Starting phenix.real_space_refine on Fri Jun 13 02:29:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fa4_50267/06_2025/9fa4_50267.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fa4_50267/06_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_50267/06_2025/9fa4_50267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fa4_50267/06_2025/9fa4_50267.map" model { file = "/net/cci-nas-00/data/ceres_data/9fa4_50267/06_2025/9fa4_50267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fa4_50267/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.70, per 1000 atoms: 0.80 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: 3.39 Conformation dependent library (CDL) restraints added in 1.9 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: 4.28 Time building geometry restraints manager: 4.06 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: 606.190 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: 0.680 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 36.490 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 646.770 ------------------------------------------------------------------------------- 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 : 1.780 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: 0.2839 time to fit residues: 69.6652 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 : 1.860 ------------------------------------------------------------------------------- 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 = 0.144557 restraints weight = 46396.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.136610 restraints weight = 66145.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.133383 restraints weight = 77463.831| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 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 : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 126 ARG cc_start: 0.6621 (mtt180) cc_final: 0.6398 (mtt-85) REVERT: D 114 MET cc_start: 0.0540 (mpp) cc_final: 0.0288 (mpp) REVERT: D 275 ASP cc_start: 0.3574 (OUTLIER) cc_final: 0.2600 (t70) REVERT: B 449 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8360 (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: 0.2868 time to fit residues: 74.0154 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 : 1.744 ------------------------------------------------------------------------------- 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: 8.9990 chunk 48 optimal weight: 7.9990 chunk 173 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 189 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4465 r_free = 0.4465 target = 0.168781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.147517 restraints weight = 50008.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.141925 restraints weight = 71833.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.140234 restraints weight = 75799.351| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14875 Z= 0.179 Angle : 0.598 9.412 20280 Z= 0.302 Chirality : 0.039 0.163 2423 Planarity : 0.004 0.047 2606 Dihedral : 5.277 56.497 2091 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.00 % Favored : 93.84 % Rotamer: Outliers : 4.04 % Allowed : 19.47 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.20), residues: 1932 helix: 1.90 (0.16), residues: 1083 sheet: -2.76 (0.40), residues: 151 loop : -1.38 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 597 HIS 0.007 0.001 HIS D 503 PHE 0.015 0.002 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 0.03667 ( 842) hydrogen bonds : angle 4.46403 ( 2475) covalent geometry : bond 0.00402 (14875) covalent geometry : angle 0.59827 (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 : 1.637 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: -0.0807 (OUTLIER) cc_final: -0.1315 (tpt90) REVERT: C 255 LYS cc_start: 0.2950 (tttm) cc_final: 0.2648 (ttpt) REVERT: D 275 ASP cc_start: 0.3717 (OUTLIER) cc_final: 0.2874 (t70) REVERT: D 403 LEU cc_start: 0.7619 (tp) cc_final: 0.7022 (tt) REVERT: D 695 HIS cc_start: 0.8546 (OUTLIER) cc_final: 0.8019 (t-90) REVERT: B 449 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8361 (t80) REVERT: B 452 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8951 (tt) outliers start: 59 outliers final: 31 residues processed: 185 average time/residue: 0.2662 time to fit residues: 72.7851 Evaluate side-chains 171 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 1.698 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 178 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 61 optimal weight: 0.4980 chunk 109 optimal weight: 0.9990 chunk 14 optimal weight: 50.0000 chunk 177 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 158 optimal weight: 0.0970 chunk 126 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 A 141 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.168265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.140844 restraints weight = 46290.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.138501 restraints weight = 75914.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.134777 restraints weight = 58847.736| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14875 Z= 0.153 Angle : 0.587 10.865 20280 Z= 0.293 Chirality : 0.039 0.161 2423 Planarity : 0.004 0.047 2606 Dihedral : 5.116 57.728 2085 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.80 % Favored : 94.10 % Rotamer: Outliers : 3.84 % Allowed : 20.15 % 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: 0.62 (0.20), residues: 1932 helix: 1.95 (0.16), residues: 1085 sheet: -2.94 (0.40), residues: 142 loop : -1.35 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 533 HIS 0.005 0.001 HIS B 41 PHE 0.019 0.001 PHE D 323 TYR 0.016 0.001 TYR A 62 ARG 0.007 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 842) hydrogen bonds : angle 4.31615 ( 2475) covalent geometry : bond 0.00344 (14875) covalent geometry : angle 0.58655 (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 193 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 137 time to evaluate : 1.777 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: -0.0674 (OUTLIER) cc_final: -0.1251 (tpt90) REVERT: D 288 MET cc_start: 0.8369 (tpp) cc_final: 0.8036 (tpp) REVERT: D 403 LEU cc_start: 0.7905 (tp) cc_final: 0.7304 (tt) REVERT: D 695 HIS cc_start: 0.8560 (OUTLIER) cc_final: 0.8095 (t-90) REVERT: A 452 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8032 (mp) REVERT: B 397 ARG cc_start: 0.8464 (mmt-90) cc_final: 0.7931 (mmt-90) REVERT: B 449 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8384 (t80) outliers start: 56 outliers final: 38 residues processed: 179 average time/residue: 0.2828 time to fit residues: 74.2578 Evaluate side-chains 177 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 1.641 ------------------------------------------------------------------------------- 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 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 355 TYR Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain 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 37 MET 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 31 optimal weight: 50.0000 chunk 20 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 192 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 149 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4360 r_free = 0.4360 target = 0.160668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.135641 restraints weight = 44519.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.128493 restraints weight = 71793.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.126176 restraints weight = 68146.284| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.124 14875 Z= 0.556 Angle : 0.948 14.195 20280 Z= 0.488 Chirality : 0.050 0.291 2423 Planarity : 0.006 0.065 2606 Dihedral : 6.182 57.635 2085 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.64 % Favored : 91.25 % Rotamer: Outliers : 5.00 % Allowed : 20.15 % Favored : 74.85 % 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: -0.25 (0.20), residues: 1932 helix: 1.24 (0.16), residues: 1085 sheet: -3.21 (0.37), residues: 167 loop : -1.65 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP D 597 HIS 0.021 0.002 HIS D 503 PHE 0.056 0.004 PHE A 421 TYR 0.038 0.003 TYR B 380 ARG 0.006 0.001 ARG B 397 Details of bonding type rmsd hydrogen bonds : bond 0.04622 ( 842) hydrogen bonds : angle 5.25433 ( 2475) covalent geometry : bond 0.01241 (14875) covalent geometry : angle 0.94801 (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 210 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 137 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 257 GLU cc_start: 0.8259 (tp30) cc_final: 0.7949 (tp30) REVERT: D 288 MET cc_start: 0.8645 (tpp) cc_final: 0.8437 (tpp) REVERT: D 423 LEU cc_start: 0.8055 (mt) cc_final: 0.7839 (tt) REVERT: B 25 TYR cc_start: 0.7201 (OUTLIER) cc_final: 0.6749 (t80) REVERT: B 449 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8432 (t80) outliers start: 73 outliers final: 50 residues processed: 196 average time/residue: 0.2804 time to fit residues: 80.3883 Evaluate side-chains 185 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 1.673 ------------------------------------------------------------------------------- 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 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 457 ILE Chi-restraints excluded: chain D residue 496 LEU 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 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 A residue 556 CYS Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 98 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 104 optimal weight: 0.7980 chunk 2 optimal weight: 40.0000 chunk 61 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 110 optimal weight: 0.0980 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 661 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.165852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.140901 restraints weight = 48161.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.134902 restraints weight = 80124.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.132252 restraints weight = 74696.276| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14875 Z= 0.179 Angle : 0.643 11.861 20280 Z= 0.321 Chirality : 0.040 0.191 2423 Planarity : 0.004 0.087 2606 Dihedral : 5.535 51.120 2084 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.37 % Favored : 93.53 % Rotamer: Outliers : 3.91 % Allowed : 22.14 % Favored : 73.95 % 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: 0.29 (0.20), residues: 1932 helix: 1.73 (0.16), residues: 1074 sheet: -3.12 (0.36), residues: 167 loop : -1.41 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 597 HIS 0.007 0.001 HIS D 503 PHE 0.027 0.002 PHE D 323 TYR 0.027 0.001 TYR B 380 ARG 0.004 0.000 ARG C 110 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 842) hydrogen bonds : angle 4.52372 ( 2475) covalent geometry : bond 0.00396 (14875) covalent geometry : angle 0.64268 (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 196 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 PHE cc_start: -0.1811 (t80) cc_final: -0.2036 (t80) REVERT: D 275 ASP cc_start: 0.5128 (OUTLIER) cc_final: 0.4223 (t70) REVERT: D 288 MET cc_start: 0.8754 (tpp) cc_final: 0.8537 (tpp) REVERT: D 403 LEU cc_start: 0.7854 (tp) cc_final: 0.7556 (tt) REVERT: D 695 HIS cc_start: 0.8570 (OUTLIER) cc_final: 0.8109 (t-90) REVERT: A 60 MET cc_start: 0.8666 (mmm) cc_final: 0.8444 (tpp) REVERT: A 452 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8207 (mp) REVERT: B 25 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6620 (t80) REVERT: B 449 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8355 (t80) outliers start: 57 outliers final: 36 residues processed: 187 average time/residue: 0.2643 time to fit residues: 73.8776 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 ------------------------------------------------------------------------------- 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 516 VAL 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 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 549 LYS Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 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 262 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 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: 3.9990 chunk 12 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 170 optimal weight: 0.6980 chunk 0 optimal weight: 40.0000 chunk 55 optimal weight: 5.9990 chunk 169 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.168397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.142034 restraints weight = 47713.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.132628 restraints weight = 75764.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.131423 restraints weight = 55687.310| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14875 Z= 0.226 Angle : 0.663 11.825 20280 Z= 0.332 Chirality : 0.041 0.231 2423 Planarity : 0.004 0.066 2606 Dihedral : 5.493 52.302 2084 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.14 % Favored : 92.75 % Rotamer: Outliers : 3.91 % Allowed : 22.07 % Favored : 74.02 % 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: 0.31 (0.21), residues: 1932 helix: 1.68 (0.16), residues: 1089 sheet: -3.12 (0.36), residues: 169 loop : -1.35 (0.26), residues: 674 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 0.020 0.002 PHE C 181 TYR 0.027 0.001 TYR B 380 ARG 0.006 0.000 ARG A 426 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 842) hydrogen bonds : angle 4.49523 ( 2475) covalent geometry : bond 0.00515 (14875) covalent geometry : angle 0.66320 (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 190 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 133 time to evaluate : 1.754 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: -0.1904 (t80) cc_final: -0.2146 (t80) REVERT: C 150 LYS cc_start: -0.7109 (mttt) cc_final: -0.7381 (mmtt) REVERT: D 275 ASP cc_start: 0.5326 (OUTLIER) cc_final: 0.4409 (t70) REVERT: D 288 MET cc_start: 0.8986 (tpp) cc_final: 0.8776 (tpp) REVERT: D 403 LEU cc_start: 0.8096 (tp) cc_final: 0.7811 (tt) REVERT: A 452 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8148 (mp) REVERT: B 25 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.6704 (t80) REVERT: B 449 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8358 (t80) REVERT: B 452 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.8961 (tt) outliers start: 57 outliers final: 42 residues processed: 180 average time/residue: 0.3114 time to fit residues: 82.5215 Evaluate side-chains 178 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 131 time to evaluate : 1.907 ------------------------------------------------------------------------------- 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 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 556 THR Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain A residue 44 LEU 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 466 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 549 LYS 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 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 249 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 262 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 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: 0.9980 chunk 134 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 96 optimal weight: 0.3980 chunk 80 optimal weight: 6.9990 chunk 127 optimal weight: 0.6980 chunk 176 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4423 r_free = 0.4423 target = 0.169474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.142983 restraints weight = 46699.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.132624 restraints weight = 72057.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.131515 restraints weight = 55725.173| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2598 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= 0.164 Angle : 0.637 12.378 20280 Z= 0.317 Chirality : 0.040 0.255 2423 Planarity : 0.004 0.054 2606 Dihedral : 5.378 51.189 2084 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.63 % Rotamer: Outliers : 3.15 % Allowed : 22.89 % Favored : 73.95 % 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: 0.40 (0.21), residues: 1932 helix: 1.73 (0.16), residues: 1088 sheet: -2.97 (0.37), residues: 169 loop : -1.28 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 533 HIS 0.005 0.001 HIS B 41 PHE 0.037 0.002 PHE C 181 TYR 0.019 0.001 TYR B 380 ARG 0.005 0.000 ARG C 126 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 842) hydrogen bonds : angle 4.36929 ( 2475) covalent geometry : bond 0.00374 (14875) covalent geometry : angle 0.63744 (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 178 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 132 time to evaluate : 1.814 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: -0.1967 (t80) cc_final: -0.2256 (t80) REVERT: C 150 LYS cc_start: -0.7075 (mttt) cc_final: -0.7325 (mmtt) REVERT: D 114 MET cc_start: 0.0344 (mpp) cc_final: 0.0139 (mpp) REVERT: D 275 ASP cc_start: 0.5378 (OUTLIER) cc_final: 0.4479 (t70) REVERT: D 288 MET cc_start: 0.9014 (tpp) cc_final: 0.8809 (tpp) REVERT: D 403 LEU cc_start: 0.8152 (tp) cc_final: 0.7863 (tt) REVERT: A 60 MET cc_start: 0.8779 (mmm) cc_final: 0.8566 (mmm) REVERT: A 452 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8061 (mp) REVERT: B 25 TYR cc_start: 0.7025 (OUTLIER) cc_final: 0.6656 (t80) REVERT: B 397 ARG cc_start: 0.8418 (mmt-90) cc_final: 0.7781 (mmp-170) REVERT: B 449 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8337 (t80) REVERT: B 452 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9031 (tt) outliers start: 46 outliers final: 36 residues processed: 171 average time/residue: 0.3066 time to fit residues: 77.0070 Evaluate side-chains 171 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 1.821 ------------------------------------------------------------------------------- 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 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 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 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 12 SER Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 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 262 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 306 ILE 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: 1.9990 chunk 125 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 chunk 46 optimal weight: 8.9990 chunk 85 optimal weight: 0.5980 chunk 177 optimal weight: 0.0980 chunk 136 optimal weight: 0.7980 chunk 36 optimal weight: 40.0000 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.166350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.142276 restraints weight = 46427.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.133793 restraints weight = 69195.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.131469 restraints weight = 78055.413| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14875 Z= 0.151 Angle : 0.630 13.014 20280 Z= 0.313 Chirality : 0.040 0.251 2423 Planarity : 0.004 0.045 2606 Dihedral : 5.259 51.118 2084 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.63 % Favored : 93.27 % Rotamer: Outliers : 3.02 % Allowed : 23.37 % Favored : 73.61 % 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: 0.50 (0.21), residues: 1932 helix: 1.79 (0.16), residues: 1092 sheet: -2.93 (0.38), residues: 160 loop : -1.24 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 533 HIS 0.005 0.001 HIS D 503 PHE 0.040 0.002 PHE C 181 TYR 0.016 0.001 TYR A 62 ARG 0.005 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 842) hydrogen bonds : angle 4.25675 ( 2475) covalent geometry : bond 0.00344 (14875) covalent geometry : angle 0.62999 (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 179 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 PHE cc_start: -0.1877 (t80) cc_final: -0.2189 (t80) REVERT: C 150 LYS cc_start: -0.6727 (mttt) cc_final: -0.6955 (mmtt) REVERT: D 114 MET cc_start: 0.0505 (mpp) cc_final: 0.0259 (mpp) REVERT: D 275 ASP cc_start: 0.5188 (OUTLIER) cc_final: 0.4411 (t70) REVERT: D 403 LEU cc_start: 0.7921 (tp) cc_final: 0.7620 (tt) REVERT: D 561 MET cc_start: 0.8215 (tpp) cc_final: 0.7952 (tpp) REVERT: A 60 MET cc_start: 0.8690 (mmm) cc_final: 0.8402 (mmm) REVERT: B 25 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.6622 (t80) REVERT: B 397 ARG cc_start: 0.8378 (mmt-90) cc_final: 0.7708 (mmp-170) REVERT: B 449 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8351 (t80) REVERT: B 452 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8947 (tt) outliers start: 44 outliers final: 34 residues processed: 172 average time/residue: 0.2780 time to fit residues: 70.2552 Evaluate side-chains 171 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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 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 343 VAL 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 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 253 GLN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 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 249 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 306 ILE 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: 1.9990 chunk 118 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 32 optimal weight: 40.0000 chunk 110 optimal weight: 0.0040 chunk 23 optimal weight: 20.0000 chunk 120 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.169855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.143008 restraints weight = 46725.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.131457 restraints weight = 72584.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.132332 restraints weight = 53751.915| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14875 Z= 0.153 Angle : 0.641 13.264 20280 Z= 0.317 Chirality : 0.040 0.221 2423 Planarity : 0.004 0.107 2606 Dihedral : 5.252 51.267 2084 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.26 % Favored : 93.63 % Rotamer: Outliers : 2.81 % Allowed : 23.92 % Favored : 73.27 % 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: 1.79 (0.16), residues: 1095 sheet: -2.87 (0.37), residues: 166 loop : -1.20 (0.26), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 533 HIS 0.011 0.001 HIS A 254 PHE 0.061 0.002 PHE C 181 TYR 0.021 0.001 TYR B 380 ARG 0.008 0.000 ARG C 126 Details of bonding type rmsd hydrogen bonds : bond 0.03244 ( 842) hydrogen bonds : angle 4.25320 ( 2475) covalent geometry : bond 0.00353 (14875) covalent geometry : angle 0.64148 (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 176 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 1.525 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 95 PHE cc_start: -0.1939 (t80) cc_final: -0.2250 (t80) REVERT: D 275 ASP cc_start: 0.5488 (OUTLIER) cc_final: 0.4541 (t70) REVERT: D 403 LEU cc_start: 0.8264 (tp) cc_final: 0.7981 (tt) REVERT: D 561 MET cc_start: 0.8163 (tpp) cc_final: 0.7926 (tpp) REVERT: A 60 MET cc_start: 0.8889 (mmm) cc_final: 0.8678 (mmm) REVERT: A 452 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7980 (mp) REVERT: B 25 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.6672 (t80) REVERT: B 397 ARG cc_start: 0.8443 (mmt-90) cc_final: 0.7716 (mmp-170) REVERT: B 449 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8348 (t80) REVERT: B 452 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.8972 (tt) outliers start: 41 outliers final: 33 residues processed: 171 average time/residue: 0.2847 time to fit residues: 70.9402 Evaluate side-chains 171 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 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 556 THR Chi-restraints excluded: chain D residue 695 HIS Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain A residue 44 LEU 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 3 THR Chi-restraints excluded: chain B residue 25 TYR 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 249 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 306 ILE 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: 0.8980 chunk 144 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 99 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 76 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 284 HIS A 171 HIS ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.165470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.140317 restraints weight = 46307.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.133199 restraints weight = 70671.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.130267 restraints weight = 63702.667| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14875 Z= 0.195 Angle : 0.669 12.872 20280 Z= 0.334 Chirality : 0.041 0.248 2423 Planarity : 0.004 0.043 2606 Dihedral : 5.282 52.095 2082 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.88 % Favored : 93.06 % Rotamer: Outliers : 2.74 % Allowed : 24.26 % Favored : 73.00 % 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: 0.50 (0.21), residues: 1932 helix: 1.78 (0.16), residues: 1092 sheet: -2.90 (0.37), residues: 167 loop : -1.22 (0.26), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 597 HIS 0.005 0.001 HIS B 41 PHE 0.044 0.002 PHE C 177 TYR 0.019 0.001 TYR A 62 ARG 0.013 0.000 ARG C 126 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 842) hydrogen bonds : angle 4.33267 ( 2475) covalent geometry : bond 0.00446 (14875) covalent geometry : angle 0.66935 (20280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6920.42 seconds wall clock time: 122 minutes 45.81 seconds (7365.81 seconds total)