Starting phenix.real_space_refine on Thu Mar 5 14:56:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y42_33600/03_2026/7y42_33600.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y42_33600/03_2026/7y42_33600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y42_33600/03_2026/7y42_33600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y42_33600/03_2026/7y42_33600.map" model { file = "/net/cci-nas-00/data/ceres_data/7y42_33600/03_2026/7y42_33600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y42_33600/03_2026/7y42_33600.cif" } resolution = 3.45 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= 0.003 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 14709 2.51 5 N 3780 2.21 5 O 4479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23058 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7538 Classifications: {'peptide': 968} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 46, 'TRANS': 921} Chain breaks: 15 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 7538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7538 Classifications: {'peptide': 968} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 46, 'TRANS': 921} Chain breaks: 15 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 7538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7538 Classifications: {'peptide': 968} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 46, 'TRANS': 921} Chain breaks: 15 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 148 Unusual residues: {'NAG': 9, 'REA': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 148 Unusual residues: {'NAG': 9, 'REA': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 148 Unusual residues: {'NAG': 9, 'REA': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 4.80, per 1000 atoms: 0.21 Number of scatterers: 23058 At special positions: 0 Unit cell: (128.04, 131.92, 177.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 4479 8.00 N 3780 7.00 C 14709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 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 A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 282 " " NAG D1304 " - " ASN D 331 " " NAG D1305 " - " ASN D 343 " " NAG D1306 " - " ASN D 603 " " NAG D1307 " - " ASN D 616 " " NAG D1308 " - " ASN D 657 " " NAG D1309 " - " ASN D 709 " Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 837.9 milliseconds 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5442 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 60 sheets defined 25.0% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.476A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.515A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.579A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.874A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.909A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 824 Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 869 through 874 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.973A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.033A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.801A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.692A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.446A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A1025 " --> pdb=" O SER A1021 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.877A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.476A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.516A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.579A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 636 through 638 No H-bonds generated for 'chain 'B' and resid 636 through 638' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.874A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.909A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 824 Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 869 through 874 Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.974A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.033A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.801A pdb=" N SER B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.692A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.446A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B1025 " --> pdb=" O SER B1021 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B1026 " --> pdb=" O ALA B1022 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.878A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 364 through 368 Processing helix chain 'D' and resid 383 through 389 removed outlier: 4.477A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 5.515A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 620 removed outlier: 3.579A pdb=" N VAL D 620 " --> pdb=" O CYS D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 636 through 638 No H-bonds generated for 'chain 'D' and resid 636 through 638' Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 746 through 755 removed outlier: 3.874A pdb=" N ASN D 751 " --> pdb=" O THR D 747 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D 755 " --> pdb=" O ASN D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.909A pdb=" N ASN D 764 " --> pdb=" O CYS D 760 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU D 767 " --> pdb=" O LEU D 763 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN D 779 " --> pdb=" O ASP D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 824 Processing helix chain 'D' and resid 849 through 856 Processing helix chain 'D' and resid 869 through 874 Processing helix chain 'D' and resid 897 through 907 removed outlier: 3.974A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 918 removed outlier: 4.033A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 939 removed outlier: 3.801A pdb=" N SER D 929 " --> pdb=" O ASN D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.692A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU D 959 " --> pdb=" O ASN D 955 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN D 960 " --> pdb=" O ALA D 956 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL D 963 " --> pdb=" O LEU D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.446A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY D 999 " --> pdb=" O ARG D 995 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN D1002 " --> pdb=" O THR D 998 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER D1003 " --> pdb=" O GLY D 999 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D1024 " --> pdb=" O ALA D1020 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA D1025 " --> pdb=" O SER D1021 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D1026 " --> pdb=" O ALA D1022 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR D1027 " --> pdb=" O ASN D1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1146 removed outlier: 3.878A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.503A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 51 removed outlier: 3.821A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.979A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 93 removed outlier: 4.332A pdb=" N GLY A 268 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 104 through 107 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.505A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 327 through 328 removed outlier: 4.012A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 removed outlier: 4.410A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.894A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 538 through 540 removed outlier: 5.797A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.650A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB8, first strand: chain 'A' and resid 717 through 722 removed outlier: 6.902A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AC1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.532A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.233A pdb=" N ILE A 788 " --> pdb=" O ASN D 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.381A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC5, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC6, first strand: chain 'B' and resid 50 through 51 removed outlier: 3.821A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.979A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 91 through 93 removed outlier: 4.332A pdb=" N GLY B 268 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 104 through 107 Processing sheet with id=AD1, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.505A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 327 through 328 removed outlier: 4.012A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 357 through 358 removed outlier: 4.410A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.894A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD7, first strand: chain 'B' and resid 538 through 540 removed outlier: 5.797A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.650A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AE2, first strand: chain 'B' and resid 717 through 722 removed outlier: 6.901A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AE4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.533A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.382A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE7, first strand: chain 'D' and resid 28 through 30 Processing sheet with id=AE8, first strand: chain 'D' and resid 50 through 51 removed outlier: 3.821A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 54 through 55 removed outlier: 3.979A pdb=" N PHE D 55 " --> pdb=" O GLN D 271 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN D 271 " --> pdb=" O PHE D 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 91 through 93 removed outlier: 4.332A pdb=" N GLY D 268 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA D 93 " --> pdb=" O TYR D 266 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 104 through 107 Processing sheet with id=AF3, first strand: chain 'D' and resid 311 through 313 removed outlier: 3.504A pdb=" N TYR D 313 " --> pdb=" O VAL D 597 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 327 through 328 removed outlier: 4.012A pdb=" N ARG D 328 " --> pdb=" O ASN D 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'D' and resid 357 through 358 removed outlier: 4.410A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 391 through 392 removed outlier: 3.893A pdb=" N VAL D 524 " --> pdb=" O PHE D 392 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AF8, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AF9, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.650A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 711 through 713 Processing sheet with id=AG2, first strand: chain 'D' and resid 717 through 722 removed outlier: 6.901A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 725 through 728 Processing sheet with id=AG4, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.533A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.381A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 1094 through 1097 715 hydrogen bonds defined for protein. 1884 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.51 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7332 1.34 - 1.46: 5714 1.46 - 1.58: 10378 1.58 - 1.70: 0 1.70 - 1.82: 114 Bond restraints: 23538 Sorted by residual: bond pdb=" C7 REA B1310 " pdb=" C8 REA B1310 " ideal model delta sigma weight residual 1.342 1.468 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C7 REA D1310 " pdb=" C8 REA D1310 " ideal model delta sigma weight residual 1.342 1.468 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C7 REA A1310 " pdb=" C8 REA A1310 " ideal model delta sigma weight residual 1.342 1.468 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" C11 REA D1310 " pdb=" C12 REA D1310 " ideal model delta sigma weight residual 1.349 1.472 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C11 REA A1310 " pdb=" C12 REA A1310 " ideal model delta sigma weight residual 1.349 1.472 -0.123 2.00e-02 2.50e+03 3.79e+01 ... (remaining 23533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 30610 1.86 - 3.72: 1207 3.72 - 5.58: 138 5.58 - 7.44: 28 7.44 - 9.30: 18 Bond angle restraints: 32001 Sorted by residual: angle pdb=" N ASN A 370 " pdb=" CA ASN A 370 " pdb=" C ASN A 370 " ideal model delta sigma weight residual 114.56 107.66 6.90 1.27e+00 6.20e-01 2.96e+01 angle pdb=" N ASN D 370 " pdb=" CA ASN D 370 " pdb=" C ASN D 370 " ideal model delta sigma weight residual 114.56 107.67 6.89 1.27e+00 6.20e-01 2.94e+01 angle pdb=" N ASN B 370 " pdb=" CA ASN B 370 " pdb=" C ASN B 370 " ideal model delta sigma weight residual 114.56 107.68 6.88 1.27e+00 6.20e-01 2.94e+01 angle pdb=" N VAL B 130 " pdb=" CA VAL B 130 " pdb=" C VAL B 130 " ideal model delta sigma weight residual 112.17 107.61 4.56 9.50e-01 1.11e+00 2.30e+01 angle pdb=" N VAL A 130 " pdb=" CA VAL A 130 " pdb=" C VAL A 130 " ideal model delta sigma weight residual 112.17 107.62 4.55 9.50e-01 1.11e+00 2.30e+01 ... (remaining 31996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 12870 17.54 - 35.08: 1107 35.08 - 52.62: 250 52.62 - 70.16: 53 70.16 - 87.70: 33 Dihedral angle restraints: 14313 sinusoidal: 5886 harmonic: 8427 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -173.70 87.70 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -173.70 87.70 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS D 291 " pdb=" SG CYS D 291 " pdb=" SG CYS D 301 " pdb=" CB CYS D 301 " ideal model delta sinusoidal sigma weight residual -86.00 -173.68 87.68 1 1.00e+01 1.00e-02 9.21e+01 ... (remaining 14310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2086 0.033 - 0.067: 1039 0.067 - 0.100: 450 0.100 - 0.133: 144 0.133 - 0.167: 22 Chirality restraints: 3741 Sorted by residual: chirality pdb=" CA VAL B 267 " pdb=" N VAL B 267 " pdb=" C VAL B 267 " pdb=" CB VAL B 267 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA VAL A 267 " pdb=" N VAL A 267 " pdb=" C VAL A 267 " pdb=" CB VAL A 267 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA VAL D 267 " pdb=" N VAL D 267 " pdb=" C VAL D 267 " pdb=" CB VAL D 267 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.73e-01 ... (remaining 3738 not shown) Planarity restraints: 4116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 REA B1310 " -0.380 2.00e-02 2.50e+03 2.25e-01 6.32e+02 pdb=" C11 REA B1310 " 0.272 2.00e-02 2.50e+03 pdb=" C19 REA B1310 " -0.012 2.00e-02 2.50e+03 pdb=" C8 REA B1310 " 0.177 2.00e-02 2.50e+03 pdb=" C9 REA B1310 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 REA A1310 " 0.380 2.00e-02 2.50e+03 2.25e-01 6.31e+02 pdb=" C11 REA A1310 " -0.272 2.00e-02 2.50e+03 pdb=" C19 REA A1310 " 0.012 2.00e-02 2.50e+03 pdb=" C8 REA A1310 " -0.177 2.00e-02 2.50e+03 pdb=" C9 REA A1310 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 REA D1310 " 0.379 2.00e-02 2.50e+03 2.25e-01 6.30e+02 pdb=" C11 REA D1310 " -0.271 2.00e-02 2.50e+03 pdb=" C19 REA D1310 " 0.012 2.00e-02 2.50e+03 pdb=" C8 REA D1310 " -0.177 2.00e-02 2.50e+03 pdb=" C9 REA D1310 " 0.057 2.00e-02 2.50e+03 ... (remaining 4113 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 585 2.68 - 3.23: 22423 3.23 - 3.79: 33564 3.79 - 4.34: 44864 4.34 - 4.90: 75304 Nonbonded interactions: 176740 Sorted by model distance: nonbonded pdb=" OG SER D 116 " pdb=" O VAL D 130 " model vdw 2.121 3.040 nonbonded pdb=" OG SER B 116 " pdb=" O VAL B 130 " model vdw 2.121 3.040 nonbonded pdb=" OG SER A 116 " pdb=" O VAL A 130 " model vdw 2.121 3.040 nonbonded pdb=" O ASN D 99 " pdb=" NH1 ARG D 102 " model vdw 2.151 3.120 nonbonded pdb=" O ASN A 99 " pdb=" NH1 ARG A 102 " model vdw 2.152 3.120 ... (remaining 176735 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.240 Find NCS groups from input model: 0.200 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 0.006 0.126 23589 Z= 0.303 Angle : 0.851 9.302 32130 Z= 0.480 Chirality : 0.048 0.167 3741 Planarity : 0.010 0.225 4089 Dihedral : 14.426 84.498 8799 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.59 % Allowed : 0.24 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.15), residues: 2814 helix: -1.29 (0.20), residues: 684 sheet: -2.01 (0.21), residues: 555 loop : -2.38 (0.14), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 995 TYR 0.031 0.002 TYR D 917 PHE 0.033 0.002 PHE A 338 TRP 0.017 0.002 TRP D 64 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00645 (23538) covalent geometry : angle 0.84385 (32001) SS BOND : bond 0.00252 ( 24) SS BOND : angle 1.81965 ( 48) hydrogen bonds : bond 0.20588 ( 715) hydrogen bonds : angle 8.49936 ( 1884) link_NAG-ASN : bond 0.00212 ( 27) link_NAG-ASN : angle 2.07705 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 994 ASP cc_start: 0.7894 (t70) cc_final: 0.7607 (t70) REVERT: B 855 PHE cc_start: 0.7965 (m-80) cc_final: 0.7407 (m-80) REVERT: B 902 MET cc_start: 0.7860 (tpp) cc_final: 0.7580 (tpt) REVERT: D 92 PHE cc_start: 0.7394 (t80) cc_final: 0.7119 (t80) REVERT: D 902 MET cc_start: 0.7922 (tpp) cc_final: 0.7483 (tpt) outliers start: 15 outliers final: 6 residues processed: 211 average time/residue: 0.1516 time to fit residues: 50.8363 Evaluate side-chains 167 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 161 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 309 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1071 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.134360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.103497 restraints weight = 42131.434| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.95 r_work: 0.3183 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23589 Z= 0.141 Angle : 0.624 9.723 32130 Z= 0.321 Chirality : 0.044 0.153 3741 Planarity : 0.005 0.058 4089 Dihedral : 7.646 86.847 3696 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.67 % Allowed : 5.59 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.15), residues: 2814 helix: -0.91 (0.20), residues: 705 sheet: -1.54 (0.23), residues: 534 loop : -2.30 (0.14), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 102 TYR 0.021 0.002 TYR D 904 PHE 0.015 0.002 PHE D 55 TRP 0.010 0.001 TRP D 436 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00318 (23538) covalent geometry : angle 0.61759 (32001) SS BOND : bond 0.00300 ( 24) SS BOND : angle 1.70588 ( 48) hydrogen bonds : bond 0.04775 ( 715) hydrogen bonds : angle 6.15422 ( 1884) link_NAG-ASN : bond 0.00367 ( 27) link_NAG-ASN : angle 1.50688 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 855 PHE cc_start: 0.8284 (m-80) cc_final: 0.7880 (m-80) REVERT: B 420 ASP cc_start: 0.8072 (m-30) cc_final: 0.7730 (t0) REVERT: B 473 TYR cc_start: 0.7838 (t80) cc_final: 0.7637 (t80) REVERT: B 855 PHE cc_start: 0.8274 (m-80) cc_final: 0.7698 (m-80) REVERT: D 104 TRP cc_start: 0.4401 (t-100) cc_final: 0.3095 (t60) REVERT: D 740 MET cc_start: 0.8825 (ttt) cc_final: 0.8625 (ttp) REVERT: D 902 MET cc_start: 0.8029 (tpp) cc_final: 0.7782 (tpt) outliers start: 17 outliers final: 13 residues processed: 204 average time/residue: 0.1353 time to fit residues: 44.9294 Evaluate side-chains 175 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 979 ASP Chi-restraints excluded: chain D residue 994 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 178 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 274 optimal weight: 4.9990 chunk 199 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 33 optimal weight: 0.1980 chunk 94 optimal weight: 7.9990 chunk 196 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.130387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.099835 restraints weight = 42856.898| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.18 r_work: 0.3091 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 23589 Z= 0.291 Angle : 0.697 9.809 32130 Z= 0.356 Chirality : 0.048 0.249 3741 Planarity : 0.005 0.057 4089 Dihedral : 7.504 88.595 3675 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 1.55 % Allowed : 9.51 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.15), residues: 2814 helix: -1.10 (0.19), residues: 723 sheet: -1.78 (0.21), residues: 534 loop : -2.29 (0.14), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1091 TYR 0.030 0.002 TYR D 369 PHE 0.023 0.002 PHE B 898 TRP 0.012 0.002 TRP B 436 HIS 0.005 0.001 HIS D1064 Details of bonding type rmsd covalent geometry : bond 0.00693 (23538) covalent geometry : angle 0.69028 (32001) SS BOND : bond 0.00334 ( 24) SS BOND : angle 1.81415 ( 48) hydrogen bonds : bond 0.05337 ( 715) hydrogen bonds : angle 6.03879 ( 1884) link_NAG-ASN : bond 0.00290 ( 27) link_NAG-ASN : angle 1.64186 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 ASN cc_start: 0.8812 (t0) cc_final: 0.8592 (t0) REVERT: A 855 PHE cc_start: 0.8342 (m-80) cc_final: 0.7971 (m-80) REVERT: A 994 ASP cc_start: 0.8513 (t70) cc_final: 0.8247 (t70) REVERT: B 92 PHE cc_start: 0.7511 (t80) cc_final: 0.6897 (t80) REVERT: B 420 ASP cc_start: 0.8075 (m-30) cc_final: 0.7766 (t0) REVERT: B 473 TYR cc_start: 0.7899 (t80) cc_final: 0.7628 (t80) REVERT: B 855 PHE cc_start: 0.8465 (m-80) cc_final: 0.7835 (m-80) REVERT: D 855 PHE cc_start: 0.8347 (m-80) cc_final: 0.7936 (m-80) outliers start: 39 outliers final: 31 residues processed: 208 average time/residue: 0.1341 time to fit residues: 46.7680 Evaluate side-chains 193 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 979 ASP Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1142 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 6 optimal weight: 20.0000 chunk 10 optimal weight: 0.7980 chunk 200 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 262 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 949 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.134831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.101717 restraints weight = 41973.564| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.05 r_work: 0.3164 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23589 Z= 0.110 Angle : 0.558 9.853 32130 Z= 0.284 Chirality : 0.043 0.148 3741 Planarity : 0.004 0.055 4089 Dihedral : 7.104 89.513 3675 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.94 % Allowed : 11.22 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.15), residues: 2814 helix: -0.66 (0.20), residues: 720 sheet: -1.48 (0.22), residues: 534 loop : -2.08 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 273 TYR 0.017 0.001 TYR D 369 PHE 0.014 0.001 PHE A 55 TRP 0.007 0.001 TRP A 104 HIS 0.002 0.000 HIS D1088 Details of bonding type rmsd covalent geometry : bond 0.00251 (23538) covalent geometry : angle 0.55010 (32001) SS BOND : bond 0.00269 ( 24) SS BOND : angle 1.52197 ( 48) hydrogen bonds : bond 0.03823 ( 715) hydrogen bonds : angle 5.48817 ( 1884) link_NAG-ASN : bond 0.00178 ( 27) link_NAG-ASN : angle 1.62505 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 0.804 Fit side-chains REVERT: A 347 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8926 (m-80) REVERT: A 542 ASN cc_start: 0.8753 (t0) cc_final: 0.8513 (t0) REVERT: A 855 PHE cc_start: 0.8285 (m-80) cc_final: 0.7895 (m-80) REVERT: B 347 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8871 (m-10) REVERT: B 396 TYR cc_start: 0.8406 (m-80) cc_final: 0.8204 (m-80) REVERT: B 420 ASP cc_start: 0.8048 (m-30) cc_final: 0.7664 (t0) REVERT: B 473 TYR cc_start: 0.7764 (t80) cc_final: 0.7513 (t80) REVERT: B 855 PHE cc_start: 0.8380 (m-80) cc_final: 0.7933 (m-80) REVERT: B 887 THR cc_start: 0.9311 (p) cc_final: 0.9042 (t) REVERT: D 347 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8878 (m-80) REVERT: D 855 PHE cc_start: 0.8298 (m-80) cc_final: 0.7955 (m-80) outliers start: 49 outliers final: 32 residues processed: 234 average time/residue: 0.1368 time to fit residues: 53.1842 Evaluate side-chains 190 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 979 ASP Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1142 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 111 optimal weight: 9.9990 chunk 99 optimal weight: 0.3980 chunk 98 optimal weight: 6.9990 chunk 131 optimal weight: 0.0040 chunk 202 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 48 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.135854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102939 restraints weight = 41532.155| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.06 r_work: 0.3191 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23589 Z= 0.102 Angle : 0.543 9.924 32130 Z= 0.275 Chirality : 0.043 0.151 3741 Planarity : 0.004 0.053 4089 Dihedral : 6.729 87.111 3675 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.86 % Allowed : 12.60 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.15), residues: 2814 helix: -0.33 (0.21), residues: 708 sheet: -1.37 (0.22), residues: 534 loop : -1.95 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 102 TYR 0.016 0.001 TYR D 904 PHE 0.014 0.001 PHE A 562 TRP 0.007 0.001 TRP A 104 HIS 0.002 0.000 HIS D1088 Details of bonding type rmsd covalent geometry : bond 0.00234 (23538) covalent geometry : angle 0.53701 (32001) SS BOND : bond 0.00299 ( 24) SS BOND : angle 1.43960 ( 48) hydrogen bonds : bond 0.03485 ( 715) hydrogen bonds : angle 5.18875 ( 1884) link_NAG-ASN : bond 0.00210 ( 27) link_NAG-ASN : angle 1.35256 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 181 time to evaluate : 0.886 Fit side-chains REVERT: A 290 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.7917 (t0) REVERT: A 347 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8878 (m-10) REVERT: A 542 ASN cc_start: 0.8677 (t0) cc_final: 0.8462 (t0) REVERT: A 745 ASP cc_start: 0.8155 (m-30) cc_final: 0.7505 (t0) REVERT: A 855 PHE cc_start: 0.8311 (m-80) cc_final: 0.7895 (m-80) REVERT: B 347 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8949 (m-10) REVERT: B 420 ASP cc_start: 0.8148 (m-30) cc_final: 0.7718 (t0) REVERT: B 473 TYR cc_start: 0.7797 (t80) cc_final: 0.7473 (t80) REVERT: B 756 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.7158 (t80) REVERT: B 795 LYS cc_start: 0.6311 (tptt) cc_final: 0.5210 (mmmt) REVERT: B 855 PHE cc_start: 0.8312 (m-80) cc_final: 0.8067 (m-80) REVERT: B 887 THR cc_start: 0.9335 (p) cc_final: 0.9040 (t) REVERT: D 347 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8945 (m-10) REVERT: D 855 PHE cc_start: 0.8271 (m-80) cc_final: 0.8029 (m-80) outliers start: 47 outliers final: 39 residues processed: 215 average time/residue: 0.1384 time to fit residues: 49.8334 Evaluate side-chains 201 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 979 ASP Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1142 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 29 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 282 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 274 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.133553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.100009 restraints weight = 42363.458| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.14 r_work: 0.3118 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23589 Z= 0.168 Angle : 0.583 9.967 32130 Z= 0.294 Chirality : 0.046 0.780 3741 Planarity : 0.004 0.054 4089 Dihedral : 6.654 88.423 3675 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.81 % Allowed : 12.76 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.15), residues: 2814 helix: -0.26 (0.21), residues: 699 sheet: -1.41 (0.22), residues: 534 loop : -1.91 (0.14), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.021 0.001 TYR D 369 PHE 0.015 0.001 PHE D 898 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00404 (23538) covalent geometry : angle 0.57185 (32001) SS BOND : bond 0.00274 ( 24) SS BOND : angle 1.52726 ( 48) hydrogen bonds : bond 0.03913 ( 715) hydrogen bonds : angle 5.23435 ( 1884) link_NAG-ASN : bond 0.00201 ( 27) link_NAG-ASN : angle 2.05664 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 173 time to evaluate : 0.789 Fit side-chains REVERT: A 347 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8947 (m-10) REVERT: A 542 ASN cc_start: 0.8714 (t0) cc_final: 0.8479 (t0) REVERT: A 745 ASP cc_start: 0.8108 (m-30) cc_final: 0.7478 (t0) REVERT: A 756 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.7377 (t80) REVERT: A 855 PHE cc_start: 0.8358 (m-80) cc_final: 0.8063 (m-80) REVERT: B 347 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.9003 (m-10) REVERT: B 420 ASP cc_start: 0.8137 (m-30) cc_final: 0.7823 (t0) REVERT: B 473 TYR cc_start: 0.7792 (t80) cc_final: 0.7489 (t80) REVERT: B 756 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.7290 (t80) REVERT: B 855 PHE cc_start: 0.8304 (m-80) cc_final: 0.8059 (m-80) REVERT: B 887 THR cc_start: 0.9305 (p) cc_final: 0.9066 (t) REVERT: D 347 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.9034 (m-10) REVERT: D 756 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.7353 (t80) outliers start: 71 outliers final: 47 residues processed: 230 average time/residue: 0.1337 time to fit residues: 52.6805 Evaluate side-chains 213 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 160 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 756 TYR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 979 ASP Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1142 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 126 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.131661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.097007 restraints weight = 42217.979| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.08 r_work: 0.3106 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23589 Z= 0.190 Angle : 0.612 18.682 32130 Z= 0.306 Chirality : 0.049 1.018 3741 Planarity : 0.004 0.054 4089 Dihedral : 6.607 87.588 3675 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.85 % Allowed : 13.79 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.15), residues: 2814 helix: -0.26 (0.21), residues: 699 sheet: -1.56 (0.21), residues: 564 loop : -1.86 (0.14), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 273 TYR 0.022 0.001 TYR D 369 PHE 0.014 0.001 PHE D 562 TRP 0.009 0.002 TRP A 104 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00455 (23538) covalent geometry : angle 0.59230 (32001) SS BOND : bond 0.00275 ( 24) SS BOND : angle 1.55405 ( 48) hydrogen bonds : bond 0.04062 ( 715) hydrogen bonds : angle 5.27662 ( 1884) link_NAG-ASN : bond 0.00812 ( 27) link_NAG-ASN : angle 2.94659 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 173 time to evaluate : 0.851 Fit side-chains REVERT: A 229 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6430 (tt) REVERT: A 347 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8994 (m-80) REVERT: A 542 ASN cc_start: 0.8521 (t0) cc_final: 0.8286 (t0) REVERT: A 606 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8275 (t0) REVERT: A 756 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.7338 (t80) REVERT: A 855 PHE cc_start: 0.8366 (m-80) cc_final: 0.8035 (m-80) REVERT: B 92 PHE cc_start: 0.7244 (t80) cc_final: 0.6755 (t80) REVERT: B 347 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.9041 (m-10) REVERT: B 405 ASP cc_start: 0.7841 (m-30) cc_final: 0.7500 (m-30) REVERT: B 420 ASP cc_start: 0.8379 (m-30) cc_final: 0.7887 (t0) REVERT: B 473 TYR cc_start: 0.7919 (t80) cc_final: 0.7497 (t80) REVERT: B 756 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.7220 (t80) REVERT: B 795 LYS cc_start: 0.6687 (tptt) cc_final: 0.5499 (mmmt) REVERT: B 855 PHE cc_start: 0.8359 (m-80) cc_final: 0.8095 (m-80) REVERT: B 887 THR cc_start: 0.9350 (p) cc_final: 0.9057 (t) REVERT: D 347 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.9074 (m-10) REVERT: D 756 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.7338 (t80) outliers start: 72 outliers final: 53 residues processed: 229 average time/residue: 0.1298 time to fit residues: 51.5716 Evaluate side-chains 227 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 166 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 756 TYR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 979 ASP Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1142 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 228 optimal weight: 0.8980 chunk 255 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 48 optimal weight: 0.0770 chunk 188 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.136577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.105408 restraints weight = 41660.427| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.91 r_work: 0.3191 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23589 Z= 0.113 Angle : 0.566 18.950 32130 Z= 0.281 Chirality : 0.048 1.184 3741 Planarity : 0.004 0.054 4089 Dihedral : 6.329 82.054 3675 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.26 % Allowed : 14.70 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.15), residues: 2814 helix: -0.11 (0.21), residues: 717 sheet: -1.42 (0.21), residues: 564 loop : -1.76 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.017 0.001 TYR A 473 PHE 0.015 0.001 PHE D 55 TRP 0.010 0.001 TRP A 104 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00263 (23538) covalent geometry : angle 0.54683 (32001) SS BOND : bond 0.00255 ( 24) SS BOND : angle 1.40397 ( 48) hydrogen bonds : bond 0.03429 ( 715) hydrogen bonds : angle 5.05006 ( 1884) link_NAG-ASN : bond 0.00780 ( 27) link_NAG-ASN : angle 2.77590 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 180 time to evaluate : 0.818 Fit side-chains REVERT: A 229 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6767 (tt) REVERT: A 347 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8919 (m-10) REVERT: A 542 ASN cc_start: 0.8656 (t0) cc_final: 0.8420 (t0) REVERT: A 756 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.7320 (t80) REVERT: A 855 PHE cc_start: 0.8274 (m-80) cc_final: 0.7984 (m-80) REVERT: B 92 PHE cc_start: 0.7263 (t80) cc_final: 0.6852 (t80) REVERT: B 347 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8912 (m-10) REVERT: B 396 TYR cc_start: 0.8140 (m-80) cc_final: 0.7913 (m-80) REVERT: B 405 ASP cc_start: 0.8055 (m-30) cc_final: 0.7710 (m-30) REVERT: B 420 ASP cc_start: 0.8030 (m-30) cc_final: 0.7724 (t0) REVERT: B 473 TYR cc_start: 0.7731 (t80) cc_final: 0.7453 (t80) REVERT: B 756 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.7194 (t80) REVERT: B 795 LYS cc_start: 0.6099 (tptt) cc_final: 0.5452 (mmmt) REVERT: B 887 THR cc_start: 0.9258 (p) cc_final: 0.9019 (t) REVERT: B 994 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7870 (t0) REVERT: D 347 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8940 (m-10) REVERT: D 756 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.7217 (t80) REVERT: D 795 LYS cc_start: 0.6073 (tptt) cc_final: 0.5102 (mmmt) outliers start: 57 outliers final: 44 residues processed: 224 average time/residue: 0.1327 time to fit residues: 51.2665 Evaluate side-chains 221 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 756 TYR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 979 ASP Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1142 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 164 optimal weight: 0.0980 chunk 48 optimal weight: 0.0870 chunk 73 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 249 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 235 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.135570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.101188 restraints weight = 42092.344| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.07 r_work: 0.3175 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23589 Z= 0.102 Angle : 0.550 13.017 32130 Z= 0.274 Chirality : 0.046 0.695 3741 Planarity : 0.004 0.053 4089 Dihedral : 6.241 89.172 3675 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.22 % Allowed : 15.26 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.15), residues: 2814 helix: 0.07 (0.21), residues: 699 sheet: -1.38 (0.20), residues: 579 loop : -1.73 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.019 0.001 TYR A 473 PHE 0.014 0.001 PHE B 55 TRP 0.011 0.001 TRP A 104 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00234 (23538) covalent geometry : angle 0.53332 (32001) SS BOND : bond 0.00256 ( 24) SS BOND : angle 1.33221 ( 48) hydrogen bonds : bond 0.03183 ( 715) hydrogen bonds : angle 4.89334 ( 1884) link_NAG-ASN : bond 0.00650 ( 27) link_NAG-ASN : angle 2.56630 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 190 time to evaluate : 0.871 Fit side-chains REVERT: A 229 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6473 (tt) REVERT: A 347 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8966 (m-10) REVERT: A 756 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.7236 (t80) REVERT: A 855 PHE cc_start: 0.8325 (m-80) cc_final: 0.8055 (m-80) REVERT: B 92 PHE cc_start: 0.6811 (t80) cc_final: 0.6427 (t80) REVERT: B 347 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.9036 (m-10) REVERT: B 405 ASP cc_start: 0.7794 (m-30) cc_final: 0.7391 (m-30) REVERT: B 420 ASP cc_start: 0.8385 (m-30) cc_final: 0.7873 (t0) REVERT: B 473 TYR cc_start: 0.7848 (t80) cc_final: 0.7399 (t80) REVERT: B 756 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.7092 (t80) REVERT: B 795 LYS cc_start: 0.6407 (tptt) cc_final: 0.5558 (mmmt) REVERT: B 855 PHE cc_start: 0.8255 (m-80) cc_final: 0.7706 (m-80) REVERT: B 887 THR cc_start: 0.9345 (p) cc_final: 0.8980 (t) REVERT: B 994 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8069 (t0) REVERT: D 347 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.9055 (m-10) REVERT: D 420 ASP cc_start: 0.8406 (t70) cc_final: 0.7677 (t0) REVERT: D 460 ASN cc_start: 0.7944 (t0) cc_final: 0.7389 (t0) REVERT: D 756 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.7266 (t80) REVERT: D 795 LYS cc_start: 0.6439 (tptt) cc_final: 0.5432 (mmmt) REVERT: D 873 TYR cc_start: 0.8692 (m-80) cc_final: 0.8364 (m-80) outliers start: 56 outliers final: 42 residues processed: 230 average time/residue: 0.1386 time to fit residues: 53.7122 Evaluate side-chains 220 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 756 TYR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 979 ASP Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1142 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 261 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 286 optimal weight: 6.9990 chunk 136 optimal weight: 0.0050 chunk 285 optimal weight: 0.8980 chunk 178 optimal weight: 0.7980 chunk 194 optimal weight: 0.0050 chunk 180 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 overall best weight: 0.5208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.136330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.101855 restraints weight = 41841.268| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.04 r_work: 0.3189 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23589 Z= 0.098 Angle : 0.541 16.349 32130 Z= 0.270 Chirality : 0.045 0.574 3741 Planarity : 0.004 0.053 4089 Dihedral : 6.030 86.779 3675 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.02 % Allowed : 15.89 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.15), residues: 2814 helix: 0.22 (0.21), residues: 699 sheet: -1.24 (0.20), residues: 555 loop : -1.70 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1019 TYR 0.018 0.001 TYR A 473 PHE 0.016 0.001 PHE D 562 TRP 0.011 0.001 TRP A 104 HIS 0.006 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00224 (23538) covalent geometry : angle 0.52091 (32001) SS BOND : bond 0.00257 ( 24) SS BOND : angle 1.31410 ( 48) hydrogen bonds : bond 0.03053 ( 715) hydrogen bonds : angle 4.82811 ( 1884) link_NAG-ASN : bond 0.00960 ( 27) link_NAG-ASN : angle 2.81433 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 0.867 Fit side-chains REVERT: A 229 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6566 (tt) REVERT: A 290 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8398 (m-30) REVERT: A 347 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8938 (m-10) REVERT: A 756 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.7255 (t80) REVERT: A 855 PHE cc_start: 0.8254 (m-80) cc_final: 0.8026 (m-80) REVERT: B 92 PHE cc_start: 0.6718 (t80) cc_final: 0.6403 (t80) REVERT: B 347 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.9011 (m-10) REVERT: B 420 ASP cc_start: 0.8379 (m-30) cc_final: 0.7868 (t0) REVERT: B 473 TYR cc_start: 0.7845 (t80) cc_final: 0.7394 (t80) REVERT: B 756 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.7050 (t80) REVERT: B 795 LYS cc_start: 0.6333 (tptt) cc_final: 0.5435 (mmmt) REVERT: B 887 THR cc_start: 0.9344 (p) cc_final: 0.8967 (t) REVERT: B 994 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8008 (t0) REVERT: D 347 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.9032 (m-10) REVERT: D 420 ASP cc_start: 0.8472 (t70) cc_final: 0.7731 (t0) REVERT: D 460 ASN cc_start: 0.7852 (t0) cc_final: 0.7359 (t0) REVERT: D 756 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.7231 (t80) REVERT: D 795 LYS cc_start: 0.6222 (tptt) cc_final: 0.5449 (mmmt) outliers start: 51 outliers final: 39 residues processed: 227 average time/residue: 0.1406 time to fit residues: 53.4272 Evaluate side-chains 221 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 173 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 756 TYR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 979 ASP Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1142 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 15 optimal weight: 10.0000 chunk 287 optimal weight: 4.9990 chunk 284 optimal weight: 0.8980 chunk 192 optimal weight: 20.0000 chunk 162 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 949 GLN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 784 GLN ** D 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.130126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.096003 restraints weight = 42132.124| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.94 r_work: 0.3085 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 23589 Z= 0.297 Angle : 0.689 15.813 32130 Z= 0.349 Chirality : 0.051 0.573 3741 Planarity : 0.005 0.054 4089 Dihedral : 6.603 89.263 3675 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 2.34 % Allowed : 15.62 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.15), residues: 2814 helix: -0.34 (0.20), residues: 726 sheet: -1.54 (0.20), residues: 567 loop : -1.77 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 102 TYR 0.029 0.002 TYR B 369 PHE 0.022 0.002 PHE D 898 TRP 0.013 0.002 TRP B 436 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00711 (23538) covalent geometry : angle 0.67260 (32001) SS BOND : bond 0.00355 ( 24) SS BOND : angle 1.70606 ( 48) hydrogen bonds : bond 0.04807 ( 715) hydrogen bonds : angle 5.45920 ( 1884) link_NAG-ASN : bond 0.00635 ( 27) link_NAG-ASN : angle 2.81377 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4736.29 seconds wall clock time: 82 minutes 7.88 seconds (4927.88 seconds total)