Starting phenix.real_space_refine on Sun Oct 25 01:24:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x9k_66669/10_2026/9x9k_66669.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x9k_66669/10_2026/9x9k_66669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x9k_66669/10_2026/9x9k_66669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x9k_66669/10_2026/9x9k_66669.map" model { file = "/net/cci-nas-00/data/ceres_data/9x9k_66669/10_2026/9x9k_66669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x9k_66669/10_2026/9x9k_66669.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 9442 2.51 5 N 2476 2.21 5 O 2874 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14840 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7280 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 43, 'TRANS': 858} Chain: "B" Number of atoms: 7280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7280 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 43, 'TRANS': 858} Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 3.25, per 1000 atoms: 0.22 Number of scatterers: 14840 At special positions: 0 Unit cell: (132.54, 149.46, 95.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2874 8.00 N 2476 7.00 C 9442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 761 " - pdb=" SG CYS A 768 " distance=2.03 Simple disulfide: pdb=" SG CYS A 798 " - pdb=" SG CYS A 834 " distance=2.04 Simple disulfide: pdb=" SG CYS B 761 " - pdb=" SG CYS B 768 " distance=2.03 Simple disulfide: pdb=" SG CYS B 798 " - pdb=" SG CYS B 834 " distance=2.04 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 681 " " NAG A1002 " - " ASN A 735 " " NAG A1003 " - " ASN A 818 " " NAG A1004 " - " ASN A 265 " " NAG A1005 " - " ASN A 625 " " NAG A1006 " - " ASN A 573 " " NAG A1007 " - " ASN A 319 " " NAG A1008 " - " ASN A 128 " " NAG A1009 " - " ASN A 234 " " NAG A1010 " - " ASN A 527 " " NAG B1001 " - " ASN B 681 " " NAG B1002 " - " ASN B 735 " " NAG B1003 " - " ASN B 818 " " NAG B1004 " - " ASN B 265 " " NAG B1005 " - " ASN B 625 " " NAG B1006 " - " ASN B 573 " " NAG B1007 " - " ASN B 319 " " NAG B1008 " - " ASN B 128 " " NAG B1009 " - " ASN B 234 " " NAG B1010 " - " ASN B 527 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 695.0 milliseconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 20 sheets defined 45.1% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 261 through 264 Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.742A pdb=" N LEU A 280 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.777A pdb=" N LEU A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 375 through 397 removed outlier: 3.691A pdb=" N GLN A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TRP A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.876A pdb=" N GLY A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 440 Processing helix chain 'A' and resid 467 through 473 removed outlier: 3.940A pdb=" N ASP A 473 " --> pdb=" O SER A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 removed outlier: 3.834A pdb=" N ALA A 481 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 removed outlier: 3.936A pdb=" N GLN A 498 " --> pdb=" O ASP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 528 removed outlier: 4.131A pdb=" N LEU A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TRP A 518 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU A 523 " --> pdb=" O ASP A 519 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A 524 " --> pdb=" O HIS A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 545 removed outlier: 3.896A pdb=" N ILE A 539 " --> pdb=" O THR A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 627 removed outlier: 3.554A pdb=" N THR A 627 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 649 Processing helix chain 'A' and resid 656 through 671 removed outlier: 4.411A pdb=" N ILE A 662 " --> pdb=" O ARG A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 685 removed outlier: 3.918A pdb=" N ALA A 679 " --> pdb=" O PRO A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 707 removed outlier: 3.934A pdb=" N TRP A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE A 705 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 738 removed outlier: 3.835A pdb=" N THR A 727 " --> pdb=" O LYS A 723 " (cutoff:3.500A) Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 746 through 762 removed outlier: 3.726A pdb=" N SER A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 782 removed outlier: 4.023A pdb=" N GLU A 770 " --> pdb=" O PRO A 766 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER A 773 " --> pdb=" O GLU A 769 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN A 782 " --> pdb=" O GLN A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 793 removed outlier: 3.934A pdb=" N ARG A 793 " --> pdb=" O PRO A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 801 removed outlier: 3.787A pdb=" N ALA A 800 " --> pdb=" O TYR A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 818 removed outlier: 4.233A pdb=" N PHE A 811 " --> pdb=" O GLU A 807 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 831 removed outlier: 3.531A pdb=" N ALA A 831 " --> pdb=" O LYS A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 848 Processing helix chain 'A' and resid 855 through 858 Processing helix chain 'A' and resid 859 through 869 removed outlier: 4.110A pdb=" N ILE A 863 " --> pdb=" O ALA A 859 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE A 864 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN A 869 " --> pdb=" O SER A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 874 Processing helix chain 'A' and resid 876 through 883 Processing helix chain 'A' and resid 884 through 891 Processing helix chain 'A' and resid 897 through 906 removed outlier: 3.523A pdb=" N THR A 906 " --> pdb=" O ILE A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 925 removed outlier: 3.721A pdb=" N ASN A 925 " --> pdb=" O PHE A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 932 No H-bonds generated for 'chain 'A' and resid 930 through 932' Processing helix chain 'A' and resid 933 through 938 removed outlier: 3.701A pdb=" N GLU A 938 " --> pdb=" O THR A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 951 Processing helix chain 'A' and resid 956 through 960 removed outlier: 3.766A pdb=" N LEU A 959 " --> pdb=" O GLU A 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 264 Processing helix chain 'B' and resid 276 through 280 removed outlier: 3.741A pdb=" N LEU B 280 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 314 through 332 removed outlier: 3.778A pdb=" N LEU B 318 " --> pdb=" O GLY B 314 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Proline residue: B 323 - end of helix Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 375 through 397 removed outlier: 3.690A pdb=" N GLN B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TRP B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 414 Processing helix chain 'B' and resid 417 through 426 removed outlier: 3.877A pdb=" N GLY B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 440 Processing helix chain 'B' and resid 467 through 473 removed outlier: 3.940A pdb=" N ASP B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 491 removed outlier: 3.834A pdb=" N ALA B 481 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 507 removed outlier: 3.936A pdb=" N GLN B 498 " --> pdb=" O ASP B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 528 removed outlier: 4.131A pdb=" N LEU B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TRP B 518 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU B 523 " --> pdb=" O ASP B 519 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA B 524 " --> pdb=" O HIS B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 545 removed outlier: 3.896A pdb=" N ILE B 539 " --> pdb=" O THR B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 627 removed outlier: 3.555A pdb=" N THR B 627 " --> pdb=" O LEU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 649 Processing helix chain 'B' and resid 656 through 671 removed outlier: 4.411A pdb=" N ILE B 662 " --> pdb=" O ARG B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 685 removed outlier: 3.917A pdb=" N ALA B 679 " --> pdb=" O PRO B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 707 removed outlier: 3.934A pdb=" N TRP B 695 " --> pdb=" O GLN B 691 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE B 705 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 738 removed outlier: 3.835A pdb=" N THR B 727 " --> pdb=" O LYS B 723 " (cutoff:3.500A) Proline residue: B 728 - end of helix Processing helix chain 'B' and resid 746 through 762 removed outlier: 3.727A pdb=" N SER B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 782 removed outlier: 4.022A pdb=" N GLU B 770 " --> pdb=" O PRO B 766 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER B 773 " --> pdb=" O GLU B 769 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY B 774 " --> pdb=" O GLU B 770 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN B 782 " --> pdb=" O GLN B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 793 removed outlier: 3.934A pdb=" N ARG B 793 " --> pdb=" O PRO B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 801 removed outlier: 3.787A pdb=" N ALA B 800 " --> pdb=" O TYR B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 818 removed outlier: 4.232A pdb=" N PHE B 811 " --> pdb=" O GLU B 807 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 831 removed outlier: 3.531A pdb=" N ALA B 831 " --> pdb=" O LYS B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 848 Processing helix chain 'B' and resid 855 through 858 Processing helix chain 'B' and resid 859 through 869 removed outlier: 4.110A pdb=" N ILE B 863 " --> pdb=" O ALA B 859 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE B 864 " --> pdb=" O THR B 860 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER B 865 " --> pdb=" O SER B 861 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN B 869 " --> pdb=" O SER B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 874 Processing helix chain 'B' and resid 876 through 883 Processing helix chain 'B' and resid 884 through 891 Processing helix chain 'B' and resid 897 through 906 removed outlier: 3.523A pdb=" N THR B 906 " --> pdb=" O ILE B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 925 removed outlier: 3.721A pdb=" N ASN B 925 " --> pdb=" O PHE B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 932 No H-bonds generated for 'chain 'B' and resid 930 through 932' Processing helix chain 'B' and resid 933 through 938 removed outlier: 3.701A pdb=" N GLU B 938 " --> pdb=" O THR B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 951 Processing helix chain 'B' and resid 956 through 960 removed outlier: 3.765A pdb=" N LEU B 959 " --> pdb=" O GLU B 956 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 82 removed outlier: 3.694A pdb=" N PHE A 111 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A 176 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER A 174 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 123 removed outlier: 4.117A pdb=" N ILE A 122 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A 162 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 193 through 199 removed outlier: 3.735A pdb=" N TYR A 198 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS A 205 " --> pdb=" O TYR A 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 245 Processing sheet with id=AA7, first strand: chain 'A' and resid 290 through 293 removed outlier: 3.857A pdb=" N ILE A 300 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU A 299 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLN A 343 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG A 301 " --> pdb=" O GLN A 343 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA9, first strand: chain 'A' and resid 606 through 608 Processing sheet with id=AB1, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AB2, first strand: chain 'B' and resid 80 through 82 removed outlier: 3.693A pdb=" N PHE B 111 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR B 176 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER B 174 " --> pdb=" O CYS B 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AB4, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AB5, first strand: chain 'B' and resid 119 through 123 removed outlier: 4.117A pdb=" N ILE B 122 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU B 162 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 193 through 199 removed outlier: 3.734A pdb=" N TYR B 198 " --> pdb=" O LYS B 205 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS B 205 " --> pdb=" O TYR B 198 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 244 through 245 Processing sheet with id=AB8, first strand: chain 'B' and resid 290 through 293 removed outlier: 3.857A pdb=" N ILE B 300 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU B 299 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLN B 343 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG B 301 " --> pdb=" O GLN B 343 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AC1, first strand: chain 'B' and resid 606 through 608 Processing sheet with id=AC2, first strand: chain 'B' and resid 591 through 592 512 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4788 1.34 - 1.47: 3834 1.47 - 1.59: 6510 1.59 - 1.71: 0 1.71 - 1.84: 84 Bond restraints: 15216 Sorted by residual: bond pdb=" N VAL A 714 " pdb=" CA VAL A 714 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.13e+00 bond pdb=" C VAL B 714 " pdb=" N TYR B 715 " ideal model delta sigma weight residual 1.335 1.292 0.042 1.42e-02 4.96e+03 8.88e+00 bond pdb=" N VAL B 714 " pdb=" CA VAL B 714 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.26e+00 bond pdb=" CB CYS A 768 " pdb=" SG CYS A 768 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB CYS B 768 " pdb=" SG CYS B 768 " ideal model delta sigma weight residual 1.808 1.770 0.038 3.30e-02 9.18e+02 1.35e+00 ... (remaining 15211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 20110 1.79 - 3.57: 496 3.57 - 5.36: 89 5.36 - 7.14: 23 7.14 - 8.93: 6 Bond angle restraints: 20724 Sorted by residual: angle pdb=" N GLU B 713 " pdb=" CA GLU B 713 " pdb=" C GLU B 713 " ideal model delta sigma weight residual 110.41 116.48 -6.07 1.23e+00 6.61e-01 2.44e+01 angle pdb=" N GLU A 713 " pdb=" CA GLU A 713 " pdb=" C GLU A 713 " ideal model delta sigma weight residual 110.41 116.46 -6.05 1.23e+00 6.61e-01 2.42e+01 angle pdb=" N VAL A 714 " pdb=" CA VAL A 714 " pdb=" C VAL A 714 " ideal model delta sigma weight residual 109.34 118.27 -8.93 2.08e+00 2.31e-01 1.84e+01 angle pdb=" C ALA A 214 " pdb=" CA ALA A 214 " pdb=" CB ALA A 214 " ideal model delta sigma weight residual 116.34 110.41 5.93 1.40e+00 5.10e-01 1.80e+01 angle pdb=" C ALA B 214 " pdb=" CA ALA B 214 " pdb=" CB ALA B 214 " ideal model delta sigma weight residual 116.34 110.44 5.90 1.40e+00 5.10e-01 1.78e+01 ... (remaining 20719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8389 17.99 - 35.98: 707 35.98 - 53.98: 152 53.98 - 71.97: 24 71.97 - 89.96: 22 Dihedral angle restraints: 9294 sinusoidal: 3976 harmonic: 5318 Sorted by residual: dihedral pdb=" CB CYS A 761 " pdb=" SG CYS A 761 " pdb=" SG CYS A 768 " pdb=" CB CYS A 768 " ideal model delta sinusoidal sigma weight residual 93.00 172.41 -79.41 1 1.00e+01 1.00e-02 7.84e+01 dihedral pdb=" CB CYS B 761 " pdb=" SG CYS B 761 " pdb=" SG CYS B 768 " pdb=" CB CYS B 768 " ideal model delta sinusoidal sigma weight residual 93.00 172.38 -79.38 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CA ASN A 526 " pdb=" C ASN A 526 " pdb=" N ASN A 527 " pdb=" CA ASN A 527 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 9291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2248 0.110 - 0.220: 64 0.220 - 0.331: 0 0.331 - 0.441: 2 0.441 - 0.551: 4 Chirality restraints: 2318 Sorted by residual: chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 681 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.59e+00 chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 681 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.48e+00 chirality pdb=" C1 NAG A1010 " pdb=" ND2 ASN A 527 " pdb=" C2 NAG A1010 " pdb=" O5 NAG A1010 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.01e+00 ... (remaining 2315 not shown) Planarity restraints: 2678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 681 " -0.025 2.00e-02 2.50e+03 2.50e-02 7.82e+00 pdb=" CG ASN A 681 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 681 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 681 " 0.021 2.00e-02 2.50e+03 pdb=" C1 NAG A1001 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 681 " 0.025 2.00e-02 2.50e+03 2.47e-02 7.62e+00 pdb=" CG ASN B 681 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN B 681 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 681 " -0.021 2.00e-02 2.50e+03 pdb=" C1 NAG B1001 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 714 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.85e+00 pdb=" C VAL B 714 " -0.045 2.00e-02 2.50e+03 pdb=" O VAL B 714 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR B 715 " 0.016 2.00e-02 2.50e+03 ... (remaining 2675 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1614 2.75 - 3.29: 15271 3.29 - 3.83: 23561 3.83 - 4.36: 26622 4.36 - 4.90: 44972 Nonbonded interactions: 112040 Sorted by model distance: nonbonded pdb=" OG SER A 578 " pdb=" O PHE A 580 " model vdw 2.213 3.040 nonbonded pdb=" OG SER B 578 " pdb=" O PHE B 580 " model vdw 2.214 3.040 nonbonded pdb=" OG1 THR B 88 " pdb=" OG SER B 106 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR A 88 " pdb=" OG SER A 106 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR B 911 " pdb=" OE1 GLU B 914 " model vdw 2.263 3.040 ... (remaining 112035 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.510 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 0.003 0.048 15240 Z= 0.137 Angle : 0.732 12.004 20792 Z= 0.369 Chirality : 0.050 0.551 2318 Planarity : 0.006 0.058 2658 Dihedral : 14.095 89.961 5842 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.20), residues: 1800 helix: 0.96 (0.21), residues: 640 sheet: -0.28 (0.39), residues: 216 loop : -1.94 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 935 TYR 0.027 0.001 TYR B 419 PHE 0.011 0.001 PHE A 962 TRP 0.026 0.001 TRP B 961 HIS 0.004 0.001 HIS B 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (15216) covalent geometry : angle 0.68946 / 0.36 (20724) SS BOND : bond 0.00315 / 0.15 ( 4) SS BOND : angle 4.35677 / 2.44 ( 8) hydrogen bonds : bond 0.19925 / 13.24 ( 512) hydrogen bonds : angle 6.59324 / 4.40 ( 1446) link_NAG-ASN : bond 0.00668 / 0.39 ( 20) link_NAG-ASN : angle 4.34983 / 3.12 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.452 Fit side-chains REVERT: A 189 ASP cc_start: 0.8888 (p0) cc_final: 0.8040 (m-30) REVERT: A 230 LYS cc_start: 0.5737 (mttp) cc_final: 0.4937 (ptmm) REVERT: A 354 MET cc_start: 0.6024 (tmm) cc_final: 0.5803 (tmm) REVERT: A 413 PHE cc_start: 0.5591 (m-80) cc_final: 0.5016 (m-80) REVERT: A 540 MET cc_start: 0.7346 (mmp) cc_final: 0.6754 (mmp) REVERT: A 693 MET cc_start: 0.8871 (tpp) cc_final: 0.8461 (tpp) REVERT: A 748 MET cc_start: 0.8706 (mmp) cc_final: 0.8249 (mmt) REVERT: A 778 GLN cc_start: 0.8594 (tt0) cc_final: 0.8304 (tt0) REVERT: A 817 ARG cc_start: 0.8966 (tpp80) cc_final: 0.8395 (tpp80) REVERT: A 903 GLN cc_start: 0.8787 (tp-100) cc_final: 0.8234 (tm-30) REVERT: B 178 MET cc_start: 0.6594 (tpt) cc_final: 0.6261 (tpt) REVERT: B 189 ASP cc_start: 0.8849 (p0) cc_final: 0.8002 (m-30) REVERT: B 230 LYS cc_start: 0.5665 (mttp) cc_final: 0.4892 (ptmm) REVERT: B 354 MET cc_start: 0.6001 (tmm) cc_final: 0.5778 (tmm) REVERT: B 413 PHE cc_start: 0.5566 (m-80) cc_final: 0.5006 (m-80) REVERT: B 540 MET cc_start: 0.7343 (mmp) cc_final: 0.6751 (mmp) REVERT: B 693 MET cc_start: 0.8849 (tpp) cc_final: 0.8431 (tpp) REVERT: B 748 MET cc_start: 0.8716 (mmp) cc_final: 0.8264 (mmt) REVERT: B 778 GLN cc_start: 0.8600 (tt0) cc_final: 0.8311 (tt0) REVERT: B 817 ARG cc_start: 0.8961 (tpp80) cc_final: 0.8388 (tpp80) REVERT: B 903 GLN cc_start: 0.8788 (tp-100) cc_final: 0.8230 (tm-30) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.0950 time to fit residues: 30.3983 Evaluate side-chains 143 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 HIS ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.145543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111278 restraints weight = 28406.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.112389 restraints weight = 20222.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.113632 restraints weight = 14848.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.114205 restraints weight = 12961.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.114604 restraints weight = 11778.899| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15240 Z= 0.227 Angle : 0.756 13.608 20792 Z= 0.387 Chirality : 0.051 0.505 2318 Planarity : 0.006 0.058 2658 Dihedral : 5.918 45.554 2378 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 1.94 % Allowed : 7.19 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.20), residues: 1800 helix: 0.66 (0.21), residues: 678 sheet: -0.64 (0.37), residues: 238 loop : -1.91 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 935 TYR 0.029 0.002 TYR A 419 PHE 0.030 0.003 PHE B 490 TRP 0.017 0.002 TRP A 543 HIS 0.007 0.001 HIS A 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (15216) covalent geometry : angle 0.72705 / 0.38 (20724) SS BOND : bond 0.00334 / 0.17 ( 4) SS BOND : angle 3.18329 / 2.08 ( 8) hydrogen bonds : bond 0.05720 / 3.85 ( 512) hydrogen bonds : angle 5.13254 / 3.47 ( 1446) link_NAG-ASN : bond 0.00468 / 0.31 ( 20) link_NAG-ASN : angle 3.78264 / 2.53 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.6022 (mttp) cc_final: 0.5406 (ptpt) REVERT: A 342 ASP cc_start: 0.6865 (t0) cc_final: 0.6619 (t0) REVERT: A 413 PHE cc_start: 0.6003 (m-80) cc_final: 0.4661 (m-80) REVERT: A 788 ILE cc_start: 0.9107 (mm) cc_final: 0.8828 (mt) REVERT: A 891 TYR cc_start: 0.6362 (m-80) cc_final: 0.6159 (t80) REVERT: A 903 GLN cc_start: 0.8852 (tp-100) cc_final: 0.8317 (tm-30) REVERT: B 230 LYS cc_start: 0.6067 (mttp) cc_final: 0.5463 (ptpt) REVERT: B 342 ASP cc_start: 0.6864 (t0) cc_final: 0.6622 (t0) REVERT: B 413 PHE cc_start: 0.6020 (m-80) cc_final: 0.4679 (m-80) REVERT: B 788 ILE cc_start: 0.9095 (mm) cc_final: 0.8819 (mt) REVERT: B 903 GLN cc_start: 0.8849 (tp-100) cc_final: 0.8311 (tm-30) outliers start: 31 outliers final: 23 residues processed: 188 average time/residue: 0.0963 time to fit residues: 29.2266 Evaluate side-chains 164 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 890 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [112, 36, 5, 149, 39, 50, 64, 79, 56, 121, 82] chunk 112 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 39 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 HIS ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.150698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.117124 restraints weight = 28517.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.118809 restraints weight = 21386.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.120077 restraints weight = 15488.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.120616 restraints weight = 14150.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.121263 restraints weight = 13021.888| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15240 Z= 0.112 Angle : 0.610 11.467 20792 Z= 0.306 Chirality : 0.045 0.416 2318 Planarity : 0.004 0.050 2658 Dihedral : 5.297 46.768 2378 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 1.06 % Allowed : 11.25 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.20), residues: 1800 helix: 1.02 (0.21), residues: 676 sheet: -0.68 (0.37), residues: 238 loop : -1.88 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 935 TYR 0.018 0.001 TYR B 161 PHE 0.031 0.002 PHE A 612 TRP 0.014 0.001 TRP B 961 HIS 0.002 0.001 HIS B 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (15216) covalent geometry : angle 0.58337 / 0.30 (20724) SS BOND : bond 0.00282 / 0.14 ( 4) SS BOND : angle 2.44245 / 1.66 ( 8) hydrogen bonds : bond 0.03812 / 2.57 ( 512) hydrogen bonds : angle 4.79315 / 3.23 ( 1446) link_NAG-ASN : bond 0.00557 / 0.36 ( 20) link_NAG-ASN : angle 3.24123 / 2.18 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 ASP cc_start: 0.6725 (t0) cc_final: 0.6383 (t0) REVERT: A 354 MET cc_start: 0.5976 (tmm) cc_final: 0.5659 (tmm) REVERT: A 575 THR cc_start: 0.8486 (p) cc_final: 0.8254 (p) REVERT: A 817 ARG cc_start: 0.8750 (tpp80) cc_final: 0.8207 (tpp80) REVERT: A 903 GLN cc_start: 0.8745 (tp-100) cc_final: 0.8432 (tm-30) REVERT: B 342 ASP cc_start: 0.6723 (t0) cc_final: 0.6384 (t0) REVERT: B 354 MET cc_start: 0.5962 (tmm) cc_final: 0.5654 (tmm) REVERT: B 575 THR cc_start: 0.8475 (p) cc_final: 0.8245 (p) REVERT: B 817 ARG cc_start: 0.8656 (tpp80) cc_final: 0.8103 (tpp80) REVERT: B 903 GLN cc_start: 0.8742 (tp-100) cc_final: 0.8417 (tm-30) outliers start: 17 outliers final: 14 residues processed: 183 average time/residue: 0.1062 time to fit residues: 30.1486 Evaluate side-chains 164 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 890 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [20, 138, 10, 57, 29, 126, 114, 58, 35, 141, 76] chunk 20 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 823 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.144869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110965 restraints weight = 28323.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.112543 restraints weight = 22212.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.113926 restraints weight = 15792.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.114192 restraints weight = 13882.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.114373 restraints weight = 12892.370| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15240 Z= 0.159 Angle : 0.641 10.963 20792 Z= 0.324 Chirality : 0.047 0.410 2318 Planarity : 0.004 0.046 2658 Dihedral : 5.411 45.900 2378 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.94 % Allowed : 12.75 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.20), residues: 1800 helix: 1.14 (0.21), residues: 678 sheet: -0.82 (0.36), residues: 230 loop : -1.81 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 829 TYR 0.026 0.002 TYR B 891 PHE 0.027 0.002 PHE A 490 TRP 0.011 0.001 TRP B 961 HIS 0.003 0.001 HIS A 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (15216) covalent geometry : angle 0.61739 / 0.32 (20724) SS BOND : bond 0.00303 / 0.15 ( 4) SS BOND : angle 2.82479 / 1.94 ( 8) hydrogen bonds : bond 0.04687 / 3.17 ( 512) hydrogen bonds : angle 4.68517 / 3.17 ( 1446) link_NAG-ASN : bond 0.00351 / 0.22 ( 20) link_NAG-ASN : angle 3.10027 / 2.09 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7196 (tmm) REVERT: A 342 ASP cc_start: 0.6778 (t0) cc_final: 0.6473 (t0) REVERT: A 397 ASN cc_start: 0.8638 (m-40) cc_final: 0.8419 (m110) REVERT: A 667 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8677 (m-40) REVERT: A 748 MET cc_start: 0.8457 (mmp) cc_final: 0.7985 (mmt) REVERT: A 903 GLN cc_start: 0.8779 (tp-100) cc_final: 0.8385 (tm-30) REVERT: B 133 GLN cc_start: 0.8379 (tm-30) cc_final: 0.8133 (tm-30) REVERT: B 230 LYS cc_start: 0.6839 (mmmm) cc_final: 0.6307 (ptpt) REVERT: B 342 ASP cc_start: 0.6781 (t0) cc_final: 0.6485 (t0) REVERT: B 397 ASN cc_start: 0.8635 (m-40) cc_final: 0.8424 (m110) REVERT: B 667 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8673 (m-40) REVERT: B 748 MET cc_start: 0.8465 (mmp) cc_final: 0.7988 (mmt) REVERT: B 903 GLN cc_start: 0.8765 (tp-100) cc_final: 0.8338 (tm-30) outliers start: 47 outliers final: 34 residues processed: 195 average time/residue: 0.0945 time to fit residues: 30.1081 Evaluate side-chains 174 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 667 ASN Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 890 ASP Chi-restraints excluded: chain B residue 959 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [56, 158, 179, 106, 63, 10, 45, 98, 144, 8, 51] chunk 56 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 10 optimal weight: 30.0000 chunk 45 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.141660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.109198 restraints weight = 28706.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109356 restraints weight = 19239.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.110394 restraints weight = 18435.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.111033 restraints weight = 14103.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.111319 restraints weight = 13095.847| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15240 Z= 0.177 Angle : 0.671 10.612 20792 Z= 0.337 Chirality : 0.047 0.420 2318 Planarity : 0.004 0.044 2658 Dihedral : 5.463 49.084 2378 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.28 % Favored : 91.67 % Rotamer: Outliers : 2.81 % Allowed : 15.25 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.20), residues: 1800 helix: 0.94 (0.21), residues: 696 sheet: -0.84 (0.35), residues: 230 loop : -1.84 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 829 TYR 0.014 0.002 TYR A 629 PHE 0.029 0.002 PHE B 413 TRP 0.012 0.001 TRP B 543 HIS 0.005 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (15216) covalent geometry : angle 0.64939 / 0.33 (20724) SS BOND : bond 0.00291 / 0.14 ( 4) SS BOND : angle 2.74663 / 1.90 ( 8) hydrogen bonds : bond 0.04661 / 3.14 ( 512) hydrogen bonds : angle 4.66477 / 3.16 ( 1446) link_NAG-ASN : bond 0.00379 / 0.24 ( 20) link_NAG-ASN : angle 3.05506 / 2.06 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7321 (tmm) REVERT: A 230 LYS cc_start: 0.7003 (mmmm) cc_final: 0.6355 (ptpt) REVERT: A 342 ASP cc_start: 0.7008 (t0) cc_final: 0.6748 (t0) REVERT: A 357 TRP cc_start: 0.6939 (OUTLIER) cc_final: 0.6642 (m-10) REVERT: A 397 ASN cc_start: 0.8802 (m-40) cc_final: 0.8080 (m110) REVERT: A 513 ILE cc_start: 0.7918 (mm) cc_final: 0.7675 (mp) REVERT: A 667 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8711 (m-40) REVERT: A 903 GLN cc_start: 0.8851 (tp-100) cc_final: 0.8323 (tm-30) REVERT: B 199 MET cc_start: 0.8145 (mmm) cc_final: 0.7274 (tmm) REVERT: B 342 ASP cc_start: 0.7004 (t0) cc_final: 0.6745 (t0) REVERT: B 357 TRP cc_start: 0.6960 (OUTLIER) cc_final: 0.6641 (m-10) REVERT: B 397 ASN cc_start: 0.8799 (m-40) cc_final: 0.8071 (m110) REVERT: B 513 ILE cc_start: 0.7912 (mm) cc_final: 0.7668 (mp) REVERT: B 667 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8710 (m-40) REVERT: B 903 GLN cc_start: 0.8847 (tp-100) cc_final: 0.8317 (tm-30) outliers start: 45 outliers final: 32 residues processed: 185 average time/residue: 0.1025 time to fit residues: 30.4332 Evaluate side-chains 178 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 357 TRP Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 667 ASN Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 890 ASP Chi-restraints excluded: chain B residue 959 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [178, 67, 76, 48, 34, 40, 138, 66, 93, 47, 103] chunk 178 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 93 optimal weight: 0.2980 chunk 47 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** 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 = 0.3893 r_free = 0.3893 target = 0.147129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113604 restraints weight = 28035.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114403 restraints weight = 23053.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.116924 restraints weight = 17134.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116946 restraints weight = 13445.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117214 restraints weight = 12712.632| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15240 Z= 0.107 Angle : 0.618 9.528 20792 Z= 0.308 Chirality : 0.044 0.383 2318 Planarity : 0.004 0.043 2658 Dihedral : 4.978 42.856 2378 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 2.38 % Allowed : 16.44 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.20), residues: 1800 helix: 1.14 (0.21), residues: 696 sheet: -0.71 (0.36), residues: 234 loop : -1.82 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 935 TYR 0.011 0.001 TYR A 289 PHE 0.029 0.002 PHE A 490 TRP 0.012 0.001 TRP B 961 HIS 0.005 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (15216) covalent geometry : angle 0.59039 / 0.30 (20724) SS BOND : bond 0.00379 / 0.19 ( 4) SS BOND : angle 5.58004 / 2.97 ( 8) hydrogen bonds : bond 0.03216 / 2.18 ( 512) hydrogen bonds : angle 4.44325 / 2.99 ( 1446) link_NAG-ASN : bond 0.00503 / 0.32 ( 20) link_NAG-ASN : angle 2.82248 / 1.93 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.7898 (mmm) cc_final: 0.7288 (tmm) REVERT: A 342 ASP cc_start: 0.6856 (t0) cc_final: 0.6538 (t0) REVERT: A 397 ASN cc_start: 0.8573 (m-40) cc_final: 0.7976 (m110) REVERT: A 467 GLN cc_start: 0.7399 (mm110) cc_final: 0.6778 (mp10) REVERT: A 513 ILE cc_start: 0.7867 (mm) cc_final: 0.7658 (mp) REVERT: A 667 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8688 (m-40) REVERT: A 817 ARG cc_start: 0.8486 (tpp80) cc_final: 0.8004 (tpp80) REVERT: A 903 GLN cc_start: 0.8742 (tp-100) cc_final: 0.8343 (tm-30) REVERT: B 199 MET cc_start: 0.7998 (mmm) cc_final: 0.7244 (tmm) REVERT: B 230 LYS cc_start: 0.6854 (mmmm) cc_final: 0.6436 (ptpt) REVERT: B 342 ASP cc_start: 0.6847 (t0) cc_final: 0.6532 (t0) REVERT: B 397 ASN cc_start: 0.8570 (m-40) cc_final: 0.7981 (m110) REVERT: B 467 GLN cc_start: 0.7351 (mm110) cc_final: 0.6800 (mp10) REVERT: B 513 ILE cc_start: 0.7875 (mm) cc_final: 0.7673 (mp) REVERT: B 667 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8691 (m-40) REVERT: B 817 ARG cc_start: 0.8496 (tpp80) cc_final: 0.8016 (tpp80) REVERT: B 903 GLN cc_start: 0.8713 (tp-100) cc_final: 0.8327 (tm-30) outliers start: 38 outliers final: 30 residues processed: 183 average time/residue: 0.1075 time to fit residues: 31.0501 Evaluate side-chains 177 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 667 ASN Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 890 ASP Chi-restraints excluded: chain B residue 959 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [27, 55, 150, 148, 37, 84, 134, 78, 6, 164, 66] chunk 27 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.143829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111629 restraints weight = 28536.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.111102 restraints weight = 21241.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.112270 restraints weight = 21721.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.112692 restraints weight = 17143.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.112947 restraints weight = 15354.156| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15240 Z= 0.131 Angle : 0.630 9.318 20792 Z= 0.314 Chirality : 0.045 0.378 2318 Planarity : 0.004 0.041 2658 Dihedral : 5.014 44.558 2378 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.75 % Allowed : 16.19 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.20), residues: 1800 helix: 1.22 (0.21), residues: 698 sheet: -0.92 (0.35), residues: 230 loop : -1.77 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 829 TYR 0.016 0.001 TYR B 514 PHE 0.026 0.002 PHE A 490 TRP 0.008 0.001 TRP B 961 HIS 0.005 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (15216) covalent geometry : angle 0.60899 / 0.31 (20724) SS BOND : bond 0.00266 / 0.13 ( 4) SS BOND : angle 3.94933 / 2.32 ( 8) hydrogen bonds : bond 0.03898 / 2.63 ( 512) hydrogen bonds : angle 4.34973 / 2.93 ( 1446) link_NAG-ASN : bond 0.00368 / 0.23 ( 20) link_NAG-ASN : angle 2.70666 / 1.85 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8583 (t0) cc_final: 0.8130 (p0) REVERT: A 178 MET cc_start: 0.6710 (tpt) cc_final: 0.6492 (tpt) REVERT: A 199 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7282 (tmm) REVERT: A 230 LYS cc_start: 0.7008 (mmmm) cc_final: 0.6337 (ptpt) REVERT: A 342 ASP cc_start: 0.6910 (t0) cc_final: 0.6595 (t0) REVERT: A 357 TRP cc_start: 0.6885 (OUTLIER) cc_final: 0.6472 (m-10) REVERT: A 397 ASN cc_start: 0.8709 (m-40) cc_final: 0.7578 (m110) REVERT: A 667 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8683 (m-40) REVERT: A 903 GLN cc_start: 0.8663 (tp-100) cc_final: 0.8299 (tm-30) REVERT: A 914 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: B 78 ASN cc_start: 0.8596 (t0) cc_final: 0.8148 (p0) REVERT: B 178 MET cc_start: 0.6706 (tpt) cc_final: 0.6492 (tpt) REVERT: B 199 MET cc_start: 0.8014 (mmm) cc_final: 0.7262 (tmm) REVERT: B 342 ASP cc_start: 0.6899 (t0) cc_final: 0.6596 (t0) REVERT: B 357 TRP cc_start: 0.6911 (OUTLIER) cc_final: 0.6481 (m-10) REVERT: B 397 ASN cc_start: 0.8701 (m-40) cc_final: 0.7536 (m110) REVERT: B 667 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8687 (m-40) REVERT: B 903 GLN cc_start: 0.8683 (tp-100) cc_final: 0.8296 (tm-30) REVERT: B 914 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7304 (mp0) outliers start: 44 outliers final: 29 residues processed: 183 average time/residue: 0.0927 time to fit residues: 27.6352 Evaluate side-chains 186 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 357 TRP Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 667 ASN Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 890 ASP Chi-restraints excluded: chain B residue 914 GLU Chi-restraints excluded: chain B residue 959 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [149, 60, 11, 4, 18, 139, 116, 119, 27, 176, 62] chunk 149 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 520 HIS B 520 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.140759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.108163 restraints weight = 29205.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.108209 restraints weight = 21391.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.109082 restraints weight = 20531.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.109560 restraints weight = 16656.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109903 restraints weight = 14680.335| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15240 Z= 0.161 Angle : 0.668 9.721 20792 Z= 0.334 Chirality : 0.046 0.399 2318 Planarity : 0.004 0.041 2658 Dihedral : 5.287 47.265 2378 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 3.00 % Allowed : 16.00 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.20), residues: 1800 helix: 1.09 (0.21), residues: 702 sheet: -0.91 (0.34), residues: 240 loop : -1.67 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 907 TYR 0.014 0.001 TYR A 514 PHE 0.025 0.002 PHE B 490 TRP 0.011 0.001 TRP B 543 HIS 0.005 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (15216) covalent geometry : angle 0.64793 / 0.33 (20724) SS BOND : bond 0.00287 / 0.14 ( 4) SS BOND : angle 3.59865 / 2.22 ( 8) hydrogen bonds : bond 0.04361 / 2.94 ( 512) hydrogen bonds : angle 4.47255 / 3.01 ( 1446) link_NAG-ASN : bond 0.00445 / 0.29 ( 20) link_NAG-ASN : angle 2.84285 / 1.92 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8648 (t0) cc_final: 0.8221 (p0) REVERT: A 199 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7223 (tmm) REVERT: A 342 ASP cc_start: 0.7100 (t0) cc_final: 0.6832 (t0) REVERT: A 357 TRP cc_start: 0.6951 (OUTLIER) cc_final: 0.6442 (m-10) REVERT: A 397 ASN cc_start: 0.8802 (m-40) cc_final: 0.7608 (m110) REVERT: A 667 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8713 (m-40) REVERT: A 709 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.8300 (p90) REVERT: A 748 MET cc_start: 0.8458 (mmp) cc_final: 0.8258 (mmm) REVERT: A 903 GLN cc_start: 0.8712 (tp-100) cc_final: 0.8231 (tm-30) REVERT: A 914 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: B 78 ASN cc_start: 0.8666 (t0) cc_final: 0.8231 (p0) REVERT: B 199 MET cc_start: 0.7979 (mmm) cc_final: 0.7218 (tmm) REVERT: B 230 LYS cc_start: 0.6889 (mmmm) cc_final: 0.6442 (ptmm) REVERT: B 342 ASP cc_start: 0.7096 (t0) cc_final: 0.6832 (t0) REVERT: B 357 TRP cc_start: 0.7027 (OUTLIER) cc_final: 0.6527 (m-10) REVERT: B 397 ASN cc_start: 0.8788 (m-40) cc_final: 0.7614 (m110) REVERT: B 667 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8724 (m-40) REVERT: B 709 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8254 (p90) REVERT: B 903 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8232 (tm-30) REVERT: B 914 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7363 (mp0) outliers start: 48 outliers final: 37 residues processed: 193 average time/residue: 0.0962 time to fit residues: 30.1360 Evaluate side-chains 198 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 152 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 357 TRP Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 667 ASN Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 890 ASP Chi-restraints excluded: chain B residue 914 GLU Chi-restraints excluded: chain B residue 959 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [50, 147, 84, 113, 5, 135, 42, 7, 173, 124, 76] chunk 50 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.136977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.104406 restraints weight = 29304.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.105211 restraints weight = 21769.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.105620 restraints weight = 20548.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.106239 restraints weight = 16628.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106508 restraints weight = 14709.462| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15240 Z= 0.204 Angle : 0.721 9.621 20792 Z= 0.363 Chirality : 0.048 0.408 2318 Planarity : 0.004 0.041 2658 Dihedral : 5.923 50.739 2378 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 2.94 % Allowed : 17.19 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.20), residues: 1800 helix: 0.99 (0.21), residues: 702 sheet: -0.92 (0.33), residues: 250 loop : -1.79 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 829 TYR 0.026 0.002 TYR B 514 PHE 0.026 0.002 PHE B 413 TRP 0.014 0.001 TRP A 543 HIS 0.005 0.001 HIS B 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 (15216) covalent geometry : angle 0.69442 / 0.36 (20724) SS BOND : bond 0.00260 / 0.13 ( 4) SS BOND : angle 3.50566 / 2.24 ( 8) hydrogen bonds : bond 0.05050 / 3.41 ( 512) hydrogen bonds : angle 4.60111 / 3.11 ( 1446) link_NAG-ASN : bond 0.00602 / 0.32 ( 20) link_NAG-ASN : angle 3.42505 / 2.32 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8855 (t0) cc_final: 0.8362 (p0) REVERT: A 199 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7124 (tmm) REVERT: A 230 LYS cc_start: 0.7611 (mmmm) cc_final: 0.6445 (ptmm) REVERT: A 342 ASP cc_start: 0.7232 (t0) cc_final: 0.7029 (t0) REVERT: A 357 TRP cc_start: 0.7128 (OUTLIER) cc_final: 0.6538 (m-10) REVERT: A 397 ASN cc_start: 0.8871 (m-40) cc_final: 0.7607 (m110) REVERT: A 667 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8685 (m-40) REVERT: A 748 MET cc_start: 0.8586 (mmp) cc_final: 0.8332 (mmm) REVERT: A 903 GLN cc_start: 0.8797 (tp-100) cc_final: 0.8166 (tm-30) REVERT: A 914 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: B 78 ASN cc_start: 0.8832 (t0) cc_final: 0.8344 (p0) REVERT: B 199 MET cc_start: 0.7862 (mmm) cc_final: 0.7173 (tmm) REVERT: B 230 LYS cc_start: 0.7768 (mmmm) cc_final: 0.6486 (pttp) REVERT: B 342 ASP cc_start: 0.7246 (t0) cc_final: 0.7027 (t0) REVERT: B 357 TRP cc_start: 0.7113 (OUTLIER) cc_final: 0.6554 (m-10) REVERT: B 397 ASN cc_start: 0.8856 (m-40) cc_final: 0.7582 (m110) REVERT: B 439 ASP cc_start: 0.9170 (m-30) cc_final: 0.8830 (m-30) REVERT: B 667 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8684 (m-40) REVERT: B 903 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8168 (tm-30) REVERT: B 914 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7573 (mp0) outliers start: 47 outliers final: 35 residues processed: 192 average time/residue: 0.0895 time to fit residues: 28.1721 Evaluate side-chains 187 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 357 TRP Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 667 ASN Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 890 ASP Chi-restraints excluded: chain B residue 914 GLU Chi-restraints excluded: chain B residue 959 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [69, 65, 109, 41, 79, 67, 30, 171, 77, 68, 45] chunk 69 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 45 optimal weight: 10.0000 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.141607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.107440 restraints weight = 28814.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.109983 restraints weight = 20740.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.110924 restraints weight = 14350.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.111403 restraints weight = 12472.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.111579 restraints weight = 11404.598| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15240 Z= 0.127 Angle : 0.685 8.831 20792 Z= 0.339 Chirality : 0.047 0.382 2318 Planarity : 0.004 0.043 2658 Dihedral : 5.419 45.699 2378 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.19 % Allowed : 18.31 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.20), residues: 1800 helix: 1.15 (0.21), residues: 702 sheet: -0.73 (0.34), residues: 250 loop : -1.73 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 829 TYR 0.025 0.001 TYR A 514 PHE 0.028 0.002 PHE A 490 TRP 0.008 0.001 TRP A 404 HIS 0.004 0.001 HIS B 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (15216) covalent geometry : angle 0.66104 / 0.33 (20724) SS BOND : bond 0.00324 / 0.16 ( 4) SS BOND : angle 3.04278 / 1.94 ( 8) hydrogen bonds : bond 0.03834 / 2.55 ( 512) hydrogen bonds : angle 4.35391 / 2.93 ( 1446) link_NAG-ASN : bond 0.00494 / 0.29 ( 20) link_NAG-ASN : angle 3.21897 / 2.21 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8889 (t0) cc_final: 0.8327 (p0) REVERT: A 199 MET cc_start: 0.7849 (mmm) cc_final: 0.7173 (tmm) REVERT: A 212 MET cc_start: 0.8412 (mmm) cc_final: 0.8174 (mmm) REVERT: A 342 ASP cc_start: 0.7220 (t0) cc_final: 0.6968 (t0) REVERT: A 397 ASN cc_start: 0.8724 (m-40) cc_final: 0.7920 (m110) REVERT: A 439 ASP cc_start: 0.9104 (m-30) cc_final: 0.8773 (m-30) REVERT: A 667 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8666 (m-40) REVERT: A 748 MET cc_start: 0.8438 (mmp) cc_final: 0.8076 (mmm) REVERT: A 817 ARG cc_start: 0.8544 (tpp80) cc_final: 0.7997 (tpp80) REVERT: A 903 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8134 (tm-30) REVERT: A 914 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: B 78 ASN cc_start: 0.8907 (t0) cc_final: 0.8387 (p0) REVERT: B 199 MET cc_start: 0.7925 (mmm) cc_final: 0.7203 (tmm) REVERT: B 212 MET cc_start: 0.8327 (mmm) cc_final: 0.8100 (mmm) REVERT: B 230 LYS cc_start: 0.7487 (mmmm) cc_final: 0.6168 (ptmm) REVERT: B 342 ASP cc_start: 0.7207 (t0) cc_final: 0.6973 (t0) REVERT: B 397 ASN cc_start: 0.8731 (m-40) cc_final: 0.7938 (m110) REVERT: B 439 ASP cc_start: 0.9139 (m-30) cc_final: 0.8836 (m-30) REVERT: B 667 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8669 (m-40) REVERT: B 817 ARG cc_start: 0.8555 (tpp80) cc_final: 0.8008 (tpp80) REVERT: B 903 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8131 (tm-30) REVERT: B 914 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7526 (mp0) outliers start: 35 outliers final: 30 residues processed: 189 average time/residue: 0.0982 time to fit residues: 29.9033 Evaluate side-chains 185 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 890 ASP Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 667 ASN Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 890 ASP Chi-restraints excluded: chain B residue 914 GLU Chi-restraints excluded: chain B residue 959 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [6, 33, 73, 105, 117, 92, 176, 130, 163, 171, 4] chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 92 optimal weight: 0.0170 chunk 176 optimal weight: 9.9990 chunk 130 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 135 HIS ** 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 = 0.3820 r_free = 0.3820 target = 0.141450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.109414 restraints weight = 28912.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109505 restraints weight = 19976.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.110583 restraints weight = 19153.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.111116 restraints weight = 14900.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.111393 restraints weight = 13808.042| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15240 Z= 0.130 Angle : 0.680 8.947 20792 Z= 0.335 Chirality : 0.047 0.371 2318 Planarity : 0.004 0.042 2658 Dihedral : 5.205 44.964 2378 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.50 % Allowed : 17.88 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1800 helix: 1.26 (0.21), residues: 696 sheet: -0.66 (0.34), residues: 250 loop : -1.68 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 829 TYR 0.025 0.001 TYR B 514 PHE 0.027 0.002 PHE A 490 TRP 0.008 0.001 TRP B 303 HIS 0.004 0.001 HIS B 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (15216) covalent geometry : angle 0.65756 / 0.33 (20724) SS BOND : bond 0.00635 / 0.32 ( 4) SS BOND : angle 3.32803 / 2.09 ( 8) hydrogen bonds : bond 0.03890 / 2.61 ( 512) hydrogen bonds : angle 4.28735 / 2.88 ( 1446) link_NAG-ASN : bond 0.00488 / 0.28 ( 20) link_NAG-ASN : angle 3.05822 / 2.11 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2050.51 seconds wall clock time: 36 minutes 22.30 seconds (2182.30 seconds total)