Starting phenix.real_space_refine on Wed Sep 17 16:59:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ejk_48103/09_2025/9ejk_48103_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ejk_48103/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ejk_48103/09_2025/9ejk_48103_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ejk_48103/09_2025/9ejk_48103_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ejk_48103/09_2025/9ejk_48103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ejk_48103/09_2025/9ejk_48103.map" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 14, 'GLU:plan': 19, 'ASP:plan': 8, 'ASN:plan1': 1, 'TYR:plan': 1, 'GLN:plan1': 2} 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, 'ASP:plan': 7, 'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 5, 'TPO:plan-1': 1, 'PHE:plan': 1} 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: {'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 2.18, per 1000 atoms: 0.22 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: 0.80 Conformation dependent library (CDL) restraints added in 368.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.40 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: 1.69 Time building geometry restraints manager: 1.03 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: 10.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.680 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.010 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.019 0.001 ARG A 854 TYR 0.011 0.001 TYR A 254 PHE 0.017 0.001 PHE A 712 TRP 0.008 0.001 TRP A 420 HIS 0.005 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00211 (10096) covalent geometry : angle 0.49214 (13748) hydrogen bonds : bond 0.14955 ( 319) hydrogen bonds : angle 7.22745 ( 900) *********************** 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 : 0.358 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: 0.1070 time to fit residues: 28.4151 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 : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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** A 629 HIS B 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.154996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.115813 restraints weight = 11045.547| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.11 r_work: 0.3139 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10096 Z= 0.163 Angle : 0.568 6.326 13748 Z= 0.293 Chirality : 0.047 0.161 1562 Planarity : 0.005 0.040 1774 Dihedral : 3.929 19.038 1379 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.12 % Allowed : 19.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.24), residues: 1268 helix: 0.94 (0.39), residues: 170 sheet: 0.18 (0.27), residues: 398 loop : -1.18 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 45 TYR 0.014 0.002 TYR A 378 PHE 0.023 0.002 PHE A 227 TRP 0.009 0.001 TRP A 216 HIS 0.007 0.001 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00400 (10096) covalent geometry : angle 0.56829 (13748) hydrogen bonds : bond 0.04282 ( 319) hydrogen bonds : angle 5.50376 ( 900) *********************** 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 152 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.333 Fit side-chains REVERT: A 74 ASN cc_start: 0.8306 (m110) cc_final: 0.8091 (m-40) REVERT: A 85 GLN cc_start: 0.8278 (mt0) cc_final: 0.7982 (mt0) REVERT: A 222 ARG cc_start: 0.8211 (mtm-85) cc_final: 0.7990 (ttp-110) REVERT: A 292 ARG cc_start: 0.7871 (ptp-110) cc_final: 0.7366 (ptp90) REVERT: A 359 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7005 (mm-30) REVERT: A 492 LYS cc_start: 0.8676 (mptt) cc_final: 0.8331 (ttmm) REVERT: A 637 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7724 (mm-30) REVERT: A 652 GLN cc_start: 0.6865 (mt0) cc_final: 0.6219 (tt0) REVERT: A 698 ARG cc_start: 0.7431 (mmt-90) cc_final: 0.7110 (mmp80) REVERT: B 282 MET cc_start: 0.8160 (ttp) cc_final: 0.7685 (ttm) REVERT: B 283 LYS cc_start: 0.7944 (tttt) cc_final: 0.7623 (mtpp) REVERT: B 304 HIS cc_start: 0.7821 (m170) cc_final: 0.7569 (m90) REVERT: B 378 ASP cc_start: 0.8733 (t0) cc_final: 0.8484 (t70) REVERT: B 532 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7934 (mm-40) REVERT: B 540 LYS cc_start: 0.8452 (tttp) cc_final: 0.8117 (tmtt) outliers start: 32 outliers final: 25 residues processed: 141 average time/residue: 0.0961 time to fit residues: 18.9771 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 : 0.428 ------------------------------------------------------------------------------- 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 144 LEU 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 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 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 223 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 8 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.0070 chunk 80 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 127 optimal weight: 0.0970 chunk 101 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.158314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118773 restraints weight = 10977.005| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.17 r_work: 0.3189 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10096 Z= 0.087 Angle : 0.467 6.380 13748 Z= 0.243 Chirality : 0.043 0.143 1562 Planarity : 0.004 0.035 1774 Dihedral : 3.575 18.640 1379 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.15 % Allowed : 19.71 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.24), residues: 1268 helix: 1.40 (0.41), residues: 170 sheet: 0.29 (0.26), residues: 400 loop : -0.97 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 45 TYR 0.012 0.001 TYR A 254 PHE 0.021 0.001 PHE A 227 TRP 0.008 0.001 TRP B 527 HIS 0.005 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00196 (10096) covalent geometry : angle 0.46742 (13748) hydrogen bonds : bond 0.03391 ( 319) hydrogen bonds : angle 4.92352 ( 900) *********************** 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 140 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 222 ARG cc_start: 0.8165 (mtm-85) cc_final: 0.7906 (ttp-110) REVERT: A 292 ARG cc_start: 0.7855 (ptp-110) cc_final: 0.7348 (ptp90) REVERT: A 492 LYS cc_start: 0.8665 (mptt) cc_final: 0.8303 (ttmm) REVERT: A 637 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 652 GLN cc_start: 0.6817 (mt0) cc_final: 0.6182 (tt0) REVERT: A 698 ARG cc_start: 0.7356 (mmt-90) cc_final: 0.7050 (mmp80) REVERT: A 886 ARG cc_start: 0.8085 (ttm110) cc_final: 0.7792 (ttt180) REVERT: B 282 MET cc_start: 0.8139 (ttp) cc_final: 0.7622 (ttm) REVERT: B 304 HIS cc_start: 0.7788 (m170) cc_final: 0.7460 (m90) REVERT: B 344 MET cc_start: 0.7743 (mmp) cc_final: 0.6987 (mmp) REVERT: B 378 ASP cc_start: 0.8705 (t0) cc_final: 0.8412 (t70) REVERT: B 532 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7917 (mm-40) REVERT: B 540 LYS cc_start: 0.8402 (tttp) cc_final: 0.8093 (tmtt) outliers start: 22 outliers final: 17 residues processed: 133 average time/residue: 0.1072 time to fit residues: 20.0025 Evaluate side-chains 127 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 213 VAL 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 615 ASP 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 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 81 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN B 517 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.150597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111865 restraints weight = 11276.335| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.27 r_work: 0.3040 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10096 Z= 0.217 Angle : 0.610 6.947 13748 Z= 0.312 Chirality : 0.048 0.165 1562 Planarity : 0.005 0.048 1774 Dihedral : 4.143 19.300 1379 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.68 % Allowed : 18.24 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.24), residues: 1268 helix: 0.75 (0.39), residues: 176 sheet: 0.02 (0.26), residues: 399 loop : -1.14 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 331 TYR 0.019 0.002 TYR B 376 PHE 0.026 0.002 PHE A 300 TRP 0.013 0.002 TRP A 216 HIS 0.007 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00548 (10096) covalent geometry : angle 0.61045 (13748) hydrogen bonds : bond 0.04652 ( 319) hydrogen bonds : angle 5.32095 ( 900) *********************** 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 161 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 113 time to evaluate : 0.329 Fit side-chains REVERT: A 85 GLN cc_start: 0.8346 (mt0) cc_final: 0.8081 (mt0) REVERT: A 359 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6983 (mm-30) REVERT: A 410 ARG cc_start: 0.8499 (mtp-110) cc_final: 0.8255 (ttm170) REVERT: A 652 GLN cc_start: 0.6878 (mt0) cc_final: 0.6153 (tt0) REVERT: A 698 ARG cc_start: 0.7440 (mmt-90) cc_final: 0.7083 (mmp80) REVERT: B 282 MET cc_start: 0.8157 (ttp) cc_final: 0.7660 (ttm) REVERT: B 304 HIS cc_start: 0.7864 (m170) cc_final: 0.7367 (m90) REVERT: B 378 ASP cc_start: 0.8766 (t0) cc_final: 0.8519 (t70) REVERT: B 532 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7913 (mm-40) REVERT: B 540 LYS cc_start: 0.8424 (tttp) cc_final: 0.8038 (tmtt) outliers start: 48 outliers final: 39 residues processed: 144 average time/residue: 0.1014 time to fit residues: 20.4700 Evaluate side-chains 149 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 144 LEU 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 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 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 866 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 917 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 125 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 0.0010 chunk 108 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 118 optimal weight: 10.0000 chunk 100 optimal weight: 0.0070 chunk 98 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.156160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.117010 restraints weight = 11032.642| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.35 r_work: 0.3146 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10096 Z= 0.090 Angle : 0.474 6.055 13748 Z= 0.245 Chirality : 0.044 0.140 1562 Planarity : 0.004 0.039 1774 Dihedral : 3.742 21.747 1379 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.61 % Allowed : 20.10 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.24), residues: 1268 helix: 1.13 (0.40), residues: 176 sheet: 0.14 (0.26), residues: 396 loop : -0.95 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 372 TYR 0.012 0.001 TYR A 254 PHE 0.031 0.001 PHE A 227 TRP 0.009 0.001 TRP B 527 HIS 0.004 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00204 (10096) covalent geometry : angle 0.47425 (13748) hydrogen bonds : bond 0.03452 ( 319) hydrogen bonds : angle 4.92200 ( 900) *********************** 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 152 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.402 Fit side-chains REVERT: A 85 GLN cc_start: 0.8289 (mt0) cc_final: 0.7973 (mt0) REVERT: A 292 ARG cc_start: 0.8232 (ptp-110) cc_final: 0.7576 (ptp90) REVERT: A 359 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7025 (mm-30) REVERT: A 410 ARG cc_start: 0.8424 (mtp-110) cc_final: 0.8178 (ttm170) REVERT: A 637 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7743 (mm-30) REVERT: A 652 GLN cc_start: 0.6894 (mt0) cc_final: 0.6201 (tt0) REVERT: A 698 ARG cc_start: 0.7436 (mmt-90) cc_final: 0.7113 (mmp80) REVERT: B 282 MET cc_start: 0.8174 (ttp) cc_final: 0.7660 (ttm) REVERT: B 304 HIS cc_start: 0.7773 (m170) cc_final: 0.7408 (m90) REVERT: B 378 ASP cc_start: 0.8736 (t0) cc_final: 0.8474 (t70) REVERT: B 532 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7903 (mm-40) REVERT: B 540 LYS cc_start: 0.8372 (tttp) cc_final: 0.8034 (tmtt) outliers start: 37 outliers final: 29 residues processed: 139 average time/residue: 0.1038 time to fit residues: 20.5096 Evaluate side-chains 137 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 236 ILE 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 615 ASP 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 917 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 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 Chi-restraints excluded: chain C residue 246 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 43 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.152705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113245 restraints weight = 11235.141| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.24 r_work: 0.3089 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10096 Z= 0.146 Angle : 0.522 6.732 13748 Z= 0.267 Chirality : 0.045 0.149 1562 Planarity : 0.004 0.040 1774 Dihedral : 3.884 25.004 1379 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.24), residues: 1268 helix: 1.02 (0.40), residues: 176 sheet: 0.11 (0.26), residues: 394 loop : -0.98 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 372 TYR 0.012 0.001 TYR B 376 PHE 0.019 0.002 PHE A 300 TRP 0.009 0.001 TRP A 216 HIS 0.004 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00358 (10096) covalent geometry : angle 0.52187 (13748) hydrogen bonds : bond 0.03873 ( 319) hydrogen bonds : angle 4.95645 ( 900) *********************** 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 152 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 0.372 Fit side-chains REVERT: A 85 GLN cc_start: 0.8323 (mt0) cc_final: 0.8081 (mt0) REVERT: A 359 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7003 (mm-30) REVERT: A 652 GLN cc_start: 0.6860 (mt0) cc_final: 0.6149 (tt0) REVERT: A 698 ARG cc_start: 0.7451 (mmt-90) cc_final: 0.7100 (mmp80) REVERT: B 282 MET cc_start: 0.8168 (ttp) cc_final: 0.7665 (ttm) REVERT: B 304 HIS cc_start: 0.7853 (m170) cc_final: 0.7477 (m90) REVERT: B 378 ASP cc_start: 0.8745 (t0) cc_final: 0.8492 (t70) REVERT: B 532 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7873 (mm-40) REVERT: B 540 LYS cc_start: 0.8376 (tttp) cc_final: 0.8005 (tmtt) outliers start: 42 outliers final: 36 residues processed: 137 average time/residue: 0.0916 time to fit residues: 18.1743 Evaluate side-chains 143 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 144 LEU 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 244 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 378 TYR 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 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 A residue 917 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 111 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 73 optimal weight: 0.0270 chunk 117 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.155758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.116555 restraints weight = 11082.400| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.21 r_work: 0.3149 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10096 Z= 0.110 Angle : 0.482 5.834 13748 Z= 0.248 Chirality : 0.044 0.140 1562 Planarity : 0.004 0.038 1774 Dihedral : 3.751 26.463 1379 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.20 % Allowed : 20.78 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.24), residues: 1268 helix: 1.03 (0.40), residues: 182 sheet: 0.18 (0.26), residues: 393 loop : -0.90 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 372 TYR 0.011 0.001 TYR A 911 PHE 0.037 0.001 PHE A 227 TRP 0.008 0.001 TRP A 216 HIS 0.004 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00265 (10096) covalent geometry : angle 0.48236 (13748) hydrogen bonds : bond 0.03506 ( 319) hydrogen bonds : angle 4.84109 ( 900) *********************** 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 151 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 108 time to evaluate : 0.326 Fit side-chains REVERT: A 85 GLN cc_start: 0.8313 (mt0) cc_final: 0.8104 (mt0) REVERT: A 359 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: A 410 ARG cc_start: 0.8437 (mtp-110) cc_final: 0.8205 (ttm170) REVERT: A 637 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7705 (mm-30) REVERT: A 652 GLN cc_start: 0.6900 (mt0) cc_final: 0.6211 (tt0) REVERT: A 698 ARG cc_start: 0.7447 (mmt-90) cc_final: 0.7107 (mmp80) REVERT: B 282 MET cc_start: 0.8198 (ttp) cc_final: 0.7711 (ttm) REVERT: B 304 HIS cc_start: 0.7828 (m170) cc_final: 0.7449 (m90) REVERT: B 378 ASP cc_start: 0.8766 (t0) cc_final: 0.8502 (t70) REVERT: B 532 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7877 (mm-40) REVERT: B 540 LYS cc_start: 0.8357 (tttp) cc_final: 0.8024 (tmtt) outliers start: 43 outliers final: 35 residues processed: 137 average time/residue: 0.0988 time to fit residues: 19.2065 Evaluate side-chains 142 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 144 LEU Chi-restraints excluded: chain A residue 210 ARG 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 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 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 A residue 917 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 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 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 94 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.0070 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.156392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.117364 restraints weight = 11018.659| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.20 r_work: 0.3156 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10096 Z= 0.101 Angle : 0.478 5.642 13748 Z= 0.247 Chirality : 0.044 0.138 1562 Planarity : 0.004 0.036 1774 Dihedral : 3.683 27.404 1379 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.00 % Allowed : 20.88 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.24), residues: 1268 helix: 1.13 (0.40), residues: 182 sheet: 0.20 (0.26), residues: 395 loop : -0.85 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 372 TYR 0.011 0.001 TYR A 254 PHE 0.014 0.001 PHE A 300 TRP 0.008 0.001 TRP A 216 HIS 0.004 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00240 (10096) covalent geometry : angle 0.47819 (13748) hydrogen bonds : bond 0.03382 ( 319) hydrogen bonds : angle 4.72942 ( 900) *********************** 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 153 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 0.384 Fit side-chains REVERT: A 85 GLN cc_start: 0.8291 (mt0) cc_final: 0.8088 (mt0) REVERT: A 359 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6995 (mm-30) REVERT: A 637 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7728 (mm-30) REVERT: A 652 GLN cc_start: 0.6919 (mt0) cc_final: 0.6206 (tt0) REVERT: A 698 ARG cc_start: 0.7446 (mmt-90) cc_final: 0.7107 (mmp80) REVERT: B 282 MET cc_start: 0.8201 (ttp) cc_final: 0.7718 (ttm) REVERT: B 304 HIS cc_start: 0.7822 (m170) cc_final: 0.7445 (m90) REVERT: B 341 MET cc_start: 0.7941 (ttt) cc_final: 0.7706 (mtt) REVERT: B 378 ASP cc_start: 0.8753 (t0) cc_final: 0.8492 (t70) REVERT: B 532 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7859 (mm-40) REVERT: B 540 LYS cc_start: 0.8350 (tttp) cc_final: 0.8025 (tmtt) outliers start: 41 outliers final: 35 residues processed: 139 average time/residue: 0.0968 time to fit residues: 19.5763 Evaluate side-chains 144 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 128 SER Chi-restraints excluded: chain A residue 144 LEU 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 246 VAL Chi-restraints excluded: chain A residue 272 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 615 ASP 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 402 GLU 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 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 76 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 0.0000 chunk 92 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 GLN B 464 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.152164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.114006 restraints weight = 11106.371| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.30 r_work: 0.3105 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10096 Z= 0.228 Angle : 0.607 7.447 13748 Z= 0.309 Chirality : 0.048 0.161 1562 Planarity : 0.005 0.046 1774 Dihedral : 4.222 27.688 1379 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.68 % Allowed : 20.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.24), residues: 1268 helix: 0.65 (0.38), residues: 181 sheet: -0.14 (0.26), residues: 386 loop : -0.97 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 222 TYR 0.018 0.002 TYR B 376 PHE 0.048 0.002 PHE A 227 TRP 0.014 0.002 TRP A 216 HIS 0.007 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00571 (10096) covalent geometry : angle 0.60686 (13748) hydrogen bonds : bond 0.04653 ( 319) hydrogen bonds : angle 5.22789 ( 900) *********************** 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 160 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 112 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7638 (tp) REVERT: A 131 GLN cc_start: 0.6241 (mm-40) cc_final: 0.5960 (mt0) REVERT: A 359 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7040 (mm-30) REVERT: A 410 ARG cc_start: 0.8550 (mtp-110) cc_final: 0.8315 (ttm170) REVERT: A 652 GLN cc_start: 0.7031 (mt0) cc_final: 0.6338 (tt0) REVERT: A 698 ARG cc_start: 0.7460 (mmt-90) cc_final: 0.7089 (mmp80) REVERT: B 282 MET cc_start: 0.8212 (ttp) cc_final: 0.7749 (ttm) REVERT: B 304 HIS cc_start: 0.7879 (m170) cc_final: 0.7569 (m-70) REVERT: B 378 ASP cc_start: 0.8767 (t0) cc_final: 0.8511 (t70) REVERT: B 532 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7883 (mm-40) REVERT: B 540 LYS cc_start: 0.8407 (tttp) cc_final: 0.8043 (tmtt) outliers start: 48 outliers final: 42 residues processed: 143 average time/residue: 0.1037 time to fit residues: 20.9963 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 : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 233 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 378 TYR 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 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 A residue 917 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 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 215 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 22 optimal weight: 0.0980 chunk 57 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 115 optimal weight: 0.1980 chunk 118 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.155974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116922 restraints weight = 10923.686| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.17 r_work: 0.3156 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2389 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= 0.095 Angle : 0.482 5.499 13748 Z= 0.250 Chirality : 0.044 0.140 1562 Planarity : 0.004 0.041 1774 Dihedral : 3.787 27.386 1379 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.41 % Allowed : 21.76 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.24), residues: 1268 helix: 1.06 (0.40), residues: 182 sheet: 0.11 (0.26), residues: 395 loop : -0.88 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 372 TYR 0.011 0.001 TYR A 254 PHE 0.042 0.001 PHE A 227 TRP 0.008 0.001 TRP A 216 HIS 0.004 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00221 (10096) covalent geometry : angle 0.48166 (13748) hydrogen bonds : bond 0.03401 ( 319) hydrogen bonds : angle 4.84435 ( 900) ********************** 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: 35 poor density : 113 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 131 GLN cc_start: 0.6120 (mm-40) cc_final: 0.5879 (mt0) REVERT: A 359 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: A 378 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7860 (p90) REVERT: A 410 ARG cc_start: 0.8430 (mtp-110) cc_final: 0.8192 (ttm170) REVERT: A 652 GLN cc_start: 0.7008 (mt0) cc_final: 0.6285 (tt0) REVERT: A 698 ARG cc_start: 0.7438 (mmt-90) cc_final: 0.7087 (mmp80) REVERT: B 282 MET cc_start: 0.8177 (ttp) cc_final: 0.7715 (ttm) REVERT: B 304 HIS cc_start: 0.7803 (m170) cc_final: 0.7499 (m-70) REVERT: B 378 ASP cc_start: 0.8752 (t0) cc_final: 0.8499 (t70) REVERT: B 532 GLN cc_start: 0.8107 (mm-40) cc_final: 0.7849 (mm-40) REVERT: B 540 LYS cc_start: 0.8356 (tttp) cc_final: 0.8007 (tmtt) outliers start: 35 outliers final: 31 residues processed: 136 average time/residue: 0.0964 time to fit residues: 18.8751 Evaluate side-chains 144 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 144 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 378 TYR 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 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 411 SER Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 215 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 101 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 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 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.154564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.115899 restraints weight = 11021.856| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.22 r_work: 0.3132 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10096 Z= 0.136 Angle : 0.512 6.013 13748 Z= 0.263 Chirality : 0.045 0.145 1562 Planarity : 0.004 0.040 1774 Dihedral : 3.852 27.606 1379 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.80 % Allowed : 21.07 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.24), residues: 1268 helix: 0.99 (0.39), residues: 183 sheet: 0.12 (0.26), residues: 394 loop : -0.90 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 372 TYR 0.011 0.001 TYR A 911 PHE 0.045 0.002 PHE A 227 TRP 0.010 0.001 TRP A 216 HIS 0.004 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00335 (10096) covalent geometry : angle 0.51205 (13748) hydrogen bonds : bond 0.03743 ( 319) hydrogen bonds : angle 4.90464 ( 900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3060.23 seconds wall clock time: 52 minutes 57.01 seconds (3177.01 seconds total)