Starting phenix.real_space_refine on Sat Feb 7 05:19:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p3r_71252/02_2026/9p3r_71252_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p3r_71252/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9p3r_71252/02_2026/9p3r_71252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p3r_71252/02_2026/9p3r_71252.map" model { file = "/net/cci-nas-00/data/ceres_data/9p3r_71252/02_2026/9p3r_71252_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p3r_71252/02_2026/9p3r_71252_neut.cif" } 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-2.0-5952/lib/python3.9/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, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 7.72, per 1000 atoms: 0.26 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: 2.21 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: 0.79 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: 5.98 Time building geometry restraints manager: 3.00 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: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 26.790 Find NCS groups from input model: 0.380 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 covalent geometry : bond 0.00701 (30884) covalent geometry : angle 1.07488 (42168) hydrogen bonds : bond 0.16315 ( 1964) hydrogen bonds : angle 6.62923 ( 5796) link_NAG-ASN : bond 0.09783 ( 4) link_NAG-ASN : angle 4.64471 ( 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 : 1.094 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: 0.1724 time to fit residues: 192.7957 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 : 1.165 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3320 r_free = 0.3320 target = 0.085763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.065621 restraints weight = 84112.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.068176 restraints weight = 39163.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.069921 restraints weight = 24219.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.071068 restraints weight = 17627.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.071690 restraints weight = 14404.107| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30888 Z= 0.189 Angle : 0.619 9.215 42180 Z= 0.315 Chirality : 0.041 0.198 5000 Planarity : 0.005 0.049 5216 Dihedral : 7.293 66.959 4358 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.16 % Allowed : 11.63 % Favored : 86.21 % 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: 1.97 (0.14), residues: 3944 helix: 1.97 (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 0.020 0.002 TYR B 559 PHE 0.014 0.001 PHE A 734 TRP 0.017 0.001 TRP A 984 HIS 0.005 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00434 (30884) covalent geometry : angle 0.61828 (42168) hydrogen bonds : bond 0.04505 ( 1964) hydrogen bonds : angle 4.09795 ( 5796) link_NAG-ASN : bond 0.00293 ( 4) link_NAG-ASN : angle 1.35611 ( 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 423 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 360 time to evaluate : 1.087 Fit side-chains REVERT: A 194 MET cc_start: 0.8701 (tpp) cc_final: 0.8352 (tpp) REVERT: A 205 TYR cc_start: 0.6922 (p90) cc_final: 0.6693 (p90) REVERT: A 493 MET cc_start: 0.8392 (mmt) cc_final: 0.7564 (mmt) REVERT: A 569 GLU cc_start: 0.8810 (tp30) cc_final: 0.8587 (tp30) REVERT: A 981 ASP cc_start: 0.8684 (m-30) cc_final: 0.8483 (m-30) REVERT: B 64 MET cc_start: 0.8300 (mtp) cc_final: 0.8071 (mtp) REVERT: B 136 MET cc_start: 0.8472 (mmt) cc_final: 0.8065 (mmp) REVERT: B 493 MET cc_start: 0.8344 (mmt) cc_final: 0.7897 (mmt) REVERT: B 829 MET cc_start: 0.9279 (tpp) cc_final: 0.8855 (ttt) REVERT: B 952 ILE cc_start: 0.9522 (mm) cc_final: 0.9291 (mt) REVERT: C 64 MET cc_start: 0.8146 (mtp) cc_final: 0.7766 (mtp) REVERT: C 86 LYS cc_start: 0.9333 (tppp) cc_final: 0.9020 (tptp) REVERT: C 89 GLN cc_start: 0.9051 (tt0) cc_final: 0.8777 (tt0) REVERT: C 370 MET cc_start: 0.9095 (tpp) cc_final: 0.8402 (tpp) REVERT: C 493 MET cc_start: 0.8343 (mmt) cc_final: 0.7794 (mmt) REVERT: C 726 MET cc_start: 0.9368 (mmm) cc_final: 0.9063 (mmt) REVERT: D 86 LYS cc_start: 0.9231 (tppt) cc_final: 0.8870 (tppt) REVERT: D 89 GLN cc_start: 0.8855 (tt0) cc_final: 0.8618 (pt0) REVERT: D 493 MET cc_start: 0.8350 (mmt) cc_final: 0.7857 (tpp) REVERT: D 523 MET cc_start: 0.8776 (mmt) cc_final: 0.8399 (mmt) REVERT: D 833 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9099 (mm) outliers start: 63 outliers final: 40 residues processed: 406 average time/residue: 0.1557 time to fit residues: 107.2336 Evaluate side-chains 348 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 307 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 219 LEU 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 856 ILE 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 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 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 Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 977 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 100 optimal weight: 20.0000 chunk 93 optimal weight: 0.0040 chunk 385 optimal weight: 3.9990 chunk 318 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 285 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 203 optimal weight: 0.5980 chunk 142 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 overall best weight: 1.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1076 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.086619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.066996 restraints weight = 83122.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.069535 restraints weight = 38614.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.071292 restraints weight = 23755.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.072482 restraints weight = 17282.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.073114 restraints weight = 14011.509| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30888 Z= 0.135 Angle : 0.534 10.348 42180 Z= 0.270 Chirality : 0.038 0.148 5000 Planarity : 0.004 0.056 5216 Dihedral : 4.947 44.757 4328 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.47 % Allowed : 13.82 % Favored : 84.71 % 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: 2.37 (0.14), residues: 3944 helix: 2.36 (0.10), residues: 2548 sheet: 0.58 (0.29), residues: 296 loop : -0.01 (0.21), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 225 TYR 0.029 0.001 TYR C 205 PHE 0.010 0.001 PHE C 828 TRP 0.016 0.001 TRP A 984 HIS 0.004 0.001 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00308 (30884) covalent geometry : angle 0.53373 (42168) hydrogen bonds : bond 0.03951 ( 1964) hydrogen bonds : angle 3.79148 ( 5796) link_NAG-ASN : bond 0.00415 ( 4) link_NAG-ASN : angle 1.77738 ( 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 387 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 344 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.8606 (tpp) cc_final: 0.8313 (tpp) REVERT: A 205 TYR cc_start: 0.6902 (p90) cc_final: 0.6674 (p90) REVERT: A 493 MET cc_start: 0.8407 (mmt) cc_final: 0.7753 (mmt) REVERT: B 89 GLN cc_start: 0.9083 (tt0) cc_final: 0.8746 (pt0) REVERT: B 493 MET cc_start: 0.8277 (mmt) cc_final: 0.8038 (tpp) REVERT: B 496 ARG cc_start: 0.8603 (mtm-85) cc_final: 0.8320 (ttm110) REVERT: B 829 MET cc_start: 0.9177 (tpp) cc_final: 0.8711 (ttt) REVERT: C 64 MET cc_start: 0.8070 (mtp) cc_final: 0.7674 (mtp) REVERT: C 81 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8439 (ttp-170) REVERT: C 89 GLN cc_start: 0.9009 (tt0) cc_final: 0.8674 (pt0) REVERT: C 493 MET cc_start: 0.8328 (mmt) cc_final: 0.7767 (mmt) REVERT: C 552 ARG cc_start: 0.8708 (ttm110) cc_final: 0.8506 (ttp80) REVERT: D 86 LYS cc_start: 0.9213 (tppt) cc_final: 0.8764 (tppt) REVERT: D 370 MET cc_start: 0.9081 (tpp) cc_final: 0.8413 (tpp) REVERT: D 493 MET cc_start: 0.8237 (mmt) cc_final: 0.7543 (mmt) REVERT: D 523 MET cc_start: 0.8703 (mmt) cc_final: 0.8327 (mmt) REVERT: D 575 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7803 (tm-30) REVERT: D 785 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7529 (tmm) REVERT: D 833 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9101 (mm) outliers start: 43 outliers final: 24 residues processed: 366 average time/residue: 0.1645 time to fit residues: 100.7019 Evaluate side-chains 330 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 303 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 624 MET Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 867 SER 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 462 LEU Chi-restraints excluded: chain B residue 809 SER 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 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 D residue 242 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 769 ILE Chi-restraints excluded: chain D residue 785 MET Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 856 ILE Chi-restraints excluded: chain D residue 867 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 277 optimal weight: 3.9990 chunk 383 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 369 optimal weight: 9.9990 chunk 354 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 324 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 943 ASN C 138 GLN D 235 GLN D1076 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.084092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.064279 restraints weight = 83042.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.066771 restraints weight = 38822.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.068501 restraints weight = 24086.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.069470 restraints weight = 17603.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.070295 restraints weight = 14638.994| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30888 Z= 0.175 Angle : 0.540 7.935 42180 Z= 0.274 Chirality : 0.038 0.156 5000 Planarity : 0.004 0.058 5216 Dihedral : 4.320 40.698 4328 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.67 % Allowed : 14.44 % Favored : 82.89 % 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: 2.46 (0.14), residues: 3944 helix: 2.45 (0.10), residues: 2556 sheet: 0.48 (0.29), residues: 292 loop : 0.01 (0.21), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 225 TYR 0.031 0.002 TYR B 205 PHE 0.016 0.001 PHE B 773 TRP 0.017 0.001 TRP A 984 HIS 0.003 0.001 HIS A 842 Details of bonding type rmsd covalent geometry : bond 0.00403 (30884) covalent geometry : angle 0.53865 (42168) hydrogen bonds : bond 0.04061 ( 1964) hydrogen bonds : angle 3.73751 ( 5796) link_NAG-ASN : bond 0.00338 ( 4) link_NAG-ASN : angle 2.23427 ( 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 388 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 310 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.8601 (tpp) cc_final: 0.8248 (tpp) REVERT: A 205 TYR cc_start: 0.6886 (p90) cc_final: 0.6654 (p90) REVERT: A 212 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7210 (mt-10) REVERT: A 493 MET cc_start: 0.8413 (mmt) cc_final: 0.7746 (mmt) REVERT: B 64 MET cc_start: 0.8225 (mtp) cc_final: 0.7615 (mtp) REVERT: B 89 GLN cc_start: 0.9084 (tt0) cc_final: 0.8742 (pt0) REVERT: B 136 MET cc_start: 0.8453 (mmt) cc_final: 0.8085 (mmp) REVERT: B 253 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8525 (mm) REVERT: B 257 MET cc_start: 0.8618 (mtt) cc_final: 0.8133 (mpp) REVERT: B 493 MET cc_start: 0.8314 (mmt) cc_final: 0.8000 (mmt) REVERT: B 496 ARG cc_start: 0.8643 (mtm-85) cc_final: 0.7985 (ttm110) REVERT: B 829 MET cc_start: 0.9158 (tpp) cc_final: 0.8818 (ttt) REVERT: C 64 MET cc_start: 0.8144 (mtp) cc_final: 0.7716 (mtp) REVERT: C 81 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8438 (ttp-170) REVERT: C 86 LYS cc_start: 0.9370 (tppp) cc_final: 0.9001 (tppp) REVERT: C 89 GLN cc_start: 0.9058 (tt0) cc_final: 0.8772 (tt0) REVERT: C 635 LEU cc_start: 0.9427 (mt) cc_final: 0.9211 (mp) REVERT: C 771 GLN cc_start: 0.8971 (mm110) cc_final: 0.8737 (mm-40) REVERT: D 81 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8311 (ttm170) REVERT: D 86 LYS cc_start: 0.9246 (tppt) cc_final: 0.9030 (tppt) REVERT: D 89 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8544 (pt0) REVERT: D 205 TYR cc_start: 0.6568 (p90) cc_final: 0.6278 (p90) REVERT: D 370 MET cc_start: 0.9180 (tpp) cc_final: 0.8271 (tpp) REVERT: D 493 MET cc_start: 0.8238 (mmt) cc_final: 0.7474 (mmt) REVERT: D 523 MET cc_start: 0.8773 (mmt) cc_final: 0.8505 (mmt) REVERT: D 575 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7906 (tm-30) REVERT: D 785 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7558 (tmm) outliers start: 78 outliers final: 45 residues processed: 361 average time/residue: 0.1638 time to fit residues: 98.4289 Evaluate side-chains 335 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 285 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 624 MET Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 732 ILE 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 952 ILE 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 253 LEU 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 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 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 856 ILE Chi-restraints excluded: chain C residue 867 SER Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 242 ILE 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 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 1045 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 250 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 chunk 328 optimal weight: 10.0000 chunk 361 optimal weight: 4.9990 chunk 271 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 365 optimal weight: 0.1980 chunk 23 optimal weight: 10.0000 chunk 278 optimal weight: 0.0980 chunk 317 optimal weight: 7.9990 chunk 370 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 943 ASN D1076 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.086218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.066674 restraints weight = 82469.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.069117 restraints weight = 39693.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.070774 restraints weight = 25050.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.071933 restraints weight = 18612.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.072538 restraints weight = 15293.454| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 30888 Z= 0.110 Angle : 0.493 11.020 42180 Z= 0.248 Chirality : 0.037 0.171 5000 Planarity : 0.004 0.060 5216 Dihedral : 4.039 33.815 4328 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.51 % Allowed : 16.29 % Favored : 82.20 % 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: 2.57 (0.10), residues: 2552 sheet: 0.92 (0.30), residues: 264 loop : 0.06 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 225 TYR 0.014 0.001 TYR B 559 PHE 0.008 0.001 PHE B 773 TRP 0.014 0.001 TRP A 984 HIS 0.002 0.000 HIS D 221 Details of bonding type rmsd covalent geometry : bond 0.00247 (30884) covalent geometry : angle 0.49204 (42168) hydrogen bonds : bond 0.03593 ( 1964) hydrogen bonds : angle 3.56684 ( 5796) link_NAG-ASN : bond 0.00348 ( 4) link_NAG-ASN : angle 2.02545 ( 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 372 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 328 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.8622 (tpp) cc_final: 0.8259 (tpp) REVERT: A 205 TYR cc_start: 0.6751 (p90) cc_final: 0.6506 (p90) REVERT: A 493 MET cc_start: 0.8396 (mmt) cc_final: 0.7747 (mmt) REVERT: A 523 MET cc_start: 0.8661 (mmm) cc_final: 0.8320 (mmt) REVERT: A 987 GLN cc_start: 0.9000 (tp40) cc_final: 0.8660 (mp10) REVERT: B 64 MET cc_start: 0.8151 (mtp) cc_final: 0.7666 (mtp) REVERT: B 89 GLN cc_start: 0.9055 (tt0) cc_final: 0.8522 (pt0) REVERT: B 370 MET cc_start: 0.9143 (tpp) cc_final: 0.8110 (tpp) REVERT: B 493 MET cc_start: 0.8251 (mmt) cc_final: 0.7795 (mmt) REVERT: B 496 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.7985 (ttm110) REVERT: B 829 MET cc_start: 0.9049 (tpp) cc_final: 0.8635 (ttm) REVERT: B 952 ILE cc_start: 0.9543 (mm) cc_final: 0.9334 (mt) REVERT: C 64 MET cc_start: 0.8087 (mtp) cc_final: 0.7702 (mtp) REVERT: C 81 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8432 (ttp-170) REVERT: C 86 LYS cc_start: 0.9336 (tppp) cc_final: 0.8905 (mmmt) REVERT: C 89 GLN cc_start: 0.8999 (tt0) cc_final: 0.8485 (pt0) REVERT: C 493 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7610 (mmt) REVERT: C 496 ARG cc_start: 0.8733 (mtm-85) cc_final: 0.7990 (ttm110) REVERT: C 785 MET cc_start: 0.7619 (tmm) cc_final: 0.7087 (tmm) REVERT: C 829 MET cc_start: 0.8631 (ttm) cc_final: 0.8311 (ttt) REVERT: D 81 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8298 (ttm170) REVERT: D 86 LYS cc_start: 0.9240 (tppt) cc_final: 0.9018 (tppt) REVERT: D 89 GLN cc_start: 0.8850 (tt0) cc_final: 0.8473 (pt0) REVERT: D 370 MET cc_start: 0.9022 (tpp) cc_final: 0.8201 (tpp) REVERT: D 493 MET cc_start: 0.8200 (mmt) cc_final: 0.7557 (mmt) REVERT: D 523 MET cc_start: 0.8633 (mmt) cc_final: 0.8378 (mmt) REVERT: D 575 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7821 (tm-30) REVERT: D 785 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7520 (tmm) REVERT: D 829 MET cc_start: 0.8659 (ttt) cc_final: 0.8438 (ttm) outliers start: 44 outliers final: 26 residues processed: 356 average time/residue: 0.1574 time to fit residues: 94.5376 Evaluate side-chains 324 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 294 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 408 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 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 809 SER Chi-restraints excluded: chain B residue 833 LEU 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 769 ILE Chi-restraints excluded: chain C residue 809 SER Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 867 SER Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 769 ILE 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 1045 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 322 optimal weight: 30.0000 chunk 159 optimal weight: 9.9990 chunk 361 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 323 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 307 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 943 ASN C 235 GLN 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 = 0.3253 r_free = 0.3253 target = 0.081212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.060973 restraints weight = 83327.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.063360 restraints weight = 39710.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.064998 restraints weight = 25089.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.066071 restraints weight = 18651.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.066650 restraints weight = 15453.405| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 30888 Z= 0.278 Angle : 0.618 8.966 42180 Z= 0.313 Chirality : 0.040 0.335 5000 Planarity : 0.005 0.061 5216 Dihedral : 4.207 33.633 4328 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.09 % Allowed : 15.98 % Favored : 80.93 % 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: 2.39 (0.14), residues: 3944 helix: 2.41 (0.10), residues: 2544 sheet: 0.43 (0.29), residues: 292 loop : -0.03 (0.20), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1080 TYR 0.017 0.002 TYR A 758 PHE 0.018 0.002 PHE A 734 TRP 0.020 0.002 TRP A 984 HIS 0.004 0.001 HIS A 837 Details of bonding type rmsd covalent geometry : bond 0.00637 (30884) covalent geometry : angle 0.61708 (42168) hydrogen bonds : bond 0.04659 ( 1964) hydrogen bonds : angle 3.89723 ( 5796) link_NAG-ASN : bond 0.00186 ( 4) link_NAG-ASN : angle 2.07886 ( 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 364 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 274 time to evaluate : 0.999 Fit side-chains REVERT: A 81 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8466 (tmm-80) REVERT: A 194 MET cc_start: 0.8660 (tpp) cc_final: 0.8220 (tpp) REVERT: A 205 TYR cc_start: 0.6884 (p90) cc_final: 0.6659 (p90) REVERT: A 493 MET cc_start: 0.8404 (mmt) cc_final: 0.7639 (mmt) REVERT: B 64 MET cc_start: 0.8228 (mtp) cc_final: 0.7689 (mtp) REVERT: B 89 GLN cc_start: 0.9082 (tt0) cc_final: 0.8748 (pt0) REVERT: B 370 MET cc_start: 0.9316 (tpp) cc_final: 0.8160 (tpp) REVERT: B 493 MET cc_start: 0.8329 (mmt) cc_final: 0.7866 (mmt) REVERT: B 496 ARG cc_start: 0.8618 (mtm-85) cc_final: 0.8351 (ttm110) REVERT: B 785 MET cc_start: 0.7849 (tmm) cc_final: 0.7470 (tmm) REVERT: B 829 MET cc_start: 0.9107 (tpp) cc_final: 0.8787 (ttt) REVERT: C 64 MET cc_start: 0.8191 (mtp) cc_final: 0.7727 (mtp) REVERT: C 81 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8471 (ttp-170) REVERT: C 86 LYS cc_start: 0.9372 (tppp) cc_final: 0.8929 (tppp) REVERT: C 89 GLN cc_start: 0.9061 (tt0) cc_final: 0.8715 (tt0) REVERT: C 493 MET cc_start: 0.8434 (tpt) cc_final: 0.8100 (mmt) REVERT: C 496 ARG cc_start: 0.8763 (mtm-85) cc_final: 0.8441 (ptp-110) REVERT: C 785 MET cc_start: 0.7817 (tmm) cc_final: 0.7286 (tmm) REVERT: D 81 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8496 (ttp-170) REVERT: D 86 LYS cc_start: 0.9285 (tppt) cc_final: 0.9049 (tppt) REVERT: D 89 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8562 (pt0) REVERT: D 493 MET cc_start: 0.8225 (mmt) cc_final: 0.7662 (mmt) REVERT: D 564 MET cc_start: 0.8891 (ttm) cc_final: 0.8664 (ttm) REVERT: D 575 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7919 (tm-30) REVERT: D 785 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7486 (tmm) REVERT: D 829 MET cc_start: 0.8787 (ttt) cc_final: 0.8577 (ttm) outliers start: 90 outliers final: 60 residues processed: 348 average time/residue: 0.1515 time to fit residues: 89.9009 Evaluate side-chains 329 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 264 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 765 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 852 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 943 ASN Chi-restraints excluded: chain A residue 952 ILE 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 97 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 242 ILE 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 798 MET 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 961 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 177 VAL 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 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 89 GLN 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 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 1076 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 247 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 243 optimal weight: 0.6980 chunk 353 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 chunk 352 optimal weight: 4.9990 chunk 359 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 154 optimal weight: 0.9980 chunk 347 optimal weight: 0.9990 chunk 342 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 943 ASN A1058 HIS D1076 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.084798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.065048 restraints weight = 82232.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.067574 restraints weight = 38151.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.069296 restraints weight = 23495.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.070446 restraints weight = 17238.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.071005 restraints weight = 14097.408| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30888 Z= 0.106 Angle : 0.502 12.614 42180 Z= 0.253 Chirality : 0.037 0.385 5000 Planarity : 0.004 0.061 5216 Dihedral : 3.927 30.036 4328 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.44 % Allowed : 17.90 % Favored : 80.66 % 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: 2.62 (0.14), residues: 3944 helix: 2.55 (0.10), residues: 2556 sheet: 0.89 (0.31), residues: 264 loop : 0.05 (0.20), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1080 TYR 0.014 0.001 TYR B 559 PHE 0.010 0.001 PHE B 773 TRP 0.013 0.001 TRP A 984 HIS 0.002 0.000 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00230 (30884) covalent geometry : angle 0.50165 (42168) hydrogen bonds : bond 0.03677 ( 1964) hydrogen bonds : angle 3.60076 ( 5796) link_NAG-ASN : bond 0.00359 ( 4) link_NAG-ASN : angle 1.70524 ( 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 346 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 304 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8395 (tmm-80) REVERT: A 89 GLN cc_start: 0.9041 (tt0) cc_final: 0.8690 (pt0) REVERT: A 194 MET cc_start: 0.8548 (tpp) cc_final: 0.8167 (tpp) REVERT: A 205 TYR cc_start: 0.6922 (p90) cc_final: 0.6667 (p90) REVERT: A 493 MET cc_start: 0.8408 (mmt) cc_final: 0.7755 (mmt) REVERT: A 968 MET cc_start: 0.8617 (mtm) cc_final: 0.8412 (mtm) REVERT: A 987 GLN cc_start: 0.9013 (tp40) cc_final: 0.8574 (mp10) REVERT: B 64 MET cc_start: 0.8249 (mtp) cc_final: 0.7734 (mtp) REVERT: B 89 GLN cc_start: 0.9079 (tt0) cc_final: 0.8512 (pt0) REVERT: B 370 MET cc_start: 0.9182 (tpp) cc_final: 0.8103 (tpp) REVERT: B 493 MET cc_start: 0.8276 (mmt) cc_final: 0.7751 (mmt) REVERT: B 785 MET cc_start: 0.7817 (tmm) cc_final: 0.7448 (tmm) REVERT: B 829 MET cc_start: 0.9076 (tpp) cc_final: 0.8743 (ttm) REVERT: C 64 MET cc_start: 0.8188 (mtp) cc_final: 0.7740 (mtp) REVERT: C 81 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8442 (ttp-170) REVERT: C 89 GLN cc_start: 0.9035 (tt0) cc_final: 0.8734 (pt0) REVERT: C 194 MET cc_start: 0.8434 (tpp) cc_final: 0.8101 (mmt) REVERT: C 493 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7696 (mmt) REVERT: C 496 ARG cc_start: 0.8740 (mtm-85) cc_final: 0.8343 (ttm110) REVERT: C 785 MET cc_start: 0.7728 (tmm) cc_final: 0.7205 (tmm) REVERT: D 81 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8460 (ttp-170) REVERT: D 86 LYS cc_start: 0.9277 (tppt) cc_final: 0.8960 (tppt) REVERT: D 89 GLN cc_start: 0.8881 (tt0) cc_final: 0.8468 (pt0) REVERT: D 493 MET cc_start: 0.8221 (mmt) cc_final: 0.7604 (mmt) REVERT: D 575 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7798 (tm-30) REVERT: D 779 MET cc_start: 0.3998 (mmp) cc_final: 0.3700 (mmp) REVERT: D 785 MET cc_start: 0.8001 (tmm) cc_final: 0.7457 (tmm) outliers start: 42 outliers final: 26 residues processed: 335 average time/residue: 0.1621 time to fit residues: 92.5821 Evaluate side-chains 320 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 290 time to evaluate : 1.699 ------------------------------------------------------------------------------- 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 867 SER 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 408 VAL Chi-restraints excluded: chain B residue 796 CYS Chi-restraints excluded: chain B residue 798 MET Chi-restraints excluded: chain B residue 809 SER Chi-restraints excluded: chain B residue 867 SER 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 769 ILE Chi-restraints excluded: chain C residue 809 SER Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 764 LEU 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 1075 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 4 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 309 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 381 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 358 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 943 ASN D 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.084260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.064611 restraints weight = 82678.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.067012 restraints weight = 40064.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.068653 restraints weight = 25326.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.069754 restraints weight = 18884.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.070316 restraints weight = 15614.287| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30888 Z= 0.126 Angle : 0.509 11.611 42180 Z= 0.253 Chirality : 0.037 0.321 5000 Planarity : 0.004 0.061 5216 Dihedral : 3.782 27.714 4328 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.51 % Allowed : 18.31 % Favored : 80.18 % 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: 2.69 (0.14), residues: 3944 helix: 2.63 (0.10), residues: 2548 sheet: 0.66 (0.30), residues: 288 loop : 0.07 (0.20), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 496 TYR 0.032 0.001 TYR A1070 PHE 0.010 0.001 PHE A 973 TRP 0.014 0.001 TRP A 984 HIS 0.002 0.000 HIS B 221 Details of bonding type rmsd covalent geometry : bond 0.00289 (30884) covalent geometry : angle 0.50881 (42168) hydrogen bonds : bond 0.03681 ( 1964) hydrogen bonds : angle 3.56286 ( 5796) link_NAG-ASN : bond 0.00297 ( 4) link_NAG-ASN : angle 1.61516 ( 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 338 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 294 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8496 (ttp-170) REVERT: A 89 GLN cc_start: 0.9029 (tt0) cc_final: 0.8700 (pt0) REVERT: A 194 MET cc_start: 0.8543 (tpp) cc_final: 0.8119 (mmt) REVERT: A 205 TYR cc_start: 0.6924 (p90) cc_final: 0.6652 (p90) REVERT: A 493 MET cc_start: 0.8388 (mmt) cc_final: 0.7634 (mmt) REVERT: B 64 MET cc_start: 0.8209 (mtp) cc_final: 0.7734 (mtp) REVERT: B 89 GLN cc_start: 0.9064 (tt0) cc_final: 0.8527 (pt0) REVERT: B 257 MET cc_start: 0.8469 (mtt) cc_final: 0.8216 (mpp) REVERT: B 370 MET cc_start: 0.9171 (tpp) cc_final: 0.8075 (tpp) REVERT: B 493 MET cc_start: 0.8249 (mmt) cc_final: 0.7805 (mmt) REVERT: B 785 MET cc_start: 0.7776 (tmm) cc_final: 0.7424 (tmm) REVERT: B 829 MET cc_start: 0.9071 (tpp) cc_final: 0.8655 (ttm) REVERT: C 64 MET cc_start: 0.8148 (mtp) cc_final: 0.7736 (mtp) REVERT: C 81 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8463 (ttp-170) REVERT: C 89 GLN cc_start: 0.9025 (tt0) cc_final: 0.8741 (pt0) REVERT: C 493 MET cc_start: 0.8311 (tpt) cc_final: 0.7755 (mmt) REVERT: C 496 ARG cc_start: 0.8691 (mtm-85) cc_final: 0.8366 (ttm110) REVERT: C 575 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7681 (tm-30) REVERT: C 785 MET cc_start: 0.7717 (tmm) cc_final: 0.7202 (tmm) REVERT: C 968 MET cc_start: 0.8580 (mtm) cc_final: 0.8372 (mtm) REVERT: D 81 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8508 (ttp-170) REVERT: D 86 LYS cc_start: 0.9272 (tppt) cc_final: 0.8950 (tppt) REVERT: D 89 GLN cc_start: 0.8876 (tt0) cc_final: 0.8447 (pt0) REVERT: D 493 MET cc_start: 0.8175 (mmt) cc_final: 0.7599 (mmt) REVERT: D 575 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7777 (tm-30) REVERT: D 779 MET cc_start: 0.4082 (mmp) cc_final: 0.3805 (mmp) REVERT: D 785 MET cc_start: 0.7960 (tmm) cc_final: 0.7433 (tmm) outliers start: 44 outliers final: 30 residues processed: 327 average time/residue: 0.1669 time to fit residues: 93.7398 Evaluate side-chains 317 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 284 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 177 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 862 PHE Chi-restraints excluded: chain A residue 867 SER 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 408 VAL Chi-restraints excluded: chain B residue 809 SER Chi-restraints excluded: chain B residue 867 SER 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 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 D residue 81 ARG Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 764 LEU 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 1045 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 345 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 227 optimal weight: 0.9980 chunk 241 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 277 optimal weight: 7.9990 chunk 166 optimal weight: 8.9990 chunk 374 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 943 ASN B 235 GLN C 943 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.081343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.061121 restraints weight = 83256.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.063514 restraints weight = 39819.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.065101 restraints weight = 25143.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.066199 restraints weight = 18858.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.066813 restraints weight = 15609.095| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 30888 Z= 0.264 Angle : 0.616 12.424 42180 Z= 0.308 Chirality : 0.040 0.361 5000 Planarity : 0.005 0.061 5216 Dihedral : 3.963 28.793 4328 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.89 % Allowed : 18.28 % Favored : 79.84 % 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: 2.48 (0.14), residues: 3944 helix: 2.51 (0.10), residues: 2536 sheet: 0.43 (0.29), residues: 288 loop : -0.01 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1080 TYR 0.037 0.002 TYR B 45 PHE 0.017 0.002 PHE A 734 TRP 0.018 0.001 TRP A 984 HIS 0.004 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00604 (30884) covalent geometry : angle 0.61522 (42168) hydrogen bonds : bond 0.04451 ( 1964) hydrogen bonds : angle 3.84712 ( 5796) link_NAG-ASN : bond 0.00249 ( 4) link_NAG-ASN : angle 1.60491 ( 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 317 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 262 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8557 (ttp-170) REVERT: A 89 GLN cc_start: 0.9073 (tt0) cc_final: 0.8697 (pt0) REVERT: A 194 MET cc_start: 0.8568 (tpp) cc_final: 0.8299 (tpt) REVERT: A 205 TYR cc_start: 0.6973 (p90) cc_final: 0.6694 (p90) REVERT: A 493 MET cc_start: 0.8334 (mmt) cc_final: 0.7573 (mmt) REVERT: B 64 MET cc_start: 0.8237 (mtp) cc_final: 0.7749 (mtp) REVERT: B 89 GLN cc_start: 0.9089 (tt0) cc_final: 0.8585 (pt0) REVERT: B 370 MET cc_start: 0.9246 (tpp) cc_final: 0.8148 (tpp) REVERT: B 785 MET cc_start: 0.7902 (tmm) cc_final: 0.7392 (tmm) REVERT: B 829 MET cc_start: 0.9102 (tpp) cc_final: 0.8815 (ttt) REVERT: C 64 MET cc_start: 0.8156 (mtp) cc_final: 0.7707 (mtp) REVERT: C 81 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8477 (ttp-170) REVERT: C 89 GLN cc_start: 0.9056 (tt0) cc_final: 0.8639 (pt0) REVERT: C 493 MET cc_start: 0.8424 (tpt) cc_final: 0.7798 (mmt) REVERT: C 496 ARG cc_start: 0.8705 (mtm-85) cc_final: 0.8427 (ptp-110) REVERT: C 785 MET cc_start: 0.7846 (tmm) cc_final: 0.7367 (tmm) REVERT: D 81 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8512 (ttp-170) REVERT: D 89 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8622 (pt0) REVERT: D 493 MET cc_start: 0.8142 (mmt) cc_final: 0.7549 (mmt) REVERT: D 575 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7876 (tm-30) REVERT: D 785 MET cc_start: 0.8060 (tmm) cc_final: 0.7643 (tmm) outliers start: 55 outliers final: 43 residues processed: 303 average time/residue: 0.1597 time to fit residues: 82.8328 Evaluate side-chains 304 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 257 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 177 VAL 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 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 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 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 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 943 ASN Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 775 THR 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 1045 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 265 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 177 optimal weight: 0.8980 chunk 374 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 343 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3259 r_free = 0.3259 target = 0.081629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.061417 restraints weight = 82468.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.063823 restraints weight = 39463.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.065457 restraints weight = 24993.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.066550 restraints weight = 18628.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.067139 restraints weight = 15467.575| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 30888 Z= 0.214 Angle : 0.709 59.195 42180 Z= 0.377 Chirality : 0.040 0.548 5000 Planarity : 0.005 0.097 5216 Dihedral : 3.979 28.867 4328 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.89 % Allowed : 18.28 % Favored : 79.84 % 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: 2.49 (0.14), residues: 3944 helix: 2.52 (0.10), residues: 2536 sheet: 0.39 (0.29), residues: 288 loop : -0.02 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1080 TYR 0.029 0.002 TYR B 45 PHE 0.015 0.001 PHE A 734 TRP 0.019 0.001 TRP A 984 HIS 0.003 0.001 HIS C 837 Details of bonding type rmsd covalent geometry : bond 0.00483 (30884) covalent geometry : angle 0.70814 (42168) hydrogen bonds : bond 0.04382 ( 1964) hydrogen bonds : angle 3.83336 ( 5796) link_NAG-ASN : bond 0.00259 ( 4) link_NAG-ASN : angle 1.59076 ( 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 313 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 258 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8550 (ttp-170) REVERT: A 89 GLN cc_start: 0.9072 (tt0) cc_final: 0.8691 (pt0) REVERT: A 194 MET cc_start: 0.8559 (tpp) cc_final: 0.8291 (tpt) REVERT: A 205 TYR cc_start: 0.6965 (p90) cc_final: 0.6688 (p90) REVERT: A 493 MET cc_start: 0.8326 (mmt) cc_final: 0.7748 (mmt) REVERT: B 64 MET cc_start: 0.8251 (mtp) cc_final: 0.7751 (mtp) REVERT: B 89 GLN cc_start: 0.9085 (tt0) cc_final: 0.8577 (pt0) REVERT: B 370 MET cc_start: 0.9245 (tpp) cc_final: 0.8139 (tpp) REVERT: B 785 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7380 (tmm) REVERT: B 829 MET cc_start: 0.9089 (tpp) cc_final: 0.8795 (ttt) REVERT: C 64 MET cc_start: 0.8160 (mtp) cc_final: 0.7701 (mtp) REVERT: C 81 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8472 (ttp-170) REVERT: C 89 GLN cc_start: 0.9055 (tt0) cc_final: 0.8633 (pt0) REVERT: C 493 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7786 (mmt) REVERT: C 496 ARG cc_start: 0.8705 (mtm-85) cc_final: 0.8428 (ptp-110) REVERT: C 785 MET cc_start: 0.7848 (tmm) cc_final: 0.7367 (tmm) REVERT: D 81 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8509 (ttp-170) REVERT: D 89 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8615 (pt0) REVERT: D 493 MET cc_start: 0.8137 (mmt) cc_final: 0.7542 (mmt) REVERT: D 575 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7866 (tm-30) REVERT: D 785 MET cc_start: 0.8061 (tmm) cc_final: 0.7642 (tmm) outliers start: 55 outliers final: 46 residues processed: 294 average time/residue: 0.1642 time to fit residues: 83.0356 Evaluate side-chains 310 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 258 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU 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 177 VAL 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 796 CYS Chi-restraints excluded: chain A residue 862 PHE Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 952 ILE 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 785 MET 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 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 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 952 ILE Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 775 THR 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 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 308 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 209 optimal weight: 8.9990 chunk 304 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 300 optimal weight: 0.9990 chunk 324 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3259 r_free = 0.3259 target = 0.081623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.061385 restraints weight = 83014.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.063787 restraints weight = 39676.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.065433 restraints weight = 25085.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.066544 restraints weight = 18702.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.067130 restraints weight = 15466.100| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 30888 Z= 0.214 Angle : 0.709 59.195 42180 Z= 0.377 Chirality : 0.040 0.548 5000 Planarity : 0.005 0.097 5216 Dihedral : 3.979 28.867 4328 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.82 % Allowed : 18.31 % Favored : 79.87 % 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: 2.49 (0.14), residues: 3944 helix: 2.52 (0.10), residues: 2536 sheet: 0.39 (0.29), residues: 288 loop : -0.02 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1080 TYR 0.029 0.002 TYR B 45 PHE 0.015 0.001 PHE A 734 TRP 0.019 0.001 TRP A 984 HIS 0.003 0.001 HIS C 837 Details of bonding type rmsd covalent geometry : bond 0.00483 (30884) covalent geometry : angle 0.70814 (42168) hydrogen bonds : bond 0.04382 ( 1964) hydrogen bonds : angle 3.83336 ( 5796) link_NAG-ASN : bond 0.00259 ( 4) link_NAG-ASN : angle 1.59076 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4448.10 seconds wall clock time: 77 minutes 44.94 seconds (4664.94 seconds total)