Starting phenix.real_space_refine on Sun Jul 5 22:40:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p3r_71252/07_2026/9p3r_71252_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p3r_71252/07_2026/9p3r_71252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p3r_71252/07_2026/9p3r_71252_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p3r_71252/07_2026/9p3r_71252_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p3r_71252/07_2026/9p3r_71252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p3r_71252/07_2026/9p3r_71252.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 176 5.16 5 C 19768 2.51 5 N 5124 2.21 5 O 5060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 124 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30132 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7518 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 524 Unresolved non-hydrogen angles: 646 Unresolved non-hydrogen dihedrals: 412 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 31, 'ARG:plan': 11, 'GLU:plan': 32, 'GLN:plan1': 14, 'HIS:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 365 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D Time building chain proxies: 8.34, per 1000 atoms: 0.28 Number of scatterers: 30132 At special positions: 0 Unit cell: (136.29, 136.29, 155.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 176 16.00 O 5060 8.00 N 5124 7.00 C 19768 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1501 " - " ASN A 921 " " NAG B1501 " - " ASN B 921 " " NAG C1501 " - " ASN C 921 " " NAG D1501 " - " ASN D 921 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.1 seconds 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7600 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 12 sheets defined 70.9% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 40 through 50 removed outlier: 3.746A pdb=" N ILE A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 91 removed outlier: 3.783A pdb=" N SER A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.630A pdb=" N LYS A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 139 through 145 removed outlier: 3.891A pdb=" N LEU A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 201 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.739A pdb=" N ILE A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 275 Processing helix chain 'A' and resid 280 through 298 Processing helix chain 'A' and resid 311 through 328 removed outlier: 3.621A pdb=" N VAL A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 333 Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 366 through 376 Processing helix chain 'A' and resid 378 through 388 Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 397 through 407 Processing helix chain 'A' and resid 412 through 429 removed outlier: 3.879A pdb=" N THR A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 463 removed outlier: 3.570A pdb=" N VAL A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 460 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.678A pdb=" N GLN A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 526 through 545 Processing helix chain 'A' and resid 547 through 555 removed outlier: 3.661A pdb=" N ALA A 551 " --> pdb=" O GLU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 574 removed outlier: 3.507A pdb=" N PHE A 562 " --> pdb=" O LYS A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 584 removed outlier: 4.168A pdb=" N SER A 580 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 602 Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 609 through 622 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 699 through 714 Processing helix chain 'A' and resid 715 through 741 Processing helix chain 'A' and resid 751 through 774 Processing helix chain 'A' and resid 780 through 791 removed outlier: 3.986A pdb=" N ASP A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 812 Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'A' and resid 816 through 839 removed outlier: 4.094A pdb=" N ILE A 836 " --> pdb=" O THR A 832 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N HIS A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE A 838 " --> pdb=" O ARG A 834 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A 839 " --> pdb=" O LEU A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 842 No H-bonds generated for 'chain 'A' and resid 840 through 842' Processing helix chain 'A' and resid 845 through 882 removed outlier: 3.601A pdb=" N ILE A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 850 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 864 " --> pdb=" O PHE A 860 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE A 865 " --> pdb=" O PHE A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 903 removed outlier: 5.068A pdb=" N ARG A 898 " --> pdb=" O ARG A 894 " (cutoff:3.500A) Proline residue: A 899 - end of helix removed outlier: 3.803A pdb=" N ILE A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 925 through 932 Processing helix chain 'A' and resid 942 through 958 removed outlier: 3.623A pdb=" N VAL A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 979 removed outlier: 3.962A pdb=" N ASN A 979 " --> pdb=" O VAL A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 997 removed outlier: 4.338A pdb=" N PHE A 983 " --> pdb=" O ASN A 979 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER A 997 " --> pdb=" O VAL A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.912A pdb=" N SER A1009 " --> pdb=" O PHE A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1062 Processing helix chain 'A' and resid 1063 through 1092 removed outlier: 3.781A pdb=" N GLN A1076 " --> pdb=" O SER A1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 50 removed outlier: 3.747A pdb=" N ILE B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 91 removed outlier: 3.783A pdb=" N SER B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 119 removed outlier: 3.630A pdb=" N LYS B 106 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 139 through 145 removed outlier: 3.891A pdb=" N LEU B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER B 145 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 248 through 260 removed outlier: 3.738A pdb=" N ILE B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 280 through 298 Processing helix chain 'B' and resid 311 through 328 removed outlier: 3.622A pdb=" N VAL B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 333 Processing helix chain 'B' and resid 334 through 345 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 366 through 376 Processing helix chain 'B' and resid 378 through 388 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 397 through 407 Processing helix chain 'B' and resid 412 through 429 removed outlier: 3.878A pdb=" N THR B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 463 removed outlier: 3.570A pdb=" N VAL B 454 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B 460 " --> pdb=" O LYS B 456 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 511 removed outlier: 3.678A pdb=" N GLN B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 523 Processing helix chain 'B' and resid 526 through 545 Processing helix chain 'B' and resid 547 through 555 removed outlier: 3.661A pdb=" N ALA B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 574 removed outlier: 3.506A pdb=" N PHE B 562 " --> pdb=" O LYS B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 584 removed outlier: 4.169A pdb=" N SER B 580 " --> pdb=" O ASP B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 602 Processing helix chain 'B' and resid 603 through 608 Processing helix chain 'B' and resid 609 through 622 Processing helix chain 'B' and resid 629 through 639 Processing helix chain 'B' and resid 640 through 645 Processing helix chain 'B' and resid 699 through 714 Processing helix chain 'B' and resid 715 through 741 Processing helix chain 'B' and resid 751 through 774 Processing helix chain 'B' and resid 780 through 791 removed outlier: 3.985A pdb=" N ASP B 791 " --> pdb=" O LEU B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 812 Processing helix chain 'B' and resid 813 through 815 No H-bonds generated for 'chain 'B' and resid 813 through 815' Processing helix chain 'B' and resid 816 through 839 removed outlier: 4.094A pdb=" N ILE B 836 " --> pdb=" O THR B 832 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N HIS B 837 " --> pdb=" O LEU B 833 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE B 838 " --> pdb=" O ARG B 834 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE B 839 " --> pdb=" O LEU B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 842 No H-bonds generated for 'chain 'B' and resid 840 through 842' Processing helix chain 'B' and resid 845 through 882 removed outlier: 3.601A pdb=" N ILE B 849 " --> pdb=" O LEU B 845 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 850 " --> pdb=" O GLY B 846 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE B 864 " --> pdb=" O PHE B 860 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE B 865 " --> pdb=" O PHE B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 903 removed outlier: 5.067A pdb=" N ARG B 898 " --> pdb=" O ARG B 894 " (cutoff:3.500A) Proline residue: B 899 - end of helix removed outlier: 3.803A pdb=" N ILE B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 917 Processing helix chain 'B' and resid 925 through 932 Processing helix chain 'B' and resid 942 through 958 removed outlier: 3.623A pdb=" N VAL B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 979 removed outlier: 3.962A pdb=" N ASN B 979 " --> pdb=" O VAL B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 997 removed outlier: 4.338A pdb=" N PHE B 983 " --> pdb=" O ASN B 979 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER B 997 " --> pdb=" O VAL B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1020 removed outlier: 3.912A pdb=" N SER B1009 " --> pdb=" O PHE B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1062 Processing helix chain 'B' and resid 1063 through 1092 removed outlier: 3.782A pdb=" N GLN B1076 " --> pdb=" O SER B1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 50 removed outlier: 3.747A pdb=" N ILE C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 91 removed outlier: 3.783A pdb=" N SER C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 119 removed outlier: 3.630A pdb=" N LYS C 106 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 139 through 145 removed outlier: 3.891A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER C 145 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 248 through 260 removed outlier: 3.739A pdb=" N ILE C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 275 Processing helix chain 'C' and resid 280 through 298 Processing helix chain 'C' and resid 311 through 328 removed outlier: 3.621A pdb=" N VAL C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 333 Processing helix chain 'C' and resid 334 through 345 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 366 through 376 Processing helix chain 'C' and resid 378 through 388 Processing helix chain 'C' and resid 391 through 396 Processing helix chain 'C' and resid 397 through 407 Processing helix chain 'C' and resid 412 through 429 removed outlier: 3.879A pdb=" N THR C 416 " --> pdb=" O ASN C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 463 removed outlier: 3.570A pdb=" N VAL C 454 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C 460 " --> pdb=" O LYS C 456 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE C 461 " --> pdb=" O VAL C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 511 removed outlier: 3.678A pdb=" N GLN C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 523 Processing helix chain 'C' and resid 526 through 545 Processing helix chain 'C' and resid 547 through 555 removed outlier: 3.661A pdb=" N ALA C 551 " --> pdb=" O GLU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 574 removed outlier: 3.507A pdb=" N PHE C 562 " --> pdb=" O LYS C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 584 removed outlier: 4.168A pdb=" N SER C 580 " --> pdb=" O ASP C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 602 Processing helix chain 'C' and resid 603 through 608 Processing helix chain 'C' and resid 609 through 622 Processing helix chain 'C' and resid 629 through 639 Processing helix chain 'C' and resid 640 through 645 Processing helix chain 'C' and resid 699 through 714 Processing helix chain 'C' and resid 715 through 741 Processing helix chain 'C' and resid 751 through 774 Processing helix chain 'C' and resid 780 through 791 removed outlier: 3.985A pdb=" N ASP C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 812 Processing helix chain 'C' and resid 813 through 815 No H-bonds generated for 'chain 'C' and resid 813 through 815' Processing helix chain 'C' and resid 816 through 839 removed outlier: 4.094A pdb=" N ILE C 836 " --> pdb=" O THR C 832 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N HIS C 837 " --> pdb=" O LEU C 833 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 838 " --> pdb=" O ARG C 834 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE C 839 " --> pdb=" O LEU C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 842 No H-bonds generated for 'chain 'C' and resid 840 through 842' Processing helix chain 'C' and resid 845 through 882 removed outlier: 3.602A pdb=" N ILE C 849 " --> pdb=" O LEU C 845 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 850 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE C 864 " --> pdb=" O PHE C 860 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE C 865 " --> pdb=" O PHE C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 903 removed outlier: 5.067A pdb=" N ARG C 898 " --> pdb=" O ARG C 894 " (cutoff:3.500A) Proline residue: C 899 - end of helix removed outlier: 3.803A pdb=" N ILE C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 917 Processing helix chain 'C' and resid 925 through 932 Processing helix chain 'C' and resid 942 through 958 removed outlier: 3.622A pdb=" N VAL C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 979 removed outlier: 3.962A pdb=" N ASN C 979 " --> pdb=" O VAL C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 997 removed outlier: 4.338A pdb=" N PHE C 983 " --> pdb=" O ASN C 979 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER C 997 " --> pdb=" O VAL C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1020 removed outlier: 3.912A pdb=" N SER C1009 " --> pdb=" O PHE C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1062 Processing helix chain 'C' and resid 1063 through 1092 removed outlier: 3.781A pdb=" N GLN C1076 " --> pdb=" O SER C1072 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 50 removed outlier: 3.747A pdb=" N ILE D 44 " --> pdb=" O ASP D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 91 removed outlier: 3.783A pdb=" N SER D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 119 removed outlier: 3.630A pdb=" N LYS D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN D 107 " --> pdb=" O GLY D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 137 No H-bonds generated for 'chain 'D' and resid 135 through 137' Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.891A pdb=" N LEU D 143 " --> pdb=" O ASN D 139 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER D 145 " --> pdb=" O ASP D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 201 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 226 through 236 Processing helix chain 'D' and resid 248 through 260 removed outlier: 3.739A pdb=" N ILE D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 275 Processing helix chain 'D' and resid 280 through 298 Processing helix chain 'D' and resid 311 through 328 removed outlier: 3.621A pdb=" N VAL D 315 " --> pdb=" O GLU D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 333 Processing helix chain 'D' and resid 334 through 345 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 366 through 376 Processing helix chain 'D' and resid 378 through 388 Processing helix chain 'D' and resid 391 through 396 Processing helix chain 'D' and resid 397 through 407 Processing helix chain 'D' and resid 412 through 429 removed outlier: 3.879A pdb=" N THR D 416 " --> pdb=" O ASN D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 463 removed outlier: 3.570A pdb=" N VAL D 454 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP D 460 " --> pdb=" O LYS D 456 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 511 removed outlier: 3.677A pdb=" N GLN D 511 " --> pdb=" O TRP D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 523 Processing helix chain 'D' and resid 526 through 545 Processing helix chain 'D' and resid 547 through 555 removed outlier: 3.661A pdb=" N ALA D 551 " --> pdb=" O GLU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 574 removed outlier: 3.507A pdb=" N PHE D 562 " --> pdb=" O LYS D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 584 removed outlier: 4.169A pdb=" N SER D 580 " --> pdb=" O ASP D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 602 Processing helix chain 'D' and resid 603 through 608 Processing helix chain 'D' and resid 609 through 622 Processing helix chain 'D' and resid 629 through 639 Processing helix chain 'D' and resid 640 through 645 Processing helix chain 'D' and resid 699 through 714 Processing helix chain 'D' and resid 715 through 741 Processing helix chain 'D' and resid 751 through 774 Processing helix chain 'D' and resid 780 through 791 removed outlier: 3.986A pdb=" N ASP D 791 " --> pdb=" O LEU D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 812 Processing helix chain 'D' and resid 813 through 815 No H-bonds generated for 'chain 'D' and resid 813 through 815' Processing helix chain 'D' and resid 816 through 839 removed outlier: 4.094A pdb=" N ILE D 836 " --> pdb=" O THR D 832 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N HIS D 837 " --> pdb=" O LEU D 833 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE D 838 " --> pdb=" O ARG D 834 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE D 839 " --> pdb=" O LEU D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 842 No H-bonds generated for 'chain 'D' and resid 840 through 842' Processing helix chain 'D' and resid 845 through 882 removed outlier: 3.600A pdb=" N ILE D 849 " --> pdb=" O LEU D 845 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE D 850 " --> pdb=" O GLY D 846 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE D 864 " --> pdb=" O PHE D 860 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE D 865 " --> pdb=" O PHE D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 903 removed outlier: 5.067A pdb=" N ARG D 898 " --> pdb=" O ARG D 894 " (cutoff:3.500A) Proline residue: D 899 - end of helix removed outlier: 3.803A pdb=" N ILE D 903 " --> pdb=" O PRO D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 917 Processing helix chain 'D' and resid 925 through 932 Processing helix chain 'D' and resid 942 through 958 removed outlier: 3.623A pdb=" N VAL D 946 " --> pdb=" O ALA D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 960 through 979 removed outlier: 3.962A pdb=" N ASN D 979 " --> pdb=" O VAL D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 997 removed outlier: 4.338A pdb=" N PHE D 983 " --> pdb=" O ASN D 979 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER D 997 " --> pdb=" O VAL D 993 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1020 removed outlier: 3.912A pdb=" N SER D1009 " --> pdb=" O PHE D1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 1034 through 1062 Processing helix chain 'D' and resid 1063 through 1092 removed outlier: 3.781A pdb=" N GLN D1076 " --> pdb=" O SER D1072 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 133 removed outlier: 6.338A pdb=" N GLY A 130 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A 177 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA A 132 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N PHE A 174 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS A 31 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU A 176 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 33 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR A 28 " --> pdb=" O PHE A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 96 removed outlier: 6.103A pdb=" N VAL A 60 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU A 218 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA A 62 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL A 220 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N MET A 64 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N LEU A 241 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N CYS A 217 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU A 243 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU A 219 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 204 Processing sheet with id=AA4, first strand: chain 'B' and resid 129 through 133 removed outlier: 6.338A pdb=" N GLY B 130 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL B 177 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA B 132 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N PHE B 174 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS B 31 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU B 176 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL B 33 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR B 28 " --> pdb=" O PHE B 22 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 93 through 96 removed outlier: 6.103A pdb=" N VAL B 60 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU B 218 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA B 62 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL B 220 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N MET B 64 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N LEU B 241 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N CYS B 217 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU B 243 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU B 219 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 204 Processing sheet with id=AA7, first strand: chain 'C' and resid 129 through 133 removed outlier: 6.338A pdb=" N GLY C 130 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL C 177 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA C 132 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N PHE C 174 " --> pdb=" O ARG C 29 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS C 31 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU C 176 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL C 33 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR C 28 " --> pdb=" O PHE C 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 93 through 96 removed outlier: 6.103A pdb=" N VAL C 60 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU C 218 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA C 62 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL C 220 " --> pdb=" O ALA C 62 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N MET C 64 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N LEU C 241 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N CYS C 217 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU C 243 " --> pdb=" O CYS C 217 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU C 219 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 202 through 204 Processing sheet with id=AB1, first strand: chain 'D' and resid 129 through 133 removed outlier: 6.337A pdb=" N GLY D 130 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL D 177 " --> pdb=" O GLY D 130 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA D 132 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N PHE D 174 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS D 31 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU D 176 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL D 33 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR D 28 " --> pdb=" O PHE D 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 93 through 96 removed outlier: 6.102A pdb=" N VAL D 60 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU D 218 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA D 62 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL D 220 " --> pdb=" O ALA D 62 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N MET D 64 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N LEU D 241 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N CYS D 217 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU D 243 " --> pdb=" O CYS D 217 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU D 219 " --> pdb=" O LEU D 243 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 202 through 204 1964 hydrogen bonds defined for protein. 5796 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: 6.75 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4576 1.31 - 1.44: 8496 1.44 - 1.56: 17520 1.56 - 1.69: 0 1.69 - 1.82: 292 Bond restraints: 30884 Sorted by residual: bond pdb=" C ASP D 387 " pdb=" O ASP D 387 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.17e-02 7.31e+03 2.30e+01 bond pdb=" C ASP A 387 " pdb=" O ASP A 387 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.17e-02 7.31e+03 2.27e+01 bond pdb=" C ASP B 387 " pdb=" O ASP B 387 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.17e-02 7.31e+03 2.26e+01 bond pdb=" C ASP C 387 " pdb=" O ASP C 387 " ideal model delta sigma weight residual 1.237 1.182 0.055 1.17e-02 7.31e+03 2.20e+01 bond pdb=" N ILE D 238 " pdb=" CA ILE D 238 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.60e-03 1.73e+04 1.89e+01 ... (remaining 30879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 37664 1.75 - 3.50: 3710 3.50 - 5.25: 719 5.25 - 7.00: 67 7.00 - 8.75: 8 Bond angle restraints: 42168 Sorted by residual: angle pdb=" CA LYS B 73 " pdb=" C LYS B 73 " pdb=" N PRO B 74 " ideal model delta sigma weight residual 117.79 124.35 -6.56 1.08e+00 8.57e-01 3.69e+01 angle pdb=" CA LYS A 73 " pdb=" C LYS A 73 " pdb=" N PRO A 74 " ideal model delta sigma weight residual 117.79 124.34 -6.55 1.08e+00 8.57e-01 3.67e+01 angle pdb=" CA LYS C 73 " pdb=" C LYS C 73 " pdb=" N PRO C 74 " ideal model delta sigma weight residual 117.79 124.32 -6.53 1.08e+00 8.57e-01 3.65e+01 angle pdb=" CA LYS D 73 " pdb=" C LYS D 73 " pdb=" N PRO D 74 " ideal model delta sigma weight residual 117.79 124.31 -6.52 1.08e+00 8.57e-01 3.65e+01 angle pdb=" CA MET D 968 " pdb=" C MET D 968 " pdb=" O MET D 968 " ideal model delta sigma weight residual 120.82 115.72 5.10 1.05e+00 9.07e-01 2.36e+01 ... (remaining 42163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 16717 21.25 - 42.51: 1175 42.51 - 63.76: 208 63.76 - 85.02: 40 85.02 - 106.27: 32 Dihedral angle restraints: 18172 sinusoidal: 6492 harmonic: 11680 Sorted by residual: dihedral pdb=" O3 NAG D1501 " pdb=" C3 NAG D1501 " pdb=" C4 NAG D1501 " pdb=" O4 NAG D1501 " ideal model delta sinusoidal sigma weight residual -64.55 -170.82 106.27 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" C5 NAG D1501 " pdb=" C3 NAG D1501 " pdb=" C4 NAG D1501 " pdb=" O3 NAG D1501 " ideal model delta sinusoidal sigma weight residual -174.13 -67.89 -106.24 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" C5 NAG A1501 " pdb=" C3 NAG A1501 " pdb=" C4 NAG A1501 " pdb=" O3 NAG A1501 " ideal model delta sinusoidal sigma weight residual -174.13 -67.89 -106.24 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 18169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3574 0.052 - 0.104: 877 0.104 - 0.156: 394 0.156 - 0.208: 115 0.208 - 0.260: 40 Chirality restraints: 5000 Sorted by residual: chirality pdb=" CA ILE C 850 " pdb=" N ILE C 850 " pdb=" C ILE C 850 " pdb=" CB ILE C 850 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ILE D 850 " pdb=" N ILE D 850 " pdb=" C ILE D 850 " pdb=" CB ILE D 850 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA LEU B 241 " pdb=" N LEU B 241 " pdb=" C LEU B 241 " pdb=" CB LEU B 241 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 4997 not shown) Planarity restraints: 5220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1501 " -0.098 2.00e-02 2.50e+03 8.09e-02 8.19e+01 pdb=" C7 NAG C1501 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG C1501 " -0.075 2.00e-02 2.50e+03 pdb=" N2 NAG C1501 " 0.128 2.00e-02 2.50e+03 pdb=" O7 NAG C1501 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1501 " 0.098 2.00e-02 2.50e+03 8.09e-02 8.19e+01 pdb=" C7 NAG B1501 " -0.028 2.00e-02 2.50e+03 pdb=" C8 NAG B1501 " 0.075 2.00e-02 2.50e+03 pdb=" N2 NAG B1501 " -0.128 2.00e-02 2.50e+03 pdb=" O7 NAG B1501 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1501 " 0.098 2.00e-02 2.50e+03 8.09e-02 8.17e+01 pdb=" C7 NAG A1501 " -0.027 2.00e-02 2.50e+03 pdb=" C8 NAG A1501 " 0.074 2.00e-02 2.50e+03 pdb=" N2 NAG A1501 " -0.128 2.00e-02 2.50e+03 pdb=" O7 NAG A1501 " -0.017 2.00e-02 2.50e+03 ... (remaining 5217 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3992 2.76 - 3.29: 31044 3.29 - 3.83: 49720 3.83 - 4.36: 58878 4.36 - 4.90: 100855 Nonbonded interactions: 244489 Sorted by model distance: nonbonded pdb=" OG SER B 362 " pdb=" OD2 ASP B 365 " model vdw 2.220 3.040 nonbonded pdb=" OG SER D 362 " pdb=" OD2 ASP D 365 " model vdw 2.220 3.040 nonbonded pdb=" OG SER A 362 " pdb=" OD2 ASP A 365 " model vdw 2.220 3.040 nonbonded pdb=" OG SER C 362 " pdb=" OD2 ASP C 365 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASP D 336 " pdb=" N GLU D 337 " model vdw 2.381 3.120 ... (remaining 244484 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 4.820 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: 0.040 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.470 Find NCS groups from input model: 0.300 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 : 0.007 0.098 30888 Z= 0.514 Angle : 1.078 8.746 42180 Z= 0.798 Chirality : 0.062 0.260 5000 Planarity : 0.006 0.081 5216 Dihedral : 15.888 106.270 10572 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.61 % Allowed : 3.70 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.02 (0.14), residues: 3944 helix: 1.15 (0.10), residues: 2528 sheet: 0.42 (0.27), residues: 300 loop : -0.15 (0.21), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 81 TYR 0.039 0.002 TYR B1070 PHE 0.021 0.002 PHE B 730 TRP 0.015 0.002 TRP D 620 HIS 0.009 0.002 HIS D 902 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.51 (30884) covalent geometry : angle 1.07488 / 0.80 (42168) hydrogen bonds : bond 0.16315 / 11.42 ( 1964) hydrogen bonds : angle 6.62923 / 4.83 ( 5796) link_NAG-ASN : bond 0.09783 / 4.90 ( 4) link_NAG-ASN : angle 4.64471 / 2.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 628 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8455 (mmmt) REVERT: A 959 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7851 (t) REVERT: B 420 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8385 (mmtm) REVERT: B 421 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8548 (mmpt) REVERT: C 89 GLN cc_start: 0.7463 (tt0) cc_final: 0.7168 (tt0) REVERT: C 421 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8576 (mmmt) REVERT: D 421 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8599 (mmmt) outliers start: 76 outliers final: 3 residues processed: 687 average time/residue: 0.1681 time to fit residues: 187.7024 Evaluate side-chains 371 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 362 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 421 LYS Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain C residue 420 LYS Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain D residue 421 LYS Chi-restraints excluded: chain D residue 796 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.0570 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 overall best weight: 2.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 943 ASN A1076 GLN B 107 ASN B 943 ASN B1076 GLN C 107 ASN C 943 ASN C1076 GLN D 107 ASN D 943 ASN D1076 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.085590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.065511 restraints weight = 84317.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.068046 restraints weight = 39109.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.069773 restraints weight = 24208.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.070939 restraints weight = 17716.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.071566 restraints weight = 14422.140| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 30888 Z= 0.195 Angle : 0.619 8.926 42180 Z= 0.315 Chirality : 0.041 0.202 5000 Planarity : 0.005 0.050 5216 Dihedral : 7.511 68.872 4358 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.92 % Allowed : 11.73 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.98 (0.14), residues: 3944 helix: 1.98 (0.10), residues: 2552 sheet: 0.50 (0.28), residues: 296 loop : 0.02 (0.21), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 225 TYR 0.019 0.002 TYR B 559 PHE 0.014 0.001 PHE C 828 TRP 0.017 0.001 TRP A 984 HIS 0.005 0.001 HIS D 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (30884) covalent geometry : angle 0.61847 / 0.31 (42168) hydrogen bonds : bond 0.04435 / 3.09 ( 1964) hydrogen bonds : angle 4.10633 / 2.98 ( 5796) link_NAG-ASN : bond 0.00032 / 0.02 ( 4) link_NAG-ASN : angle 1.11314 / 0.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 361 time to evaluate : 1.178 Fit side-chains REVERT: A 194 MET cc_start: 0.8695 (tpp) cc_final: 0.8386 (tpp) REVERT: A 205 TYR cc_start: 0.6895 (p90) cc_final: 0.6648 (p90) REVERT: A 493 MET cc_start: 0.8386 (mmt) cc_final: 0.7546 (mmt) REVERT: A 496 ARG cc_start: 0.8455 (ptp-110) cc_final: 0.8115 (mtm-85) REVERT: A 569 GLU cc_start: 0.8791 (tp30) cc_final: 0.8588 (tp30) REVERT: B 64 MET cc_start: 0.8292 (mtp) cc_final: 0.8065 (mtp) REVERT: B 493 MET cc_start: 0.8356 (mmt) cc_final: 0.7872 (mmt) REVERT: B 829 MET cc_start: 0.9271 (tpp) cc_final: 0.8812 (ttt) REVERT: C 64 MET cc_start: 0.8143 (mtp) cc_final: 0.7728 (mtp) REVERT: C 86 LYS cc_start: 0.9331 (tppp) cc_final: 0.8848 (mmmt) REVERT: C 89 GLN cc_start: 0.9051 (tt0) cc_final: 0.8630 (pt0) REVERT: C 370 MET cc_start: 0.9102 (tpp) cc_final: 0.8394 (tpp) REVERT: C 493 MET cc_start: 0.8328 (mmt) cc_final: 0.7789 (mmt) REVERT: C 726 MET cc_start: 0.9364 (mmm) cc_final: 0.9067 (mmt) REVERT: D 86 LYS cc_start: 0.9228 (tppt) cc_final: 0.8844 (tppt) REVERT: D 89 GLN cc_start: 0.8860 (tt0) cc_final: 0.8517 (tt0) REVERT: D 493 MET cc_start: 0.8316 (mmt) cc_final: 0.7835 (tpp) REVERT: D 523 MET cc_start: 0.8778 (mmt) cc_final: 0.8403 (mmt) REVERT: D 833 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9043 (mm) outliers start: 56 outliers final: 35 residues processed: 403 average time/residue: 0.1539 time to fit residues: 105.3654 Evaluate side-chains 341 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 305 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 809 SER Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 809 SER Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 867 SER Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 769 ILE Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 868 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 100 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 385 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 153 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 235 GLN D1076 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.083520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.063686 restraints weight = 83869.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.066152 restraints weight = 39211.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.067879 restraints weight = 24236.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.068995 restraints weight = 17791.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.069495 restraints weight = 14589.620| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30888 Z= 0.203 Angle : 0.573 7.923 42180 Z= 0.293 Chirality : 0.040 0.154 5000 Planarity : 0.004 0.056 5216 Dihedral : 4.873 47.181 4328 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.40 % Allowed : 13.55 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 2.32 (0.14), residues: 3944 helix: 2.30 (0.10), residues: 2556 sheet: 0.48 (0.28), residues: 292 loop : 0.04 (0.21), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 225 TYR 0.034 0.002 TYR D 205 PHE 0.013 0.001 PHE A 734 TRP 0.018 0.001 TRP A 984 HIS 0.003 0.001 HIS D 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (30884) covalent geometry : angle 0.57208 / 0.29 (42168) hydrogen bonds : bond 0.04370 / 3.04 ( 1964) hydrogen bonds : angle 3.91775 / 2.85 ( 5796) link_NAG-ASN : bond 0.00413 / 0.21 ( 4) link_NAG-ASN : angle 1.97402 / 1.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 302 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.8500 (mmm) cc_final: 0.8273 (mmm) REVERT: A 194 MET cc_start: 0.8553 (tpp) cc_final: 0.8242 (tpp) REVERT: A 205 TYR cc_start: 0.6935 (p90) cc_final: 0.6692 (p90) REVERT: A 493 MET cc_start: 0.8402 (mmt) cc_final: 0.7687 (mmt) REVERT: B 64 MET cc_start: 0.8160 (mtp) cc_final: 0.7562 (mtp) REVERT: B 136 MET cc_start: 0.8462 (mmt) cc_final: 0.8099 (mmp) REVERT: B 493 MET cc_start: 0.8334 (mmt) cc_final: 0.8000 (mmt) REVERT: B 812 MET cc_start: 0.8785 (mmp) cc_final: 0.8555 (mmp) REVERT: B 829 MET cc_start: 0.9168 (tpp) cc_final: 0.8823 (ttt) REVERT: C 64 MET cc_start: 0.8102 (mtp) cc_final: 0.7685 (mtp) REVERT: C 81 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8428 (ttp-170) REVERT: C 89 GLN cc_start: 0.9058 (tt0) cc_final: 0.8752 (pt0) REVERT: C 493 MET cc_start: 0.8341 (mmt) cc_final: 0.7722 (mmt) REVERT: C 496 ARG cc_start: 0.8375 (ptp-110) cc_final: 0.8167 (ptp-110) REVERT: C 552 ARG cc_start: 0.8721 (ttm110) cc_final: 0.8510 (ttp80) REVERT: D 86 LYS cc_start: 0.9227 (tppt) cc_final: 0.8744 (tppt) REVERT: D 89 GLN cc_start: 0.8873 (tt0) cc_final: 0.8643 (tt0) REVERT: D 370 MET cc_start: 0.9055 (tpp) cc_final: 0.8490 (tpp) REVERT: D 493 MET cc_start: 0.8238 (mmt) cc_final: 0.7534 (mmt) REVERT: D 575 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7895 (tm-30) REVERT: D 785 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7561 (tmm) REVERT: D 829 MET cc_start: 0.8886 (tpt) cc_final: 0.8681 (ttt) outliers start: 70 outliers final: 43 residues processed: 356 average time/residue: 0.1645 time to fit residues: 97.7761 Evaluate side-chains 323 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 278 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 809 SER Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 809 SER Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 867 SER Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 769 ILE Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 785 MET Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 867 SER Chi-restraints excluded: chain D residue 951 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 277 optimal weight: 4.9990 chunk 383 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 369 optimal weight: 8.9990 chunk 354 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 324 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 235 GLN D1076 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.082197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.062242 restraints weight = 83198.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.064713 restraints weight = 39180.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.066378 restraints weight = 24460.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.067459 restraints weight = 18049.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.068005 restraints weight = 14879.988| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 30888 Z= 0.219 Angle : 0.565 7.505 42180 Z= 0.289 Chirality : 0.039 0.195 5000 Planarity : 0.004 0.057 5216 Dihedral : 4.483 41.553 4328 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.61 % Allowed : 14.61 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 2.36 (0.14), residues: 3944 helix: 2.37 (0.10), residues: 2552 sheet: 0.41 (0.28), residues: 292 loop : -0.02 (0.21), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 225 TYR 0.026 0.002 TYR B 205 PHE 0.014 0.001 PHE B 773 TRP 0.018 0.001 TRP A 984 HIS 0.003 0.001 HIS A 837 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 (30884) covalent geometry : angle 0.56385 / 0.29 (42168) hydrogen bonds : bond 0.04364 / 3.06 ( 1964) hydrogen bonds : angle 3.87620 / 2.82 ( 5796) link_NAG-ASN : bond 0.00313 / 0.16 ( 4) link_NAG-ASN : angle 2.27066 / 1.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 292 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.8599 (tpp) cc_final: 0.8236 (tpp) REVERT: A 205 TYR cc_start: 0.7001 (p90) cc_final: 0.6759 (p90) REVERT: A 493 MET cc_start: 0.8418 (mmt) cc_final: 0.7765 (mmt) REVERT: A 496 ARG cc_start: 0.8336 (ptp-110) cc_final: 0.8000 (mtm-85) REVERT: A 785 MET cc_start: 0.7662 (tmm) cc_final: 0.7246 (tmm) REVERT: B 64 MET cc_start: 0.8228 (mtp) cc_final: 0.7656 (mtp) REVERT: B 89 GLN cc_start: 0.9094 (tt0) cc_final: 0.8760 (pt0) REVERT: B 257 MET cc_start: 0.8688 (mtt) cc_final: 0.8158 (mpp) REVERT: B 493 MET cc_start: 0.8361 (mmt) cc_final: 0.8029 (mmt) REVERT: B 496 ARG cc_start: 0.8595 (mtm-85) cc_final: 0.8246 (ttm-80) REVERT: B 785 MET cc_start: 0.7848 (tmm) cc_final: 0.7463 (tmm) REVERT: B 829 MET cc_start: 0.9122 (tpp) cc_final: 0.8750 (ttm) REVERT: C 64 MET cc_start: 0.8144 (mtp) cc_final: 0.7701 (mtp) REVERT: C 81 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8454 (ttp-170) REVERT: C 86 LYS cc_start: 0.9422 (tppp) cc_final: 0.8981 (tppp) REVERT: C 552 ARG cc_start: 0.8706 (ttm110) cc_final: 0.8493 (ttp80) REVERT: D 81 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8351 (ttm170) REVERT: D 86 LYS cc_start: 0.9257 (tppt) cc_final: 0.8896 (tppt) REVERT: D 89 GLN cc_start: 0.8935 (tt0) cc_final: 0.8545 (pt0) REVERT: D 370 MET cc_start: 0.9169 (tpp) cc_final: 0.8259 (tpp) REVERT: D 575 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7941 (tm-30) REVERT: D 785 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7451 (tmm) outliers start: 76 outliers final: 55 residues processed: 351 average time/residue: 0.1615 time to fit residues: 94.9013 Evaluate side-chains 329 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 271 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 862 PHE Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 796 CYS Chi-restraints excluded: chain B residue 809 SER Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 809 SER Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 867 SER Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 769 ILE Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 785 MET Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 867 SER Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 952 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 250 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 chunk 328 optimal weight: 10.0000 chunk 361 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 365 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 278 optimal weight: 0.7980 chunk 317 optimal weight: 3.9990 chunk 370 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 943 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.083377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.063612 restraints weight = 83269.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.066102 restraints weight = 39144.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.067766 restraints weight = 24092.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.068756 restraints weight = 17664.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.069585 restraints weight = 14699.245| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 30888 Z= 0.157 Angle : 0.516 7.975 42180 Z= 0.263 Chirality : 0.038 0.221 5000 Planarity : 0.004 0.060 5216 Dihedral : 4.237 35.721 4328 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.57 % Allowed : 15.36 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 2.47 (0.14), residues: 3944 helix: 2.47 (0.10), residues: 2556 sheet: 0.48 (0.29), residues: 288 loop : -0.01 (0.21), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 552 TYR 0.016 0.001 TYR B 205 PHE 0.009 0.001 PHE C 734 TRP 0.016 0.001 TRP A 984 HIS 0.002 0.001 HIS D 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (30884) covalent geometry : angle 0.51459 / 0.26 (42168) hydrogen bonds : bond 0.04017 / 2.80 ( 1964) hydrogen bonds : angle 3.74190 / 2.72 ( 5796) link_NAG-ASN : bond 0.00297 / 0.15 ( 4) link_NAG-ASN : angle 2.08433 / 1.47 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 290 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8441 (tmm-80) REVERT: A 194 MET cc_start: 0.8620 (tpp) cc_final: 0.8175 (tpp) REVERT: A 205 TYR cc_start: 0.6903 (p90) cc_final: 0.6641 (p90) REVERT: A 493 MET cc_start: 0.8390 (mmt) cc_final: 0.7789 (mmt) REVERT: A 785 MET cc_start: 0.7761 (tmm) cc_final: 0.7305 (tmm) REVERT: B 64 MET cc_start: 0.8203 (mtp) cc_final: 0.7682 (mtp) REVERT: B 89 GLN cc_start: 0.9085 (tt0) cc_final: 0.8746 (pt0) REVERT: B 493 MET cc_start: 0.8403 (mmt) cc_final: 0.8063 (mmt) REVERT: B 496 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.8248 (ttm-80) REVERT: B 785 MET cc_start: 0.7849 (tmm) cc_final: 0.7500 (tmm) REVERT: B 829 MET cc_start: 0.9114 (tpp) cc_final: 0.8758 (ttm) REVERT: C 64 MET cc_start: 0.8188 (mtp) cc_final: 0.7741 (mtp) REVERT: C 81 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8454 (ttp-170) REVERT: C 86 LYS cc_start: 0.9403 (tppp) cc_final: 0.8972 (tppp) REVERT: C 493 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7582 (mmt) REVERT: C 552 ARG cc_start: 0.8707 (ttm110) cc_final: 0.8505 (ttp80) REVERT: C 785 MET cc_start: 0.7799 (tmm) cc_final: 0.7278 (tmm) REVERT: C 829 MET cc_start: 0.8746 (ttm) cc_final: 0.8466 (ttt) REVERT: D 81 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8287 (ttm170) REVERT: D 86 LYS cc_start: 0.9271 (tppt) cc_final: 0.8774 (tppt) REVERT: D 89 GLN cc_start: 0.8948 (tt0) cc_final: 0.8439 (tt0) REVERT: D 370 MET cc_start: 0.9085 (tpp) cc_final: 0.8238 (tpp) REVERT: D 493 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7781 (mmt) REVERT: D 575 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7871 (tm-30) REVERT: D 785 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7449 (tmm) REVERT: D 829 MET cc_start: 0.8767 (ttt) cc_final: 0.8527 (ttm) outliers start: 75 outliers final: 48 residues processed: 347 average time/residue: 0.1630 time to fit residues: 95.0157 Evaluate side-chains 329 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 275 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 862 PHE Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 796 CYS Chi-restraints excluded: chain B residue 809 SER Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 493 MET Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 809 SER Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 867 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 769 ILE Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 785 MET Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 867 SER Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 1045 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 322 optimal weight: 0.9980 chunk 159 optimal weight: 20.0000 chunk 361 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 323 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 307 optimal weight: 10.0000 chunk 185 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 943 ASN B 235 GLN D1076 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.082570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.062668 restraints weight = 82717.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.065125 restraints weight = 38803.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.066788 restraints weight = 24213.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.067883 restraints weight = 17849.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.068456 restraints weight = 14702.713| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30888 Z= 0.168 Angle : 0.530 12.148 42180 Z= 0.267 Chirality : 0.038 0.355 5000 Planarity : 0.004 0.062 5216 Dihedral : 4.076 32.826 4328 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.74 % Allowed : 16.39 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 2.55 (0.14), residues: 3944 helix: 2.55 (0.10), residues: 2552 sheet: 0.47 (0.29), residues: 288 loop : -0.03 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 552 TYR 0.013 0.001 TYR D 559 PHE 0.010 0.001 PHE A 734 TRP 0.016 0.001 TRP A 984 HIS 0.002 0.001 HIS C1060 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (30884) covalent geometry : angle 0.52874 / 0.27 (42168) hydrogen bonds : bond 0.04023 / 2.81 ( 1964) hydrogen bonds : angle 3.71371 / 2.71 ( 5796) link_NAG-ASN : bond 0.00278 / 0.14 ( 4) link_NAG-ASN : angle 1.97855 / 1.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 286 time to evaluate : 1.196 Fit side-chains REVERT: A 81 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8440 (tmm-80) REVERT: A 194 MET cc_start: 0.8581 (tpp) cc_final: 0.8243 (tpp) REVERT: A 205 TYR cc_start: 0.6942 (p90) cc_final: 0.6676 (p90) REVERT: A 493 MET cc_start: 0.8407 (mmt) cc_final: 0.7791 (mmt) REVERT: A 785 MET cc_start: 0.7855 (tmm) cc_final: 0.7423 (tmm) REVERT: B 64 MET cc_start: 0.8241 (mtp) cc_final: 0.7727 (mtp) REVERT: B 89 GLN cc_start: 0.9090 (tt0) cc_final: 0.8521 (pt0) REVERT: B 493 MET cc_start: 0.8337 (mmt) cc_final: 0.7872 (mmt) REVERT: B 496 ARG cc_start: 0.8594 (mtm-85) cc_final: 0.8238 (ttm-80) REVERT: B 785 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7488 (tmm) REVERT: B 829 MET cc_start: 0.9106 (tpp) cc_final: 0.8745 (ttm) REVERT: C 64 MET cc_start: 0.8180 (mtp) cc_final: 0.7714 (mtp) REVERT: C 81 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8462 (ttp-170) REVERT: C 86 LYS cc_start: 0.9420 (tppp) cc_final: 0.8973 (tppp) REVERT: C 136 MET cc_start: 0.8521 (mmt) cc_final: 0.8119 (mmp) REVERT: C 493 MET cc_start: 0.8417 (tpt) cc_final: 0.8063 (mmt) REVERT: C 552 ARG cc_start: 0.8696 (ttm110) cc_final: 0.8489 (ttp80) REVERT: C 785 MET cc_start: 0.7821 (tmm) cc_final: 0.7292 (tmm) REVERT: C 829 MET cc_start: 0.8770 (ttm) cc_final: 0.8545 (ttt) REVERT: D 81 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8284 (ttm170) REVERT: D 86 LYS cc_start: 0.9303 (tppt) cc_final: 0.8832 (tppt) REVERT: D 89 GLN cc_start: 0.8970 (tt0) cc_final: 0.8382 (tt0) REVERT: D 493 MET cc_start: 0.8321 (tpt) cc_final: 0.7909 (mmt) REVERT: D 564 MET cc_start: 0.8869 (ttm) cc_final: 0.8663 (ttm) REVERT: D 575 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7856 (tm-30) REVERT: D 785 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7486 (tmm) REVERT: D 829 MET cc_start: 0.8755 (ttt) cc_final: 0.8537 (ttm) outliers start: 80 outliers final: 55 residues processed: 344 average time/residue: 0.1655 time to fit residues: 95.8974 Evaluate side-chains 333 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 273 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 862 PHE Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 796 CYS Chi-restraints excluded: chain B residue 809 SER Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 952 ILE Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 809 SER Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 867 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 769 ILE Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 785 MET Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 867 SER Chi-restraints excluded: chain D residue 943 ASN Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 952 ILE Chi-restraints excluded: chain D residue 1045 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 247 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 243 optimal weight: 2.9990 chunk 353 optimal weight: 5.9990 chunk 13 optimal weight: 30.0000 chunk 352 optimal weight: 0.9980 chunk 359 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 347 optimal weight: 10.0000 chunk 342 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 943 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.083255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.063492 restraints weight = 82739.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.065969 restraints weight = 38577.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.067693 restraints weight = 23918.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.068786 restraints weight = 17510.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.069296 restraints weight = 14378.353| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30888 Z= 0.148 Angle : 0.518 12.874 42180 Z= 0.260 Chirality : 0.038 0.348 5000 Planarity : 0.004 0.061 5216 Dihedral : 3.939 30.310 4328 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.43 % Allowed : 17.22 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 2.63 (0.14), residues: 3944 helix: 2.60 (0.10), residues: 2552 sheet: 0.54 (0.29), residues: 288 loop : 0.03 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 496 TYR 0.012 0.001 TYR B 559 PHE 0.011 0.001 PHE A 973 TRP 0.015 0.001 TRP A 984 HIS 0.002 0.000 HIS D1060 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (30884) covalent geometry : angle 0.51708 / 0.26 (42168) hydrogen bonds : bond 0.03846 / 2.68 ( 1964) hydrogen bonds : angle 3.65372 / 2.66 ( 5796) link_NAG-ASN : bond 0.00297 / 0.15 ( 4) link_NAG-ASN : angle 1.80636 / 1.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 291 time to evaluate : 1.088 Fit side-chains REVERT: A 81 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8431 (tmm-80) REVERT: A 194 MET cc_start: 0.8492 (tpp) cc_final: 0.8258 (tpt) REVERT: A 205 TYR cc_start: 0.6878 (p90) cc_final: 0.6638 (p90) REVERT: A 493 MET cc_start: 0.8379 (mmt) cc_final: 0.7745 (mmt) REVERT: A 785 MET cc_start: 0.7911 (tmm) cc_final: 0.7535 (tmm) REVERT: A 987 GLN cc_start: 0.9022 (tp40) cc_final: 0.8691 (mp10) REVERT: B 64 MET cc_start: 0.8232 (mtp) cc_final: 0.7735 (mtp) REVERT: B 89 GLN cc_start: 0.9085 (tt0) cc_final: 0.8500 (pt0) REVERT: B 370 MET cc_start: 0.9235 (tpp) cc_final: 0.8278 (tpp) REVERT: B 493 MET cc_start: 0.8359 (mmt) cc_final: 0.7881 (mmt) REVERT: B 785 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7509 (tmm) REVERT: B 829 MET cc_start: 0.9103 (tpp) cc_final: 0.8740 (ttm) REVERT: C 64 MET cc_start: 0.8209 (mtp) cc_final: 0.7763 (mtp) REVERT: C 81 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8458 (ttp-170) REVERT: C 493 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7702 (mmt) REVERT: C 496 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.8318 (ttm110) REVERT: C 552 ARG cc_start: 0.8691 (ttm110) cc_final: 0.8482 (ttp80) REVERT: C 785 MET cc_start: 0.7801 (tmm) cc_final: 0.7293 (tmm) REVERT: C 968 MET cc_start: 0.8605 (mtm) cc_final: 0.8399 (mtm) REVERT: D 81 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8435 (ttp-170) REVERT: D 86 LYS cc_start: 0.9316 (tppt) cc_final: 0.8777 (tppt) REVERT: D 493 MET cc_start: 0.8303 (tpt) cc_final: 0.7893 (mmt) REVERT: D 564 MET cc_start: 0.8860 (ttm) cc_final: 0.8639 (ttm) REVERT: D 575 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7815 (tm-30) REVERT: D 785 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7684 (tmm) REVERT: D 829 MET cc_start: 0.8768 (ttt) cc_final: 0.8551 (ttm) REVERT: D 968 MET cc_start: 0.8367 (ttm) cc_final: 0.8166 (ttm) outliers start: 71 outliers final: 51 residues processed: 339 average time/residue: 0.1674 time to fit residues: 96.0000 Evaluate side-chains 330 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 273 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 862 PHE Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 796 CYS Chi-restraints excluded: chain B residue 809 SER Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 952 ILE Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 493 MET Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 799 VAL Chi-restraints excluded: chain C residue 809 SER Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 867 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 785 MET Chi-restraints excluded: chain D residue 796 CYS Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 867 SER Chi-restraints excluded: chain D residue 952 ILE Chi-restraints excluded: chain D residue 1045 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 309 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 381 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 358 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 GLN A 943 ASN C 943 ASN D1076 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.082953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.063292 restraints weight = 82902.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.065665 restraints weight = 40281.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.067329 restraints weight = 25578.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.068380 restraints weight = 18990.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.068907 restraints weight = 15739.039| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30888 Z= 0.158 Angle : 0.528 12.199 42180 Z= 0.263 Chirality : 0.038 0.303 5000 Planarity : 0.004 0.061 5216 Dihedral : 3.854 28.656 4328 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.47 % Allowed : 17.28 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 2.65 (0.14), residues: 3944 helix: 2.63 (0.10), residues: 2552 sheet: 0.44 (0.29), residues: 296 loop : 0.03 (0.21), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 552 TYR 0.016 0.001 TYR A1070 PHE 0.010 0.001 PHE A 973 TRP 0.015 0.001 TRP A 984 HIS 0.002 0.001 HIS B1060 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (30884) covalent geometry : angle 0.52713 / 0.26 (42168) hydrogen bonds : bond 0.03895 / 2.72 ( 1964) hydrogen bonds : angle 3.64662 / 2.66 ( 5796) link_NAG-ASN : bond 0.00297 / 0.15 ( 4) link_NAG-ASN : angle 1.63223 / 1.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 279 time to evaluate : 1.413 Fit side-chains REVERT: A 81 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8537 (ttp-170) REVERT: A 194 MET cc_start: 0.8501 (tpp) cc_final: 0.8288 (tpt) REVERT: A 205 TYR cc_start: 0.6857 (p90) cc_final: 0.6626 (p90) REVERT: A 493 MET cc_start: 0.8371 (mmt) cc_final: 0.7770 (mmt) REVERT: A 523 MET cc_start: 0.8782 (mmm) cc_final: 0.8517 (mmt) REVERT: A 785 MET cc_start: 0.7896 (tmm) cc_final: 0.7509 (tmm) REVERT: A 983 PHE cc_start: 0.8641 (m-80) cc_final: 0.8315 (m-80) REVERT: A 987 GLN cc_start: 0.8973 (tp40) cc_final: 0.8629 (mp10) REVERT: B 64 MET cc_start: 0.8184 (mtp) cc_final: 0.7731 (mtp) REVERT: B 89 GLN cc_start: 0.9060 (tt0) cc_final: 0.8518 (pt0) REVERT: B 493 MET cc_start: 0.8356 (mmt) cc_final: 0.7891 (mmt) REVERT: B 785 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7452 (tmm) REVERT: B 829 MET cc_start: 0.9064 (tpp) cc_final: 0.8690 (ttm) REVERT: C 64 MET cc_start: 0.8153 (mtp) cc_final: 0.7740 (mtp) REVERT: C 81 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8480 (ttp-170) REVERT: C 493 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7684 (mmt) REVERT: C 552 ARG cc_start: 0.8664 (ttm110) cc_final: 0.8457 (ttp80) REVERT: C 575 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7648 (tm-30) REVERT: C 785 MET cc_start: 0.7787 (tmm) cc_final: 0.7299 (tmm) REVERT: C 968 MET cc_start: 0.8577 (mtm) cc_final: 0.8350 (mtm) REVERT: D 81 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8476 (ttp-170) REVERT: D 89 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8736 (pt0) REVERT: D 493 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7798 (mmt) REVERT: D 575 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7801 (tm-30) REVERT: D 785 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7719 (tmm) REVERT: D 829 MET cc_start: 0.8706 (ttt) cc_final: 0.8497 (ttm) outliers start: 72 outliers final: 55 residues processed: 329 average time/residue: 0.1640 time to fit residues: 91.4485 Evaluate side-chains 328 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 265 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 862 PHE Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 796 CYS Chi-restraints excluded: chain B residue 809 SER Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 952 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 493 MET Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 809 SER Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 867 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 785 MET Chi-restraints excluded: chain D residue 796 CYS Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 867 SER Chi-restraints excluded: chain D residue 943 ASN Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 952 ILE Chi-restraints excluded: chain D residue 1045 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 345 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 81 optimal weight: 0.0970 chunk 92 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 277 optimal weight: 0.1980 chunk 166 optimal weight: 7.9990 chunk 374 optimal weight: 3.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN A 943 ASN C 943 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.082568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.062637 restraints weight = 82810.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.065084 restraints weight = 38974.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.066730 restraints weight = 24336.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.067824 restraints weight = 17994.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.068380 restraints weight = 14847.056| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30888 Z= 0.161 Angle : 0.528 11.608 42180 Z= 0.265 Chirality : 0.038 0.287 5000 Planarity : 0.004 0.061 5216 Dihedral : 3.823 27.435 4328 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.54 % Allowed : 17.66 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 2.60 (0.14), residues: 3944 helix: 2.55 (0.10), residues: 2576 sheet: 0.43 (0.30), residues: 296 loop : 0.08 (0.21), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 552 TYR 0.013 0.001 TYR D 559 PHE 0.010 0.001 PHE A 734 TRP 0.015 0.001 TRP A 984 HIS 0.002 0.001 HIS C1060 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (30884) covalent geometry : angle 0.52745 / 0.26 (42168) hydrogen bonds : bond 0.03901 / 2.72 ( 1964) hydrogen bonds : angle 3.65288 / 2.66 ( 5796) link_NAG-ASN : bond 0.00304 / 0.15 ( 4) link_NAG-ASN : angle 1.48721 / 1.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 269 time to evaluate : 1.146 Fit side-chains REVERT: A 81 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8515 (ttp-170) REVERT: A 194 MET cc_start: 0.8514 (tpp) cc_final: 0.8282 (tpt) REVERT: A 205 TYR cc_start: 0.6816 (p90) cc_final: 0.6584 (p90) REVERT: A 493 MET cc_start: 0.8378 (mmt) cc_final: 0.7659 (mmt) REVERT: A 523 MET cc_start: 0.8813 (mmm) cc_final: 0.8566 (mmt) REVERT: A 785 MET cc_start: 0.7944 (tmm) cc_final: 0.7544 (tmm) REVERT: A 983 PHE cc_start: 0.8696 (m-80) cc_final: 0.8373 (m-80) REVERT: A 987 GLN cc_start: 0.9024 (tp40) cc_final: 0.8669 (mp10) REVERT: B 64 MET cc_start: 0.8248 (mtp) cc_final: 0.7741 (mtp) REVERT: B 89 GLN cc_start: 0.9078 (tt0) cc_final: 0.8509 (pt0) REVERT: B 257 MET cc_start: 0.8620 (mtt) cc_final: 0.8208 (mpp) REVERT: B 370 MET cc_start: 0.9206 (tpp) cc_final: 0.8353 (tpp) REVERT: B 785 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7486 (tmm) REVERT: B 829 MET cc_start: 0.9097 (tpp) cc_final: 0.8737 (ttm) REVERT: C 64 MET cc_start: 0.8228 (mtp) cc_final: 0.7776 (mtp) REVERT: C 81 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8457 (ttp-170) REVERT: C 493 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7759 (mmt) REVERT: C 552 ARG cc_start: 0.8696 (ttm110) cc_final: 0.8489 (ttp80) REVERT: C 785 MET cc_start: 0.7828 (tmm) cc_final: 0.7341 (tmm) REVERT: D 81 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8462 (ttp-170) REVERT: D 89 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8710 (pt0) REVERT: D 493 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7823 (mmt) REVERT: D 575 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7813 (tm-30) REVERT: D 785 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7812 (tmm) REVERT: D 829 MET cc_start: 0.8754 (ttt) cc_final: 0.8535 (ttm) outliers start: 74 outliers final: 62 residues processed: 322 average time/residue: 0.1588 time to fit residues: 88.2794 Evaluate side-chains 332 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 262 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 862 PHE Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 796 CYS Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 809 SER Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 952 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 493 MET Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 809 SER Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 867 SER Chi-restraints excluded: chain C residue 943 ASN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 785 MET Chi-restraints excluded: chain D residue 796 CYS Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 867 SER Chi-restraints excluded: chain D residue 943 ASN Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 952 ILE Chi-restraints excluded: chain D residue 1045 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 265 optimal weight: 7.9990 chunk 256 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 177 optimal weight: 0.8980 chunk 374 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 343 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 943 ASN C 943 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.082781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.062819 restraints weight = 82207.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.065279 restraints weight = 38767.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.066932 restraints weight = 24230.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.068076 restraints weight = 17903.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.068657 restraints weight = 14651.737| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30888 Z= 0.155 Angle : 0.530 14.402 42180 Z= 0.265 Chirality : 0.038 0.346 5000 Planarity : 0.004 0.061 5216 Dihedral : 3.779 26.301 4328 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.43 % Allowed : 17.87 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 2.60 (0.14), residues: 3944 helix: 2.55 (0.10), residues: 2576 sheet: 0.43 (0.30), residues: 296 loop : 0.06 (0.21), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 552 TYR 0.055 0.001 TYR C 45 PHE 0.009 0.001 PHE A 734 TRP 0.015 0.001 TRP A 984 HIS 0.002 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (30884) covalent geometry : angle 0.52977 / 0.26 (42168) hydrogen bonds : bond 0.03882 / 2.70 ( 1964) hydrogen bonds : angle 3.64489 / 2.65 ( 5796) link_NAG-ASN : bond 0.00304 / 0.15 ( 4) link_NAG-ASN : angle 1.36113 / 0.95 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 266 time to evaluate : 1.188 Fit side-chains REVERT: A 81 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8517 (ttp-170) REVERT: A 194 MET cc_start: 0.8495 (tpp) cc_final: 0.8278 (tpt) REVERT: A 205 TYR cc_start: 0.6784 (p90) cc_final: 0.6563 (p90) REVERT: A 493 MET cc_start: 0.8355 (mmt) cc_final: 0.7663 (mmt) REVERT: A 523 MET cc_start: 0.8800 (mmm) cc_final: 0.8562 (mmt) REVERT: A 785 MET cc_start: 0.7957 (tmm) cc_final: 0.7554 (tmm) REVERT: A 829 MET cc_start: 0.8785 (tpp) cc_final: 0.8575 (ttt) REVERT: A 983 PHE cc_start: 0.8693 (m-80) cc_final: 0.8359 (m-80) REVERT: A 987 GLN cc_start: 0.9014 (tp40) cc_final: 0.8655 (mp10) REVERT: B 64 MET cc_start: 0.8252 (mtp) cc_final: 0.7752 (mtp) REVERT: B 89 GLN cc_start: 0.9077 (tt0) cc_final: 0.8517 (pt0) REVERT: B 785 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7478 (tmm) REVERT: B 829 MET cc_start: 0.9094 (tpp) cc_final: 0.8724 (ttm) REVERT: C 64 MET cc_start: 0.8230 (mtp) cc_final: 0.7779 (mtp) REVERT: C 81 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8455 (ttp-170) REVERT: C 493 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7764 (mmt) REVERT: C 552 ARG cc_start: 0.8691 (ttm110) cc_final: 0.8471 (ttp80) REVERT: C 785 MET cc_start: 0.7818 (tmm) cc_final: 0.7329 (tmm) REVERT: D 81 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8472 (ttp-170) REVERT: D 89 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8707 (pt0) REVERT: D 493 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7866 (mmt) REVERT: D 575 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7806 (tm-30) REVERT: D 785 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7826 (tmm) REVERT: D 829 MET cc_start: 0.8752 (ttt) cc_final: 0.8531 (ttm) outliers start: 71 outliers final: 60 residues processed: 316 average time/residue: 0.1633 time to fit residues: 89.2424 Evaluate side-chains 332 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 264 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 862 PHE Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 877 THR Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 796 CYS Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 809 SER Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 952 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 493 MET Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 799 VAL Chi-restraints excluded: chain C residue 809 SER Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 867 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 785 MET Chi-restraints excluded: chain D residue 796 CYS Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 867 SER Chi-restraints excluded: chain D residue 943 ASN Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 1045 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 308 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 304 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 300 optimal weight: 0.6980 chunk 324 optimal weight: 7.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 943 ASN D 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.082698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.062597 restraints weight = 82902.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.065064 restraints weight = 39129.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.066700 restraints weight = 24519.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.067828 restraints weight = 18186.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.068438 restraints weight = 14970.366| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 30888 Z= 0.194 Angle : 0.642 59.075 42180 Z= 0.355 Chirality : 0.039 0.507 5000 Planarity : 0.005 0.096 5216 Dihedral : 3.781 26.266 4328 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.33 % Allowed : 17.90 % Favored : 79.77 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.33 % 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: 2.58 (0.14), residues: 3944 helix: 2.53 (0.10), residues: 2576 sheet: 0.43 (0.29), residues: 296 loop : 0.05 (0.21), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 552 TYR 0.043 0.001 TYR C 45 PHE 0.009 0.001 PHE A 734 TRP 0.015 0.001 TRP A 984 HIS 0.003 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (30884) covalent geometry : angle 0.64160 / 0.35 (42168) hydrogen bonds : bond 0.03906 / 2.71 ( 1964) hydrogen bonds : angle 3.65017 / 2.66 ( 5796) link_NAG-ASN : bond 0.00297 / 0.15 ( 4) link_NAG-ASN : angle 1.36597 / 0.96 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4696.93 seconds wall clock time: 82 minutes 12.21 seconds (4932.21 seconds total)