Starting phenix.real_space_refine on Mon Jul 28 01:55:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ejk_48103/07_2025/9ejk_48103_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ejk_48103/07_2025/9ejk_48103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ejk_48103/07_2025/9ejk_48103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ejk_48103/07_2025/9ejk_48103.map" model { file = "/net/cci-nas-00/data/ceres_data/9ejk_48103/07_2025/9ejk_48103_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ejk_48103/07_2025/9ejk_48103_neut.cif" } resolution = 3.08 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= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 39 5.16 5 C 6322 2.51 5 N 1710 2.21 5 O 1782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9854 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 865, 6596 Classifications: {'peptide': 865} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 5, 'PTRANS': 51, 'TRANS': 808} Chain breaks: 3 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8, 'GLU:plan': 19, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 188 Chain: "B" Number of atoms: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2483 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 16, 'TRANS': 303} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'TPO:plan-1': 1, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 775 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain breaks: 3 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 7.78, per 1000 atoms: 0.79 Number of scatterers: 9854 At special positions: 0 Unit cell: (87.2135, 106.1, 114.433, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 1 15.00 O 1782 8.00 N 1710 7.00 C 6322 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: 2.61 Conformation dependent library (CDL) restraints added in 1.3 seconds 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2402 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 22 sheets defined 17.1% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 removed outlier: 3.763A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.726A pdb=" N THR A 130 " --> pdb=" O PRO A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.812A pdb=" N ARG A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 397 through 410 Processing helix chain 'A' and resid 502 through 505 removed outlier: 3.560A pdb=" N LEU A 505 " --> pdb=" O ASP A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 502 through 505' Processing helix chain 'A' and resid 633 through 637 removed outlier: 3.731A pdb=" N LEU A 636 " --> pdb=" O GLN A 633 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 637 " --> pdb=" O LEU A 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 633 through 637' Processing helix chain 'A' and resid 751 through 755 removed outlier: 3.656A pdb=" N ARG A 755 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 798 removed outlier: 3.669A pdb=" N HIS A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 840 Processing helix chain 'A' and resid 895 through 900 Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 339 through 348 removed outlier: 3.888A pdb=" N HIS B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 372 Processing helix chain 'B' and resid 416 through 420 Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.637A pdb=" N LEU B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 449 removed outlier: 3.944A pdb=" N TRP B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 477 removed outlier: 3.777A pdb=" N LEU B 470 " --> pdb=" O THR B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 497 Processing helix chain 'B' and resid 511 through 518 Processing helix chain 'B' and resid 526 through 532 Processing helix chain 'B' and resid 545 through 552 removed outlier: 5.571A pdb=" N ASP B 550 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 558 Processing helix chain 'C' and resid 201 through 207 Processing helix chain 'C' and resid 227 through 238 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 27 removed outlier: 3.745A pdb=" N LEU A 923 " --> pdb=" O GLN A 22 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN A 24 " --> pdb=" O PHE A 921 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHE A 921 " --> pdb=" O ASN A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 41 removed outlier: 6.543A pdb=" N GLY A 50 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU A 38 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA A 48 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR A 40 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 46 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 55 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 81 removed outlier: 3.524A pdb=" N GLN A 78 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A 97 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER A 116 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 99 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 137 removed outlier: 4.072A pdb=" N VAL A 134 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N VAL A 153 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N ASP A 166 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL A 155 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 191 through 196 removed outlier: 4.063A pdb=" N TYR A 225 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ASP A 217 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL A 223 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 233 through 238 removed outlier: 7.058A pdb=" N CYS A 248 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE A 236 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 246 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TRP A 238 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU A 244 " --> pdb=" O TRP A 238 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 270 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 285 through 289 removed outlier: 4.164A pdb=" N ARG A 285 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N HIS A 313 " --> pdb=" O PHE A 328 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 334 through 338 removed outlier: 3.516A pdb=" N GLY A 334 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 352 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 387 through 394 removed outlier: 3.584A pdb=" N CYS A 389 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 446 " --> pdb=" O HIS A 442 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A 447 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS A 462 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE A 449 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 458 " --> pdb=" O ASP A 451 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 426 through 427 Processing sheet with id=AB2, first strand: chain 'A' and resid 499 through 500 Processing sheet with id=AB3, first strand: chain 'A' and resid 507 through 513 removed outlier: 3.801A pdb=" N TYR A 518 " --> pdb=" O CYS A 513 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLN A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 528 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU A 582 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL A 530 " --> pdb=" O PHE A 580 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU A 543 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLN A 584 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 545 " --> pdb=" O GLN A 584 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N GLN A 586 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA A 547 " --> pdb=" O GLN A 586 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 538 through 540 Processing sheet with id=AB5, first strand: chain 'A' and resid 593 through 597 removed outlier: 6.866A pdb=" N PHE A 611 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL A 624 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU A 613 " --> pdb=" O VAL A 622 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 697 through 699 removed outlier: 6.526A pdb=" N TYR C 172 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 10.543A pdb=" N GLU C 217 " --> pdb=" O PRO C 190 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE C 192 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU C 214 " --> pdb=" O ARG C 247 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR C 245 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL C 218 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE C 243 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 697 through 699 removed outlier: 6.526A pdb=" N TYR C 172 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 10.543A pdb=" N GLU C 217 " --> pdb=" O PRO C 190 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE C 192 " --> pdb=" O VAL C 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 713 through 721 removed outlier: 6.425A pdb=" N GLY A 736 " --> pdb=" O ARG A 714 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU A 716 " --> pdb=" O TRP A 734 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TRP A 734 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N PHE A 718 " --> pdb=" O SER A 732 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER A 732 " --> pdb=" O PHE A 718 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ASP A 720 " --> pdb=" O CYS A 730 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N CYS A 730 " --> pdb=" O ASP A 720 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR A 741 " --> pdb=" O THR A 737 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N SER A 746 " --> pdb=" O GLN A 764 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLN A 764 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ARG A 748 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA A 762 " --> pdb=" O ARG A 748 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE C 296 " --> pdb=" O GLN A 769 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 776 through 781 removed outlier: 4.268A pdb=" N GLN A 818 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N THR A 823 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA A 829 " --> pdb=" O THR A 823 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 843 through 852 removed outlier: 6.817A pdb=" N LEU A 867 " --> pdb=" O ARG A 844 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL A 846 " --> pdb=" O ALA A 865 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 865 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N VAL A 848 " --> pdb=" O HIS A 863 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N HIS A 863 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N HIS A 850 " --> pdb=" O GLU A 861 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU A 861 " --> pdb=" O HIS A 850 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 873 " --> pdb=" O ARG A 886 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG A 886 " --> pdb=" O ILE A 873 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 875 " --> pdb=" O GLN A 884 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 912 through 914 removed outlier: 3.860A pdb=" N SER A 914 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 254 through 262 removed outlier: 6.611A pdb=" N LEU B 270 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL B 259 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL B 268 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N GLY B 261 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA B 266 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 384 through 386 removed outlier: 3.668A pdb=" N LEU B 385 " --> pdb=" O LYS B 393 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 900 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: 4.08 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3235 1.34 - 1.46: 2097 1.46 - 1.58: 4706 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 10096 Sorted by residual: bond pdb=" CA LYS C 167 " pdb=" C LYS C 167 " ideal model delta sigma weight residual 1.525 1.542 -0.017 2.10e-02 2.27e+03 6.32e-01 bond pdb=" CB ASP A 783 " pdb=" CG ASP A 783 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 6.05e-01 bond pdb=" CG1 ILE A 56 " pdb=" CD1 ILE A 56 " ideal model delta sigma weight residual 1.513 1.484 0.029 3.90e-02 6.57e+02 5.51e-01 bond pdb=" CG PRO A 587 " pdb=" CD PRO A 587 " ideal model delta sigma weight residual 1.512 1.492 0.020 2.70e-02 1.37e+03 5.27e-01 bond pdb=" CG ARG A 886 " pdb=" CD ARG A 886 " ideal model delta sigma weight residual 1.520 1.540 -0.020 3.00e-02 1.11e+03 4.51e-01 ... (remaining 10091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 13183 1.07 - 2.13: 421 2.13 - 3.20: 122 3.20 - 4.26: 18 4.26 - 5.33: 4 Bond angle restraints: 13748 Sorted by residual: angle pdb=" C LEU B 273 " pdb=" N LYS B 274 " pdb=" CA LYS B 274 " ideal model delta sigma weight residual 120.44 123.43 -2.99 1.30e+00 5.92e-01 5.29e+00 angle pdb=" C GLN B 347 " pdb=" N ARG B 348 " pdb=" CA ARG B 348 " ideal model delta sigma weight residual 121.54 125.90 -4.36 1.91e+00 2.74e-01 5.21e+00 angle pdb=" C SER A 271 " pdb=" N LEU A 272 " pdb=" CA LEU A 272 " ideal model delta sigma weight residual 121.85 118.48 3.37 1.77e+00 3.19e-01 3.63e+00 angle pdb=" CA TYR A 254 " pdb=" CB TYR A 254 " pdb=" CG TYR A 254 " ideal model delta sigma weight residual 113.90 117.14 -3.24 1.80e+00 3.09e-01 3.24e+00 angle pdb=" N THR B 276 " pdb=" CA THR B 276 " pdb=" C THR B 276 " ideal model delta sigma weight residual 114.12 111.62 2.50 1.39e+00 5.18e-01 3.23e+00 ... (remaining 13743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5295 17.91 - 35.81: 518 35.81 - 53.72: 131 53.72 - 71.62: 28 71.62 - 89.53: 11 Dihedral angle restraints: 5983 sinusoidal: 2266 harmonic: 3717 Sorted by residual: dihedral pdb=" CA CYS A 384 " pdb=" C CYS A 384 " pdb=" N SER A 385 " pdb=" CA SER A 385 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA VAL B 335 " pdb=" C VAL B 335 " pdb=" N ASN B 336 " pdb=" CA ASN B 336 " ideal model delta harmonic sigma weight residual -180.00 -164.06 -15.94 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CB GLU A 919 " pdb=" CG GLU A 919 " pdb=" CD GLU A 919 " pdb=" OE1 GLU A 919 " ideal model delta sinusoidal sigma weight residual 0.00 87.06 -87.06 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 5980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 979 0.032 - 0.064: 371 0.064 - 0.095: 99 0.095 - 0.127: 102 0.127 - 0.159: 11 Chirality restraints: 1562 Sorted by residual: chirality pdb=" CA VAL A 273 " pdb=" N VAL A 273 " pdb=" C VAL A 273 " pdb=" CB VAL A 273 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA ILE A 79 " pdb=" N ILE A 79 " pdb=" C ILE A 79 " pdb=" CB ILE A 79 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA VAL A 624 " pdb=" N VAL A 624 " pdb=" C VAL A 624 " pdb=" CB VAL A 624 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 1559 not shown) Planarity restraints: 1774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 854 " 0.167 9.50e-02 1.11e+02 7.54e-02 4.59e+00 pdb=" NE ARG A 854 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 854 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A 854 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 854 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 758 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 759 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 759 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 759 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 396 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.11e+00 pdb=" N PRO A 397 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 397 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 397 " 0.020 5.00e-02 4.00e+02 ... (remaining 1771 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 636 2.74 - 3.28: 8826 3.28 - 3.82: 15162 3.82 - 4.36: 18324 4.36 - 4.90: 32973 Nonbonded interactions: 75921 Sorted by model distance: nonbonded pdb=" OH TYR B 376 " pdb=" O THR B 395 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR A 275 " pdb=" OG SER A 316 " model vdw 2.283 3.040 nonbonded pdb=" O ALA C 203 " pdb=" OG1 THR C 206 " model vdw 2.320 3.040 nonbonded pdb=" NE2 GLN A 508 " pdb=" OG1 THR A 524 " model vdw 2.337 3.120 nonbonded pdb=" NE2 GLN A 22 " pdb=" OD1 ASN A 24 " model vdw 2.351 3.120 ... (remaining 75916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.120 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.390 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 0.002 0.029 10096 Z= 0.095 Angle : 0.492 5.326 13748 Z= 0.262 Chirality : 0.044 0.159 1562 Planarity : 0.005 0.075 1774 Dihedral : 15.770 89.528 3581 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.49 % Allowed : 17.56 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % 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: -1.07 (0.24), residues: 1268 helix: 0.11 (0.38), residues: 171 sheet: 0.05 (0.26), residues: 415 loop : -1.44 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 420 HIS 0.005 0.001 HIS A 561 PHE 0.017 0.001 PHE A 712 TYR 0.011 0.001 TYR A 254 ARG 0.019 0.001 ARG A 854 Details of bonding type rmsd hydrogen bonds : bond 0.14955 ( 319) hydrogen bonds : angle 7.22745 ( 900) covalent geometry : bond 0.00211 (10096) covalent geometry : angle 0.49214 (13748) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 192 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7464 (mp10) cc_final: 0.7260 (mt0) REVERT: A 85 GLN cc_start: 0.8073 (mt0) cc_final: 0.7857 (mt0) REVERT: A 222 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7946 (ttp-110) REVERT: A 492 LYS cc_start: 0.8607 (mptt) cc_final: 0.8220 (ttmm) REVERT: A 574 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8271 (mm-30) REVERT: A 637 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7770 (mm-30) REVERT: A 652 GLN cc_start: 0.6909 (mt0) cc_final: 0.6178 (tt0) REVERT: A 698 ARG cc_start: 0.7533 (mmt-90) cc_final: 0.7132 (mmp80) REVERT: B 282 MET cc_start: 0.8230 (ttp) cc_final: 0.7687 (ttm) REVERT: B 378 ASP cc_start: 0.8502 (t0) cc_final: 0.8289 (t70) REVERT: B 388 SER cc_start: 0.8498 (t) cc_final: 0.8181 (m) REVERT: B 540 LYS cc_start: 0.8322 (tttp) cc_final: 0.7968 (tmtt) REVERT: B 553 ASP cc_start: 0.7841 (t70) cc_final: 0.7273 (t0) REVERT: B 555 GLN cc_start: 0.7124 (pt0) cc_final: 0.6485 (pt0) outliers start: 5 outliers final: 0 residues processed: 197 average time/residue: 0.2422 time to fit residues: 64.6626 Evaluate side-chains 125 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 0.2980 chunk 53 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.0020 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.0040 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 overall best weight: 0.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 195 GLN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 GLN B 464 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.161386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.121877 restraints weight = 10847.109| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.08 r_work: 0.3236 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10096 Z= 0.087 Angle : 0.482 4.905 13748 Z= 0.252 Chirality : 0.044 0.161 1562 Planarity : 0.004 0.032 1774 Dihedral : 3.536 18.256 1379 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.76 % Allowed : 19.12 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1268 helix: 1.25 (0.40), residues: 170 sheet: 0.43 (0.27), residues: 396 loop : -1.02 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 401 HIS 0.006 0.001 HIS A 561 PHE 0.023 0.001 PHE A 227 TYR 0.011 0.001 TYR A 254 ARG 0.005 0.000 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 319) hydrogen bonds : angle 5.23504 ( 900) covalent geometry : bond 0.00186 (10096) covalent geometry : angle 0.48179 (13748) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.010 Fit side-chains REVERT: A 85 GLN cc_start: 0.8118 (mt0) cc_final: 0.7891 (mt0) REVERT: A 202 ASN cc_start: 0.8563 (t0) cc_final: 0.8334 (t0) REVERT: A 222 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7979 (ttp-110) REVERT: A 292 ARG cc_start: 0.7800 (ptp-110) cc_final: 0.7312 (ptp90) REVERT: A 492 LYS cc_start: 0.8659 (mptt) cc_final: 0.8291 (ttmm) REVERT: A 574 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8277 (mm-30) REVERT: A 637 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7703 (mm-30) REVERT: A 652 GLN cc_start: 0.6864 (mt0) cc_final: 0.6223 (tt0) REVERT: A 698 ARG cc_start: 0.7348 (mmt-90) cc_final: 0.7034 (mmp80) REVERT: B 282 MET cc_start: 0.8075 (ttp) cc_final: 0.7594 (ttm) REVERT: B 283 LYS cc_start: 0.7907 (tttt) cc_final: 0.7587 (mtpp) REVERT: B 304 HIS cc_start: 0.7815 (m170) cc_final: 0.7553 (m90) REVERT: B 378 ASP cc_start: 0.8675 (t0) cc_final: 0.8414 (t70) REVERT: B 540 LYS cc_start: 0.8340 (tttp) cc_final: 0.8036 (tmtt) outliers start: 18 outliers final: 12 residues processed: 142 average time/residue: 0.2105 time to fit residues: 42.8776 Evaluate side-chains 127 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 561 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 70 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.156558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116555 restraints weight = 11044.986| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.21 r_work: 0.3148 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10096 Z= 0.127 Angle : 0.510 6.820 13748 Z= 0.262 Chirality : 0.045 0.148 1562 Planarity : 0.004 0.035 1774 Dihedral : 3.677 18.659 1379 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.02 % Allowed : 19.22 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % 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 (0.24), residues: 1268 helix: 1.40 (0.41), residues: 170 sheet: 0.35 (0.27), residues: 401 loop : -0.96 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 527 HIS 0.005 0.001 HIS A 616 PHE 0.024 0.002 PHE A 227 TYR 0.012 0.002 TYR B 376 ARG 0.003 0.000 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 319) hydrogen bonds : angle 5.02868 ( 900) covalent geometry : bond 0.00311 (10096) covalent geometry : angle 0.51031 (13748) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 222 ARG cc_start: 0.8093 (mtm-85) cc_final: 0.7853 (ttp-110) REVERT: A 292 ARG cc_start: 0.7858 (ptp-110) cc_final: 0.7349 (ptp90) REVERT: A 359 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6898 (mm-30) REVERT: A 492 LYS cc_start: 0.8568 (mptt) cc_final: 0.8262 (ttmm) REVERT: A 637 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7644 (mm-30) REVERT: A 652 GLN cc_start: 0.6795 (mt0) cc_final: 0.6241 (tt0) REVERT: A 698 ARG cc_start: 0.7293 (mmt-90) cc_final: 0.6975 (mmp80) REVERT: B 282 MET cc_start: 0.8062 (ttp) cc_final: 0.7529 (ttm) REVERT: B 304 HIS cc_start: 0.7697 (m170) cc_final: 0.7405 (m90) REVERT: B 378 ASP cc_start: 0.8555 (t0) cc_final: 0.8307 (t70) REVERT: B 540 LYS cc_start: 0.8398 (tttp) cc_final: 0.8105 (tmtt) outliers start: 31 outliers final: 25 residues processed: 138 average time/residue: 0.2478 time to fit residues: 48.6018 Evaluate side-chains 136 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 67 optimal weight: 0.0470 chunk 117 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.157359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.117897 restraints weight = 10942.102| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.16 r_work: 0.3175 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10096 Z= 0.103 Angle : 0.482 6.611 13748 Z= 0.249 Chirality : 0.044 0.144 1562 Planarity : 0.004 0.034 1774 Dihedral : 3.618 18.856 1379 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.12 % Allowed : 20.20 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % 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: -0.28 (0.24), residues: 1268 helix: 1.44 (0.41), residues: 170 sheet: 0.33 (0.26), residues: 403 loop : -0.91 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 527 HIS 0.004 0.001 HIS A 561 PHE 0.016 0.001 PHE A 300 TYR 0.012 0.001 TYR A 254 ARG 0.003 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 319) hydrogen bonds : angle 4.87596 ( 900) covalent geometry : bond 0.00246 (10096) covalent geometry : angle 0.48245 (13748) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.974 Fit side-chains REVERT: A 85 GLN cc_start: 0.8206 (mt0) cc_final: 0.7968 (mt0) REVERT: A 202 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8343 (t0) REVERT: A 292 ARG cc_start: 0.7935 (ptp-110) cc_final: 0.7478 (ptp90) REVERT: A 359 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7035 (mm-30) REVERT: A 492 LYS cc_start: 0.8668 (mptt) cc_final: 0.8306 (ttmm) REVERT: A 637 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7686 (mm-30) REVERT: A 652 GLN cc_start: 0.6836 (mt0) cc_final: 0.6204 (tt0) REVERT: A 698 ARG cc_start: 0.7380 (mmt-90) cc_final: 0.7077 (mmp80) REVERT: B 282 MET cc_start: 0.8166 (ttp) cc_final: 0.7618 (ttm) REVERT: B 304 HIS cc_start: 0.7790 (m170) cc_final: 0.7475 (m90) REVERT: B 344 MET cc_start: 0.7292 (mmp) cc_final: 0.6918 (mmp) REVERT: B 378 ASP cc_start: 0.8703 (t0) cc_final: 0.8459 (t70) REVERT: B 540 LYS cc_start: 0.8421 (tttp) cc_final: 0.8109 (tmtt) outliers start: 32 outliers final: 25 residues processed: 137 average time/residue: 0.2128 time to fit residues: 42.1935 Evaluate side-chains 137 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 GLN B 464 GLN B 542 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.155190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.116264 restraints weight = 10960.528| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.16 r_work: 0.3136 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10096 Z= 0.149 Angle : 0.523 7.815 13748 Z= 0.267 Chirality : 0.045 0.146 1562 Planarity : 0.004 0.037 1774 Dihedral : 3.787 19.045 1379 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.29 % Allowed : 19.71 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % 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: -0.43 (0.24), residues: 1268 helix: 1.09 (0.40), residues: 176 sheet: 0.23 (0.26), residues: 397 loop : -0.95 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 216 HIS 0.005 0.001 HIS A 616 PHE 0.035 0.002 PHE A 227 TYR 0.014 0.002 TYR B 376 ARG 0.004 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 319) hydrogen bonds : angle 4.94752 ( 900) covalent geometry : bond 0.00367 (10096) covalent geometry : angle 0.52318 (13748) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 112 time to evaluate : 1.098 Fit side-chains REVERT: A 85 GLN cc_start: 0.8281 (mt0) cc_final: 0.8067 (mt0) REVERT: A 202 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8312 (t0) REVERT: A 292 ARG cc_start: 0.7984 (ptp-110) cc_final: 0.7504 (ptp90) REVERT: A 359 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7036 (mm-30) REVERT: A 410 ARG cc_start: 0.8463 (mtp-110) cc_final: 0.8216 (ttm170) REVERT: A 652 GLN cc_start: 0.6849 (mt0) cc_final: 0.6206 (tt0) REVERT: A 698 ARG cc_start: 0.7423 (mmt-90) cc_final: 0.7098 (mmp80) REVERT: B 282 MET cc_start: 0.8205 (ttp) cc_final: 0.7677 (ttm) REVERT: B 304 HIS cc_start: 0.7803 (m170) cc_final: 0.7468 (m90) REVERT: B 378 ASP cc_start: 0.8759 (t0) cc_final: 0.8522 (t70) REVERT: B 540 LYS cc_start: 0.8435 (tttp) cc_final: 0.8096 (tmtt) outliers start: 44 outliers final: 36 residues processed: 143 average time/residue: 0.3341 time to fit residues: 69.0047 Evaluate side-chains 144 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 14 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 115 optimal weight: 0.0470 chunk 94 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 GLN B 542 ASN B 555 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.153757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.114275 restraints weight = 11096.820| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.35 r_work: 0.3101 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10096 Z= 0.188 Angle : 0.566 7.897 13748 Z= 0.289 Chirality : 0.047 0.155 1562 Planarity : 0.004 0.043 1774 Dihedral : 4.008 22.143 1379 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.07 % Allowed : 18.93 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % 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 (0.24), residues: 1268 helix: 0.87 (0.39), residues: 174 sheet: 0.07 (0.26), residues: 398 loop : -1.03 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 216 HIS 0.006 0.001 HIS A 616 PHE 0.023 0.002 PHE A 300 TYR 0.016 0.002 TYR B 376 ARG 0.003 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.04274 ( 319) hydrogen bonds : angle 5.11385 ( 900) covalent geometry : bond 0.00469 (10096) covalent geometry : angle 0.56566 (13748) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 116 time to evaluate : 1.033 Fit side-chains REVERT: A 202 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8367 (t0) REVERT: A 292 ARG cc_start: 0.7940 (ptp-110) cc_final: 0.7459 (ptp90) REVERT: A 359 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6910 (mm-30) REVERT: A 410 ARG cc_start: 0.8439 (mtp-110) cc_final: 0.8227 (ttm170) REVERT: A 652 GLN cc_start: 0.6864 (mt0) cc_final: 0.6268 (tt0) REVERT: A 698 ARG cc_start: 0.7371 (mmt-90) cc_final: 0.7023 (mmp80) REVERT: B 282 MET cc_start: 0.8160 (ttp) cc_final: 0.7633 (ttm) REVERT: B 304 HIS cc_start: 0.7735 (m170) cc_final: 0.7392 (m90) REVERT: B 378 ASP cc_start: 0.8623 (t0) cc_final: 0.8359 (t70) REVERT: B 540 LYS cc_start: 0.8402 (tttp) cc_final: 0.8070 (tmtt) outliers start: 52 outliers final: 46 residues processed: 152 average time/residue: 0.2195 time to fit residues: 47.4607 Evaluate side-chains 157 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 109 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 246 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 110 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.154773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.115157 restraints weight = 11211.262| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.28 r_work: 0.3118 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10096 Z= 0.138 Angle : 0.522 7.045 13748 Z= 0.268 Chirality : 0.045 0.144 1562 Planarity : 0.004 0.041 1774 Dihedral : 3.938 23.822 1379 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.59 % Allowed : 19.80 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % 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: -0.52 (0.24), residues: 1268 helix: 0.99 (0.40), residues: 174 sheet: 0.07 (0.26), residues: 394 loop : -0.93 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 216 HIS 0.005 0.001 HIS A 616 PHE 0.034 0.002 PHE A 227 TYR 0.011 0.001 TYR A 911 ARG 0.004 0.000 ARG B 372 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 319) hydrogen bonds : angle 4.99917 ( 900) covalent geometry : bond 0.00338 (10096) covalent geometry : angle 0.52216 (13748) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 114 time to evaluate : 1.010 Fit side-chains REVERT: A 12 MET cc_start: 0.5335 (mpp) cc_final: 0.4235 (mpp) REVERT: A 202 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8347 (t0) REVERT: A 359 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6911 (mm-30) REVERT: A 410 ARG cc_start: 0.8399 (mtp-110) cc_final: 0.8187 (ttm170) REVERT: A 652 GLN cc_start: 0.6893 (mt0) cc_final: 0.6319 (tt0) REVERT: A 698 ARG cc_start: 0.7362 (mmt-90) cc_final: 0.7018 (mmp80) REVERT: B 282 MET cc_start: 0.8149 (ttp) cc_final: 0.7604 (ttm) REVERT: B 304 HIS cc_start: 0.7723 (m170) cc_final: 0.7413 (m90) REVERT: B 341 MET cc_start: 0.7804 (ttt) cc_final: 0.7577 (mtt) REVERT: B 378 ASP cc_start: 0.8627 (t0) cc_final: 0.8363 (t70) REVERT: B 540 LYS cc_start: 0.8386 (tttp) cc_final: 0.8074 (tmtt) outliers start: 47 outliers final: 39 residues processed: 146 average time/residue: 0.2209 time to fit residues: 45.7241 Evaluate side-chains 151 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 246 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 120 optimal weight: 0.0040 chunk 107 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.156383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116677 restraints weight = 11052.785| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.30 r_work: 0.3144 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10096 Z= 0.099 Angle : 0.486 6.607 13748 Z= 0.250 Chirality : 0.044 0.140 1562 Planarity : 0.004 0.037 1774 Dihedral : 3.767 25.217 1379 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.29 % Allowed : 20.00 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % 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: -0.42 (0.24), residues: 1268 helix: 1.21 (0.40), residues: 174 sheet: 0.13 (0.26), residues: 398 loop : -0.90 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 401 HIS 0.004 0.001 HIS A 561 PHE 0.014 0.001 PHE A 227 TYR 0.011 0.001 TYR A 254 ARG 0.004 0.000 ARG B 372 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 319) hydrogen bonds : angle 4.84420 ( 900) covalent geometry : bond 0.00234 (10096) covalent geometry : angle 0.48638 (13748) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 110 time to evaluate : 1.036 Fit side-chains REVERT: A 202 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8347 (t0) REVERT: A 292 ARG cc_start: 0.8191 (ptp-110) cc_final: 0.7559 (ptp90) REVERT: A 359 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6894 (mm-30) REVERT: A 410 ARG cc_start: 0.8346 (mtp-110) cc_final: 0.8128 (ttm170) REVERT: A 652 GLN cc_start: 0.6885 (mt0) cc_final: 0.6296 (tt0) REVERT: A 698 ARG cc_start: 0.7354 (mmt-90) cc_final: 0.7019 (mmp80) REVERT: B 282 MET cc_start: 0.8140 (ttp) cc_final: 0.7605 (ttm) REVERT: B 304 HIS cc_start: 0.7719 (m170) cc_final: 0.7382 (m90) REVERT: B 341 MET cc_start: 0.7728 (ttt) cc_final: 0.7519 (mtt) REVERT: B 378 ASP cc_start: 0.8568 (t0) cc_final: 0.8289 (t70) REVERT: B 540 LYS cc_start: 0.8351 (tttp) cc_final: 0.8044 (tmtt) outliers start: 44 outliers final: 36 residues processed: 140 average time/residue: 0.2194 time to fit residues: 43.6567 Evaluate side-chains 148 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 246 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 94 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 126 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 72 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 0.0980 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.156971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.117283 restraints weight = 11068.814| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.26 r_work: 0.3142 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10096 Z= 0.096 Angle : 0.484 7.705 13748 Z= 0.247 Chirality : 0.044 0.139 1562 Planarity : 0.004 0.036 1774 Dihedral : 3.680 26.138 1379 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.29 % Allowed : 20.39 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % 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: -0.37 (0.24), residues: 1268 helix: 1.14 (0.40), residues: 182 sheet: 0.17 (0.26), residues: 398 loop : -0.87 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 401 HIS 0.004 0.001 HIS A 561 PHE 0.017 0.001 PHE A 227 TYR 0.018 0.001 TYR B 334 ARG 0.004 0.000 ARG B 372 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 319) hydrogen bonds : angle 4.72415 ( 900) covalent geometry : bond 0.00227 (10096) covalent geometry : angle 0.48401 (13748) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 1.176 Fit side-chains REVERT: A 202 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8339 (t0) REVERT: A 292 ARG cc_start: 0.8180 (ptp-110) cc_final: 0.7549 (ptp90) REVERT: A 359 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6925 (mm-30) REVERT: A 410 ARG cc_start: 0.8344 (mtp-110) cc_final: 0.8116 (ttm170) REVERT: A 652 GLN cc_start: 0.6928 (mt0) cc_final: 0.6276 (tt0) REVERT: A 698 ARG cc_start: 0.7360 (mmt-90) cc_final: 0.7027 (mmp80) REVERT: B 282 MET cc_start: 0.8136 (ttp) cc_final: 0.7611 (ttm) REVERT: B 304 HIS cc_start: 0.7716 (m170) cc_final: 0.7389 (m90) REVERT: B 341 MET cc_start: 0.7734 (ttt) cc_final: 0.7517 (mtt) REVERT: B 378 ASP cc_start: 0.8583 (t0) cc_final: 0.8301 (t70) REVERT: B 540 LYS cc_start: 0.8345 (tttp) cc_final: 0.8041 (tmtt) outliers start: 44 outliers final: 36 residues processed: 138 average time/residue: 0.2358 time to fit residues: 47.5914 Evaluate side-chains 146 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 246 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 54 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.155210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115457 restraints weight = 11107.754| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.32 r_work: 0.3124 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10096 Z= 0.141 Angle : 0.521 7.889 13748 Z= 0.265 Chirality : 0.045 0.146 1562 Planarity : 0.004 0.038 1774 Dihedral : 3.803 26.695 1379 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.10 % Allowed : 20.10 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % 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: -0.41 (0.24), residues: 1268 helix: 1.04 (0.39), residues: 180 sheet: 0.13 (0.26), residues: 394 loop : -0.85 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 216 HIS 0.005 0.001 HIS A 616 PHE 0.051 0.002 PHE A 227 TYR 0.017 0.001 TYR B 334 ARG 0.004 0.000 ARG B 372 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 319) hydrogen bonds : angle 4.84919 ( 900) covalent geometry : bond 0.00349 (10096) covalent geometry : angle 0.52137 (13748) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 106 time to evaluate : 1.032 Fit side-chains REVERT: A 202 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8320 (t0) REVERT: A 359 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6904 (mm-30) REVERT: A 410 ARG cc_start: 0.8380 (mtp-110) cc_final: 0.8163 (ttm170) REVERT: A 652 GLN cc_start: 0.6966 (mt0) cc_final: 0.6340 (tt0) REVERT: A 698 ARG cc_start: 0.7354 (mmt-90) cc_final: 0.7008 (mmp80) REVERT: B 282 MET cc_start: 0.8126 (ttp) cc_final: 0.7598 (ttm) REVERT: B 304 HIS cc_start: 0.7735 (m170) cc_final: 0.7456 (m-70) REVERT: B 341 MET cc_start: 0.7764 (ttt) cc_final: 0.7558 (mtt) REVERT: B 378 ASP cc_start: 0.8594 (t0) cc_final: 0.8318 (t70) REVERT: B 540 LYS cc_start: 0.8368 (tttp) cc_final: 0.8056 (tmtt) outliers start: 42 outliers final: 38 residues processed: 133 average time/residue: 0.2070 time to fit residues: 40.0318 Evaluate side-chains 144 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 246 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 72 optimal weight: 0.0980 chunk 115 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 0.0570 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 578 GLN ** 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 = 0.3847 r_free = 0.3847 target = 0.155772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117273 restraints weight = 11094.994| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.26 r_work: 0.3154 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10096 Z= 0.118 Angle : 0.504 7.613 13748 Z= 0.256 Chirality : 0.045 0.141 1562 Planarity : 0.004 0.038 1774 Dihedral : 3.764 26.795 1379 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.90 % Allowed : 20.68 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % 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: -0.36 (0.24), residues: 1268 helix: 1.09 (0.39), residues: 180 sheet: 0.14 (0.26), residues: 395 loop : -0.80 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 216 HIS 0.004 0.001 HIS A 616 PHE 0.047 0.002 PHE A 227 TYR 0.016 0.001 TYR B 334 ARG 0.004 0.000 ARG B 372 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 319) hydrogen bonds : angle 4.79979 ( 900) covalent geometry : bond 0.00287 (10096) covalent geometry : angle 0.50425 (13748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6281.57 seconds wall clock time: 111 minutes 33.56 seconds (6693.56 seconds total)