.41, per 1000 atoms: 0.85 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: 3.61 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.41 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: 4.62 Time building geometry restraints manager: 4.23 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: 23.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 37.490 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.830 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.001 TRP D 597 HIS 0.005 0.001 HIS B 29 PHE 0.027 0.001 PHE C 51 TYR 0.014 0.001 TYR A 62 ARG 0.006 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.17858 ( 842) hydrogen bonds : angle 6.38785 ( 2475) covalent geometry : bond 0.00371 (14875) covalent geometry : angle 0.66977 (20280) *********************** 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 : 1.790 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: 0.2877 time to fit residues: 69.9632 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 : 1.714 ------------------------------------------------------------------------------- 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 164 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 99 optimal weight: 0.0770 chunk 78 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN B 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.168914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.144553 restraints weight = 46396.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.136591 restraints weight = 66168.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.133338 restraints weight = 77727.004| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14875 Z= 0.165 Angle : 0.608 9.994 20280 Z= 0.307 Chirality : 0.039 0.164 2423 Planarity : 0.004 0.048 2606 Dihedral : 5.786 57.518 2115 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.31 % Favored : 93.53 % Rotamer: Outliers : 3.15 % Allowed : 20.22 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.20), residues: 1932 helix: 1.86 (0.16), residues: 1074 sheet: -2.77 (0.41), residues: 140 loop : -1.28 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 420 HIS 0.006 0.001 HIS B 41 PHE 0.014 0.001 PHE B 201 TYR 0.015 0.001 TYR A 62 ARG 0.010 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 842) hydrogen bonds : angle 4.72065 ( 2475) covalent geometry : bond 0.00365 (14875) covalent geometry : angle 0.60804 (20280) *********************** 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 188 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 2.725 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 126 ARG cc_start: 0.6624 (mtt180) cc_final: 0.6400 (mtt-85) REVERT: D 114 MET cc_start: 0.0540 (mpp) cc_final: 0.0287 (mpp) REVERT: D 275 ASP cc_start: 0.3576 (OUTLIER) cc_final: 0.2601 (t70) REVERT: B 449 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8361 (t80) REVERT: B 452 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9041 (tt) outliers start: 46 outliers final: 28 residues processed: 176 average time/residue: 0.2909 time to fit residues: 75.4795 Evaluate side-chains 166 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 1.751 ------------------------------------------------------------------------------- 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 249 THR Chi-restraints excluded: chain B residue 253 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 9 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 110 optimal weight: 0.0570 chunk 189 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 HIS D 168 ASN A 493 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.168593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.143166 restraints weight = 46160.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.135379 restraints weight = 68819.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.131270 restraints weight = 58938.723| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14875 Z= 0.160 Angle : 0.588 9.365 20280 Z= 0.297 Chirality : 0.039 0.180 2423 Planarity : 0.004 0.048 2606 Dihedral : 5.239 56.677 2091 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.95 % Favored : 93.89 % Rotamer: Outliers : 4.04 % Allowed : 19.40 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.20), residues: 1932 helix: 1.91 (0.16), residues: 1083 sheet: -2.91 (0.40), residues: 142 loop : -1.36 (0.25), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 597 HIS 0.005 0.001 HIS D 503 PHE 0.013 0.001 PHE A 421 TYR 0.016 0.001 TYR A 62 ARG 0.003 0.000 ARG C 110 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 842) hydrogen bonds : angle 4.41708 ( 2475) covalent geometry : bond 0.00358 (14875) covalent geometry : angle 0.58790 (20280) *********************** 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 198 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 139 time to evaluate : 1.621 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: -0.0767 (OUTLIER) cc_final: -0.1234 (tpt90) REVERT: C 255 LYS cc_start: 0.2865 (tttm) cc_final: 0.2608 (ttpt) REVERT: D 274 MET cc_start: 0.5389 (mmp) cc_final: 0.4872 (mpp) REVERT: D 275 ASP cc_start: 0.3940 (OUTLIER) cc_final: 0.2955 (t70) REVERT: D 403 LEU cc_start: 0.7928 (tp) cc_final: 0.7332 (tt) REVERT: B 449 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8416 (t80) REVERT: B 452 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9077 (tt) outliers start: 59 outliers final: 34 residues processed: 185 average time/residue: 0.2778 time to fit residues: 75.4644 Evaluate side-chains 172 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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 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 372 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 513 ILE 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 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 197 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 119 optimal weight: 4.9990 chunk 178 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 168 optimal weight: 0.7980 chunk 61 optimal weight: 0.0030 chunk 109 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 177 optimal weight: 0.0970 chunk 139 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 = 0.4468 r_free = 0.4468 target = 0.169028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.130997 restraints weight = 45783.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.122717 restraints weight = 43927.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.123524 restraints weight = 44102.338| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1448 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= 0.128 Angle : 0.574 10.894 20280 Z= 0.285 Chirality : 0.039 0.233 2423 Planarity : 0.003 0.047 2606 Dihedral : 5.051 57.742 2085 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.36 % Rotamer: Outliers : 3.63 % Allowed : 20.36 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1932 helix: 2.04 (0.16), residues: 1074 sheet: -2.70 (0.39), residues: 152 loop : -1.25 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 533 HIS 0.004 0.001 HIS B 41 PHE 0.019 0.001 PHE D 323 TYR 0.014 0.001 TYR A 62 ARG 0.007 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 842) hydrogen bonds : angle 4.25059 ( 2475) covalent geometry : bond 0.00284 (14875) covalent geometry : angle 0.57416 (20280) *********************** 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 190 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 1.750 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: -0.0081 (OUTLIER) cc_final: -0.0698 (tpt90) REVERT: D 177 ASP cc_start: 0.5658 (OUTLIER) cc_final: 0.5297 (p0) REVERT: D 274 MET cc_start: 0.6950 (mmp) cc_final: 0.6398 (mpp) REVERT: D 288 MET cc_start: 0.8836 (tpp) cc_final: 0.8452 (tpp) REVERT: D 403 LEU cc_start: 0.8146 (tp) cc_final: 0.7539 (tt) REVERT: D 503 HIS cc_start: 0.8167 (OUTLIER) cc_final: 0.7896 (m170) REVERT: D 695 HIS cc_start: 0.8633 (OUTLIER) cc_final: 0.8183 (t-90) REVERT: A 60 MET cc_start: 0.8955 (mmm) cc_final: 0.8693 (mmm) REVERT: B 449 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8463 (t80) outliers start: 53 outliers final: 33 residues processed: 177 average time/residue: 0.2826 time to fit residues: 74.2015 Evaluate side-chains 172 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 1.817 ------------------------------------------------------------------------------- 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 148 VAL Chi-restraints excluded: chain D residue 177 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 503 HIS 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 37 MET 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 220 HIS 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 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 31 optimal weight: 50.0000 chunk 20 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 149 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 566 HIS ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN ** B 333 HIS ** 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 = 0.4363 r_free = 0.4363 target = 0.160854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.136112 restraints weight = 44875.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.128176 restraints weight = 70329.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.125369 restraints weight = 72066.459| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.127 14875 Z= 0.551 Angle : 0.951 14.067 20280 Z= 0.490 Chirality : 0.049 0.292 2423 Planarity : 0.006 0.064 2606 Dihedral : 6.156 57.133 2085 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.59 % Favored : 91.30 % Rotamer: Outliers : 4.80 % Allowed : 20.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.20), residues: 1932 helix: 1.29 (0.16), residues: 1082 sheet: -3.19 (0.36), residues: 173 loop : -1.64 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP D 597 HIS 0.011 0.002 HIS A 208 PHE 0.059 0.004 PHE A 421 TYR 0.035 0.003 TYR B 153 ARG 0.007 0.001 ARG B 270 Details of bonding type rmsd hydrogen bonds : bond 0.04610 ( 842) hydrogen bonds : angle 5.22071 ( 2475) covalent geometry : bond 0.01235 (14875) covalent geometry : angle 0.95078 (20280) *********************** 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 206 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 136 time to evaluate : 1.704 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: -0.0424 (OUTLIER) cc_final: -0.1126 (tpt90) REVERT: C 308 LYS cc_start: -0.4185 (pttm) cc_final: -0.5802 (pttt) REVERT: D 257 GLU cc_start: 0.8270 (tp30) cc_final: 0.7952 (tp30) REVERT: D 275 ASP cc_start: 0.4713 (OUTLIER) cc_final: 0.3930 (t70) REVERT: D 288 MET cc_start: 0.8671 (tpp) cc_final: 0.8440 (tpp) REVERT: D 403 LEU cc_start: 0.8093 (tp) cc_final: 0.7885 (tp) REVERT: D 423 LEU cc_start: 0.8018 (mt) cc_final: 0.7801 (tt) REVERT: D 503 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.8284 (m-70) REVERT: B 335 MET cc_start: 0.8586 (ttp) cc_final: 0.8332 (ttp) REVERT: B 449 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8443 (t80) outliers start: 70 outliers final: 44 residues processed: 191 average time/residue: 0.2758 time to fit residues: 77.2501 Evaluate side-chains 177 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 129 time to evaluate : 1.701 ------------------------------------------------------------------------------- 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 136 LEU Chi-restraints excluded: chain D residue 148 VAL 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 303 HIS 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 496 LEU Chi-restraints excluded: chain D residue 503 HIS Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain B residue 3 THR 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 220 HIS 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 311 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 350 MET 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 180 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 25 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 chunk 2 optimal weight: 40.0000 chunk 61 optimal weight: 0.9980 chunk 139 optimal weight: 0.0470 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 GLN D 661 HIS A 141 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.166455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.140520 restraints weight = 47935.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.133651 restraints weight = 75549.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.129928 restraints weight = 65638.384| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14875 Z= 0.161 Angle : 0.648 11.681 20280 Z= 0.323 Chirality : 0.040 0.198 2423 Planarity : 0.004 0.081 2606 Dihedral : 5.475 50.620 2084 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.85 % Favored : 94.05 % Rotamer: Outliers : 3.77 % Allowed : 21.73 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1932 helix: 1.73 (0.16), residues: 1084 sheet: -3.05 (0.36), residues: 164 loop : -1.38 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 597 HIS 0.006 0.001 HIS B 41 PHE 0.027 0.002 PHE D 323 TYR 0.020 0.001 TYR C 254 ARG 0.004 0.000 ARG C 110 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 842) hydrogen bonds : angle 4.46251 ( 2475) covalent geometry : bond 0.00362 (14875) covalent geometry : angle 0.64751 (20280) *********************** 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 195 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 140 time to evaluate : 1.797 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 95 PHE cc_start: -0.1856 (t80) cc_final: -0.2074 (t80) REVERT: D 275 ASP cc_start: 0.5031 (OUTLIER) cc_final: 0.4161 (t70) REVERT: D 288 MET cc_start: 0.8817 (tpp) cc_final: 0.8577 (tpp) REVERT: D 503 HIS cc_start: 0.8505 (OUTLIER) cc_final: 0.8286 (m-70) REVERT: D 695 HIS cc_start: 0.8570 (OUTLIER) cc_final: 0.8149 (t-90) REVERT: A 452 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8101 (mp) REVERT: B 25 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.6633 (t80) REVERT: B 449 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8372 (t80) outliers start: 55 outliers final: 35 residues processed: 183 average time/residue: 0.2889 time to fit residues: 77.1936 Evaluate side-chains 173 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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 D residue 162 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 275 ASP 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 503 HIS Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 635 PHE Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 46 TYR 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 220 HIS 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 352 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 116 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 64 optimal weight: 0.0570 chunk 26 optimal weight: 5.9990 chunk 170 optimal weight: 0.5980 chunk 0 optimal weight: 40.0000 chunk 55 optimal weight: 7.9990 chunk 169 optimal weight: 0.2980 chunk 189 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4430 r_free = 0.4430 target = 0.170036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.142574 restraints weight = 47369.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.133647 restraints weight = 72303.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.131130 restraints weight = 55048.536| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14875 Z= 0.154 Angle : 0.637 11.899 20280 Z= 0.316 Chirality : 0.040 0.221 2423 Planarity : 0.004 0.059 2606 Dihedral : 5.292 51.434 2084 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.37 % Favored : 93.53 % Rotamer: Outliers : 4.18 % Allowed : 21.45 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.21), residues: 1932 helix: 1.84 (0.16), residues: 1087 sheet: -2.93 (0.37), residues: 161 loop : -1.26 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 597 HIS 0.005 0.001 HIS B 41 PHE 0.021 0.002 PHE C 177 TYR 0.023 0.001 TYR B 380 ARG 0.005 0.000 ARG A 426 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 842) hydrogen bonds : angle 4.28287 ( 2475) covalent geometry : bond 0.00348 (14875) covalent geometry : angle 0.63658 (20280) *********************** 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 197 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 136 time to evaluate : 1.594 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 95 PHE cc_start: -0.1881 (t80) cc_final: -0.2130 (t80) REVERT: C 150 LYS cc_start: -0.7290 (mttt) cc_final: -0.7578 (mmtt) REVERT: C 257 LYS cc_start: 0.2460 (pttm) cc_final: 0.1673 (pttm) REVERT: D 275 ASP cc_start: 0.5194 (OUTLIER) cc_final: 0.4269 (t70) REVERT: D 288 MET cc_start: 0.8923 (tpp) cc_final: 0.8692 (tpp) REVERT: D 503 HIS cc_start: 0.8462 (OUTLIER) cc_final: 0.8250 (m170) REVERT: D 695 HIS cc_start: 0.8674 (OUTLIER) cc_final: 0.8139 (t-90) REVERT: A 452 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8125 (mp) REVERT: B 25 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6655 (t80) REVERT: B 37 MET cc_start: 0.7928 (ttm) cc_final: 0.7485 (ttt) REVERT: B 449 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8331 (t80) REVERT: B 452 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9033 (tt) outliers start: 61 outliers final: 38 residues processed: 186 average time/residue: 0.2701 time to fit residues: 74.1318 Evaluate side-chains 177 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 1.618 ------------------------------------------------------------------------------- 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 136 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 303 HIS Chi-restraints excluded: chain D residue 326 VAL 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 503 HIS Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 635 PHE Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 46 TYR 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 220 HIS 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 352 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 70 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 chunk 96 optimal weight: 0.0970 chunk 80 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 176 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 253 GLN ** 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 = 0.4437 r_free = 0.4437 target = 0.170428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.144087 restraints weight = 47369.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.131779 restraints weight = 70942.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.129877 restraints weight = 53310.084| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14875 Z= 0.147 Angle : 0.630 12.589 20280 Z= 0.314 Chirality : 0.040 0.207 2423 Planarity : 0.004 0.047 2606 Dihedral : 5.227 51.250 2084 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.95 % Favored : 93.94 % Rotamer: Outliers : 3.22 % Allowed : 22.21 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1932 helix: 1.85 (0.16), residues: 1088 sheet: -2.86 (0.38), residues: 153 loop : -1.20 (0.26), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 533 HIS 0.004 0.001 HIS B 41 PHE 0.040 0.002 PHE C 181 TYR 0.018 0.001 TYR B 380 ARG 0.005 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.03267 ( 842) hydrogen bonds : angle 4.22193 ( 2475) covalent geometry : bond 0.00334 (14875) covalent geometry : angle 0.62966 (20280) *********************** 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 179 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 1.828 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 95 PHE cc_start: -0.1951 (t80) cc_final: -0.2223 (t80) REVERT: C 126 ARG cc_start: 0.6641 (mtt180) cc_final: 0.6433 (mtt180) REVERT: D 275 ASP cc_start: 0.5451 (OUTLIER) cc_final: 0.4496 (t70) REVERT: D 288 MET cc_start: 0.9129 (tpp) cc_final: 0.8888 (tpp) REVERT: D 503 HIS cc_start: 0.8526 (OUTLIER) cc_final: 0.8304 (m170) REVERT: D 561 MET cc_start: 0.8292 (tpp) cc_final: 0.8087 (tpp) REVERT: A 452 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8194 (mp) REVERT: B 25 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.6785 (t80) REVERT: B 449 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8395 (t80) REVERT: B 452 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9089 (tt) outliers start: 47 outliers final: 36 residues processed: 170 average time/residue: 0.2858 time to fit residues: 71.6363 Evaluate side-chains 172 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 1.757 ------------------------------------------------------------------------------- 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 162 GLU Chi-restraints excluded: chain D residue 177 ASP 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 503 HIS Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 635 PHE Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 46 TYR 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 220 HIS 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 352 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 106 optimal weight: 0.0020 chunk 125 optimal weight: 0.8980 chunk 153 optimal weight: 0.0040 chunk 46 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4438 r_free = 0.4438 target = 0.170594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.145278 restraints weight = 47016.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.134026 restraints weight = 67100.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.131195 restraints weight = 66095.781| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14875 Z= 0.146 Angle : 0.642 13.096 20280 Z= 0.321 Chirality : 0.040 0.203 2423 Planarity : 0.004 0.061 2606 Dihedral : 5.178 51.341 2084 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.63 % Rotamer: Outliers : 2.95 % Allowed : 22.62 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1932 helix: 1.82 (0.16), residues: 1092 sheet: -2.74 (0.39), residues: 148 loop : -1.20 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 533 HIS 0.004 0.001 HIS B 41 PHE 0.051 0.002 PHE C 181 TYR 0.018 0.001 TYR C 254 ARG 0.005 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.03253 ( 842) hydrogen bonds : angle 4.20568 ( 2475) covalent geometry : bond 0.00331 (14875) covalent geometry : angle 0.64173 (20280) *********************** 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 175 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 1.729 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 95 PHE cc_start: -0.2001 (t80) cc_final: -0.2296 (t80) REVERT: C 150 LYS cc_start: -0.6965 (mttt) cc_final: -0.7328 (mmtt) REVERT: C 257 LYS cc_start: 0.1802 (pttm) cc_final: 0.1044 (pttm) REVERT: D 275 ASP cc_start: 0.5331 (OUTLIER) cc_final: 0.4424 (t70) REVERT: D 503 HIS cc_start: 0.8430 (OUTLIER) cc_final: 0.8230 (m170) REVERT: A 452 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8197 (mp) REVERT: B 25 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.6696 (t80) REVERT: B 449 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8364 (t80) REVERT: B 452 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9004 (tt) outliers start: 43 outliers final: 34 residues processed: 169 average time/residue: 0.2970 time to fit residues: 72.8720 Evaluate side-chains 170 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 1.692 ------------------------------------------------------------------------------- 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 136 LEU 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 503 HIS Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 635 PHE Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 452 LEU 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 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 220 HIS 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 352 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 129 optimal weight: 0.9990 chunk 118 optimal weight: 0.0870 chunk 8 optimal weight: 8.9990 chunk 140 optimal weight: 0.0170 chunk 32 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 120 optimal weight: 0.0870 chunk 122 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 284 HIS A 500 ASN ** 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 = 0.4453 r_free = 0.4453 target = 0.167573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.142771 restraints weight = 46405.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.134663 restraints weight = 69846.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.131959 restraints weight = 58882.548| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14875 Z= 0.128 Angle : 0.638 13.533 20280 Z= 0.317 Chirality : 0.040 0.198 2423 Planarity : 0.004 0.044 2606 Dihedral : 5.067 50.977 2082 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.69 % Favored : 94.20 % Rotamer: Outliers : 2.81 % Allowed : 23.03 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.20), residues: 1932 helix: 1.83 (0.16), residues: 1093 sheet: -2.61 (0.40), residues: 147 loop : -1.19 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 533 HIS 0.004 0.001 HIS B 41 PHE 0.040 0.002 PHE C 181 TYR 0.016 0.001 TYR A 62 ARG 0.010 0.000 ARG C 126 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 842) hydrogen bonds : angle 4.15813 ( 2475) covalent geometry : bond 0.00290 (14875) covalent geometry : angle 0.63779 (20280) ********************** 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 174 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 1.700 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 150 LYS cc_start: -0.6861 (mttt) cc_final: -0.7223 (mmtt) REVERT: C 257 LYS cc_start: 0.1716 (pttm) cc_final: 0.0947 (pttm) REVERT: D 275 ASP cc_start: 0.5308 (OUTLIER) cc_final: 0.4512 (t70) REVERT: A 452 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7948 (mp) REVERT: B 25 TYR cc_start: 0.7005 (OUTLIER) cc_final: 0.6659 (t80) REVERT: B 449 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8310 (t80) REVERT: B 452 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.8982 (tt) outliers start: 41 outliers final: 30 residues processed: 167 average time/residue: 0.2836 time to fit residues: 69.3285 Evaluate side-chains 167 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 1.721 ------------------------------------------------------------------------------- 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 319 PHE Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 136 LEU 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 D residue 703 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 452 LEU 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 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 220 HIS 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 352 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 130 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** 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 = 0.4434 r_free = 0.4434 target = 0.166254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.145382 restraints weight = 50053.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.141987 restraints weight = 84645.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.139839 restraints weight = 68818.182| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14875 Z= 0.219 Angle : 0.682 13.092 20280 Z= 0.341 Chirality : 0.041 0.212 2423 Planarity : 0.004 0.042 2606 Dihedral : 5.217 52.887 2082 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.68 % Favored : 93.22 % Rotamer: Outliers : 2.74 % Allowed : 22.96 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1932 helix: 1.84 (0.16), residues: 1094 sheet: -2.82 (0.37), residues: 163 loop : -1.17 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 533 HIS 0.008 0.001 HIS D 503 PHE 0.038 0.002 PHE C 181 TYR 0.022 0.001 TYR B 380 ARG 0.006 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 842) hydrogen bonds : angle 4.27737 ( 2475) covalent geometry : bond 0.00497 (14875) covalent geometry : angle 0.68154 (20280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5664.93 seconds wall clock time: 100 minutes 35.24 seconds (6035.24 seconds total)