Starting phenix.real_space_refine on Fri Jun 20 03:12:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y42_33600/06_2025/7y42_33600.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y42_33600/06_2025/7y42_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_33600/06_2025/7y42_33600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y42_33600/06_2025/7y42_33600.map" model { file = "/net/cci-nas-00/data/ceres_data/7y42_33600/06_2025/7y42_33600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y42_33600/06_2025/7y42_33600.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.46, per 1000 atoms: 0.58 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: 6.24 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 3.89 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: 10.56 Time building geometry restraints manager: 7.39 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: 0.15 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: 2.150 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: 0.030 Extract box with map and model: 1.030 Check model and map are aligned: 0.180 Set scattering table: 0.200 Process input model: 56.710 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.100 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: 0.020 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.790 ------------------------------------------------------------------------------- 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 : 11.84 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.002 TRP D 64 HIS 0.004 0.001 HIS B1064 PHE 0.033 0.002 PHE A 338 TYR 0.031 0.002 TYR D 917 ARG 0.009 0.001 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 27) link_NAG-ASN : angle 2.07705 ( 81) hydrogen bonds : bond 0.20588 ( 715) hydrogen bonds : angle 8.49936 ( 1884) SS BOND : bond 0.00252 ( 24) SS BOND : angle 1.81965 ( 48) covalent geometry : bond 0.00645 (23538) covalent geometry : angle 0.84385 (32001) *********************** 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 : 2.654 Fit side-chains 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: 0.7578 (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: 0.7482 (tpt) outliers start: 15 outliers final: 5 residues processed: 211 average time/residue: 0.3459 time to fit residues: 115.2867 Evaluate side-chains 166 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 161 time to evaluate : 2.671 ------------------------------------------------------------------------------- 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 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 243 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 137 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** B 544 ASN B1071 GLN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1071 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.134128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.103446 restraints weight = 42111.111| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.95 r_work: 0.3178 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1099 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 : 0.625 9.689 32130 Z= 0.322 Chirality : 0.044 0.150 3741 Planarity : 0.005 0.058 4089 Dihedral : 7.710 87.822 3692 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.71 % Allowed : 5.35 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.15), residues: 2814 helix: -0.92 (0.20), residues: 705 sheet: -1.54 (0.23), residues: 534 loop : -2.29 (0.14), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 HIS 0.003 0.001 HIS B 49 PHE 0.015 0.002 PHE A 92 TYR 0.021 0.002 TYR D 904 ARG 0.006 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 27) link_NAG-ASN : angle 1.63108 ( 81) hydrogen bonds : bond 0.05169 ( 715) hydrogen bonds : angle 6.22055 ( 1884) SS BOND : bond 0.00300 ( 24) SS BOND : angle 1.72228 ( 48) covalent geometry : bond 0.00321 (23538) covalent geometry : angle 0.61762 (32001) *********************** 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 212 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 4.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 855 PHE cc_start: 0.8235 (m-80) cc_final: 0.7838 (m-80) REVERT: B 420 ASP cc_start: 0.8005 (m-30) cc_final: 0.7726 (t0) REVERT: B 855 PHE cc_start: 0.8236 (m-80) cc_final: 0.7688 (m-80) REVERT: D 104 TRP cc_start: 0.4438 (t-100) cc_final: 0.3153 (t60) REVERT: D 855 PHE cc_start: 0.8335 (m-80) cc_final: 0.7876 (m-80) REVERT: D 902 MET cc_start: 0.7983 (tpp) cc_final: 0.7760 (tpt) outliers start: 18 outliers final: 14 residues processed: 202 average time/residue: 0.4391 time to fit residues: 149.5114 Evaluate side-chains 170 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 2.721 ------------------------------------------------------------------------------- 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 544 ASN 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 97 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 190 optimal weight: 0.0980 chunk 87 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 154 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.133010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.102754 restraints weight = 42066.716| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.06 r_work: 0.3159 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23589 Z= 0.175 Angle : 0.607 9.835 32130 Z= 0.310 Chirality : 0.045 0.140 3741 Planarity : 0.005 0.056 4089 Dihedral : 7.230 89.236 3675 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.35 % Allowed : 8.60 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.15), residues: 2814 helix: -0.86 (0.19), residues: 723 sheet: -1.55 (0.22), residues: 534 loop : -2.21 (0.14), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS D1064 PHE 0.016 0.002 PHE B 543 TYR 0.022 0.002 TYR D 369 ARG 0.007 0.001 ARG D 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 27) link_NAG-ASN : angle 1.52497 ( 81) hydrogen bonds : bond 0.04573 ( 715) hydrogen bonds : angle 5.78126 ( 1884) SS BOND : bond 0.00301 ( 24) SS BOND : angle 1.64954 ( 48) covalent geometry : bond 0.00417 (23538) covalent geometry : angle 0.60013 (32001) *********************** 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 213 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.7878 (t0) cc_final: 0.7661 (t70) REVERT: A 542 ASN cc_start: 0.8775 (t0) cc_final: 0.8565 (t0) REVERT: A 855 PHE cc_start: 0.8217 (m-80) cc_final: 0.7843 (m-80) REVERT: B 420 ASP cc_start: 0.8050 (m-30) cc_final: 0.7694 (t0) REVERT: B 855 PHE cc_start: 0.8353 (m-80) cc_final: 0.7751 (m-80) REVERT: D 420 ASP cc_start: 0.7650 (t0) cc_final: 0.7403 (t70) REVERT: D 460 ASN cc_start: 0.8228 (m-40) cc_final: 0.7906 (m-40) REVERT: D 855 PHE cc_start: 0.8355 (m-80) cc_final: 0.7958 (m-80) REVERT: D 902 MET cc_start: 0.8054 (tpp) cc_final: 0.7817 (tpp) outliers start: 34 outliers final: 25 residues processed: 200 average time/residue: 0.2994 time to fit residues: 100.4892 Evaluate side-chains 186 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 571 ASP 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 1142 GLN Chi-restraints excluded: chain B residue 42 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 1142 GLN Chi-restraints excluded: chain D residue 42 VAL 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 194 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 263 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3825 r_free = 0.3825 target = 0.133645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.103171 restraints weight = 42430.004| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.03 r_work: 0.3162 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23589 Z= 0.158 Angle : 0.578 9.903 32130 Z= 0.294 Chirality : 0.044 0.149 3741 Planarity : 0.004 0.055 4089 Dihedral : 6.935 86.996 3675 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.18 % Allowed : 10.15 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.15), residues: 2814 helix: -0.68 (0.20), residues: 720 sheet: -1.48 (0.22), residues: 534 loop : -2.11 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.002 0.001 HIS B1064 PHE 0.014 0.001 PHE A 55 TYR 0.021 0.001 TYR D 369 ARG 0.008 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00128 ( 27) link_NAG-ASN : angle 1.48138 ( 81) hydrogen bonds : bond 0.04157 ( 715) hydrogen bonds : angle 5.53775 ( 1884) SS BOND : bond 0.00281 ( 24) SS BOND : angle 1.59734 ( 48) covalent geometry : bond 0.00377 (23538) covalent geometry : angle 0.57063 (32001) *********************** 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: 55 poor density : 194 time to evaluate : 2.551 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8812 (m-80) REVERT: A 542 ASN cc_start: 0.8742 (t0) cc_final: 0.8521 (t0) REVERT: A 855 PHE cc_start: 0.8258 (m-80) cc_final: 0.7923 (m-80) REVERT: A 906 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8624 (m-10) REVERT: B 420 ASP cc_start: 0.7910 (m-30) cc_final: 0.7604 (t0) REVERT: B 855 PHE cc_start: 0.8313 (m-80) cc_final: 0.7826 (m-80) REVERT: D 420 ASP cc_start: 0.7753 (t0) cc_final: 0.7437 (t70) REVERT: D 855 PHE cc_start: 0.8279 (m-80) cc_final: 0.7947 (m-80) outliers start: 55 outliers final: 40 residues processed: 235 average time/residue: 0.3094 time to fit residues: 122.4596 Evaluate side-chains 204 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 512 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 945 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 291 CYS 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 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 945 LEU 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 D residue 277 LEU Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 395 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 235 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 246 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 253 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 ASN ** 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 = 0.3772 r_free = 0.3772 target = 0.129539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.095829 restraints weight = 42616.407| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.82 r_work: 0.3092 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 23589 Z= 0.315 Angle : 0.699 9.898 32130 Z= 0.357 Chirality : 0.048 0.168 3741 Planarity : 0.005 0.056 4089 Dihedral : 7.154 85.485 3675 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 2.46 % Allowed : 12.33 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.15), residues: 2814 helix: -0.94 (0.19), residues: 720 sheet: -1.79 (0.21), residues: 543 loop : -2.18 (0.14), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 436 HIS 0.005 0.001 HIS D1064 PHE 0.020 0.002 PHE D 898 TYR 0.030 0.002 TYR D 369 ARG 0.007 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 27) link_NAG-ASN : angle 1.74608 ( 81) hydrogen bonds : bond 0.05176 ( 715) hydrogen bonds : angle 5.80978 ( 1884) SS BOND : bond 0.00326 ( 24) SS BOND : angle 1.82050 ( 48) covalent geometry : bond 0.00755 (23538) covalent geometry : angle 0.69144 (32001) *********************** 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 232 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 170 time to evaluate : 2.578 Fit side-chains REVERT: A 347 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.9014 (m-80) REVERT: A 542 ASN cc_start: 0.8853 (t0) cc_final: 0.8592 (t0) REVERT: A 756 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.7322 (t80) REVERT: A 855 PHE cc_start: 0.8414 (m-80) cc_final: 0.8066 (m-80) REVERT: A 994 ASP cc_start: 0.8548 (t70) cc_final: 0.8199 (t70) REVERT: B 92 PHE cc_start: 0.7553 (t80) cc_final: 0.6960 (t80) REVERT: B 347 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8936 (m-10) REVERT: B 420 ASP cc_start: 0.8135 (m-30) cc_final: 0.7802 (t0) REVERT: B 756 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.7244 (t80) REVERT: B 855 PHE cc_start: 0.8455 (m-80) cc_final: 0.8155 (m-80) REVERT: D 347 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.9030 (m-10) REVERT: D 756 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.7410 (t80) REVERT: D 855 PHE cc_start: 0.8332 (m-80) cc_final: 0.8030 (m-80) outliers start: 62 outliers final: 49 residues processed: 216 average time/residue: 0.2999 time to fit residues: 109.4428 Evaluate side-chains 203 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 148 time to evaluate : 2.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 512 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 756 TYR 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 395 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 756 TYR Chi-restraints excluded: chain B residue 849 LEU 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 945 LEU 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 1141 LEU Chi-restraints excluded: chain D residue 42 VAL 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 452 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 756 TYR Chi-restraints excluded: chain D residue 849 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 70 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.134119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.103342 restraints weight = 41620.439| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.96 r_work: 0.3153 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23589 Z= 0.137 Angle : 0.594 15.953 32130 Z= 0.298 Chirality : 0.049 0.922 3741 Planarity : 0.004 0.055 4089 Dihedral : 6.750 83.930 3675 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.66 % Allowed : 13.36 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.15), residues: 2814 helix: -0.48 (0.20), residues: 702 sheet: -1.48 (0.22), residues: 531 loop : -2.04 (0.14), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 436 HIS 0.002 0.000 HIS A1088 PHE 0.013 0.001 PHE D 55 TYR 0.022 0.001 TYR B 473 ARG 0.004 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 27) link_NAG-ASN : angle 3.13857 ( 81) hydrogen bonds : bond 0.04013 ( 715) hydrogen bonds : angle 5.43986 ( 1884) SS BOND : bond 0.00270 ( 24) SS BOND : angle 1.53457 ( 48) covalent geometry : bond 0.00322 (23538) covalent geometry : angle 0.57120 (32001) *********************** 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 241 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 174 time to evaluate : 2.818 Fit side-chains REVERT: A 542 ASN cc_start: 0.8780 (t0) cc_final: 0.8536 (t0) REVERT: A 756 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.7232 (t80) REVERT: A 855 PHE cc_start: 0.8315 (m-80) cc_final: 0.7960 (m-80) REVERT: B 65 PHE cc_start: 0.6556 (m-80) cc_final: 0.6309 (m-80) REVERT: B 92 PHE cc_start: 0.7613 (t80) cc_final: 0.7083 (t80) REVERT: B 347 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8855 (m-10) REVERT: B 405 ASP cc_start: 0.8117 (m-30) cc_final: 0.7793 (m-30) REVERT: B 420 ASP cc_start: 0.7944 (m-30) cc_final: 0.7700 (t0) REVERT: B 756 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.7048 (t80) REVERT: B 855 PHE cc_start: 0.8280 (m-80) cc_final: 0.8013 (m-80) REVERT: D 347 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8896 (m-80) REVERT: D 756 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.7257 (t80) REVERT: D 855 PHE cc_start: 0.8262 (m-80) cc_final: 0.8041 (m-80) outliers start: 67 outliers final: 44 residues processed: 227 average time/residue: 0.3081 time to fit residues: 117.8320 Evaluate side-chains 207 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL 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 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 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 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 1104 VAL 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 425 LEU 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 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 1142 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 115 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 205 optimal weight: 0.0000 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 204 optimal weight: 8.9990 chunk 85 optimal weight: 0.0870 chunk 194 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.0166 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.135381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.105051 restraints weight = 42153.117| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.00 r_work: 0.3181 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23589 Z= 0.119 Angle : 0.586 18.196 32130 Z= 0.290 Chirality : 0.047 0.798 3741 Planarity : 0.004 0.054 4089 Dihedral : 6.536 78.798 3675 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.70 % Allowed : 13.75 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.15), residues: 2814 helix: -0.22 (0.21), residues: 702 sheet: -1.44 (0.21), residues: 555 loop : -1.88 (0.14), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.002 0.000 HIS A1088 PHE 0.015 0.001 PHE D 55 TYR 0.018 0.001 TYR D 904 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00928 ( 27) link_NAG-ASN : angle 3.01156 ( 81) hydrogen bonds : bond 0.03626 ( 715) hydrogen bonds : angle 5.21326 ( 1884) SS BOND : bond 0.00281 ( 24) SS BOND : angle 1.44449 ( 48) covalent geometry : bond 0.00276 (23538) covalent geometry : angle 0.56430 (32001) *********************** 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 253 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 185 time to evaluate : 2.533 Fit side-chains REVERT: A 229 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6764 (tt) REVERT: A 542 ASN cc_start: 0.8680 (t0) cc_final: 0.8434 (t0) REVERT: A 855 PHE cc_start: 0.8219 (m-80) cc_final: 0.7873 (m-80) REVERT: B 65 PHE cc_start: 0.6531 (m-80) cc_final: 0.6282 (m-80) REVERT: B 92 PHE cc_start: 0.7410 (t80) cc_final: 0.6953 (t80) REVERT: B 290 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8150 (t0) REVERT: B 347 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8856 (m-10) REVERT: B 420 ASP cc_start: 0.7925 (m-30) cc_final: 0.7678 (t0) REVERT: B 756 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.7103 (t80) REVERT: B 795 LYS cc_start: 0.6181 (tptt) cc_final: 0.5264 (mmmt) REVERT: B 855 PHE cc_start: 0.8203 (m-80) cc_final: 0.7999 (m-80) REVERT: B 887 THR cc_start: 0.9220 (p) cc_final: 0.8996 (t) REVERT: B 994 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7903 (t0) REVERT: D 347 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8893 (m-10) REVERT: D 756 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.7282 (t80) outliers start: 68 outliers final: 49 residues processed: 237 average time/residue: 0.2896 time to fit residues: 116.2883 Evaluate side-chains 217 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 161 time to evaluate : 2.499 ------------------------------------------------------------------------------- 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 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE 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 290 ASP 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 425 LEU 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 425 LEU 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 13 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 166 optimal weight: 0.2980 chunk 18 optimal weight: 0.0370 chunk 200 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 180 optimal weight: 2.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.133745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.099490 restraints weight = 41813.124| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.01 r_work: 0.3158 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23589 Z= 0.116 Angle : 0.552 10.182 32130 Z= 0.277 Chirality : 0.045 0.587 3741 Planarity : 0.004 0.053 4089 Dihedral : 6.322 83.964 3675 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.50 % Allowed : 14.70 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.15), residues: 2814 helix: -0.11 (0.21), residues: 717 sheet: -1.39 (0.20), residues: 561 loop : -1.77 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 104 HIS 0.002 0.000 HIS B1088 PHE 0.015 0.001 PHE D 562 TYR 0.022 0.001 TYR B 473 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 27) link_NAG-ASN : angle 2.05912 ( 81) hydrogen bonds : bond 0.03494 ( 715) hydrogen bonds : angle 5.07717 ( 1884) SS BOND : bond 0.00284 ( 24) SS BOND : angle 1.41563 ( 48) covalent geometry : bond 0.00275 (23538) covalent geometry : angle 0.54088 (32001) *********************** 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 244 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 181 time to evaluate : 2.794 Fit side-chains REVERT: A 229 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6540 (tt) REVERT: A 542 ASN cc_start: 0.8472 (t0) cc_final: 0.8248 (t0) REVERT: A 756 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.7201 (t80) REVERT: A 855 PHE cc_start: 0.8365 (m-80) cc_final: 0.8055 (m-80) REVERT: A 1050 MET cc_start: 0.8390 (ptm) cc_final: 0.8104 (ptt) REVERT: B 65 PHE cc_start: 0.6767 (m-80) cc_final: 0.6462 (m-80) REVERT: B 92 PHE cc_start: 0.6886 (t80) cc_final: 0.6445 (t80) REVERT: B 347 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8948 (m-10) REVERT: B 405 ASP cc_start: 0.7822 (m-30) cc_final: 0.7412 (m-30) REVERT: B 420 ASP cc_start: 0.8352 (m-30) cc_final: 0.7824 (t0) REVERT: B 756 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.7105 (t80) REVERT: B 795 LYS cc_start: 0.6544 (tptt) cc_final: 0.5377 (mmmt) REVERT: B 855 PHE cc_start: 0.8325 (m-80) cc_final: 0.8072 (m-80) REVERT: B 887 THR cc_start: 0.9370 (p) cc_final: 0.9030 (t) REVERT: B 994 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8138 (t0) REVERT: B 1019 ARG cc_start: 0.8533 (tpp-160) cc_final: 0.8256 (tpp-160) REVERT: D 347 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.9033 (m-10) REVERT: D 756 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.7245 (t80) REVERT: D 795 LYS cc_start: 0.6467 (tptt) cc_final: 0.5188 (mmmt) outliers start: 63 outliers final: 48 residues processed: 230 average time/residue: 0.2994 time to fit residues: 115.4914 Evaluate side-chains 224 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 169 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 229 LEU 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 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 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 290 ASP 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 425 LEU 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 150 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 205 optimal weight: 0.4980 chunk 49 optimal weight: 0.0170 chunk 232 optimal weight: 0.5980 chunk 279 optimal weight: 0.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.135292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.101496 restraints weight = 41803.939| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.92 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: 0.7825 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 23589 Z= 0.098 Angle : 0.555 12.379 32130 Z= 0.276 Chirality : 0.045 0.577 3741 Planarity : 0.004 0.052 4089 Dihedral : 6.228 89.960 3675 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.18 % Allowed : 15.66 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.15), residues: 2814 helix: 0.07 (0.21), residues: 717 sheet: -1.33 (0.20), residues: 573 loop : -1.71 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 104 HIS 0.002 0.000 HIS B1088 PHE 0.015 0.001 PHE D 55 TYR 0.024 0.001 TYR B 473 ARG 0.002 0.000 ARG D 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00727 ( 27) link_NAG-ASN : angle 2.60407 ( 81) hydrogen bonds : bond 0.03189 ( 715) hydrogen bonds : angle 4.95518 ( 1884) SS BOND : bond 0.00270 ( 24) SS BOND : angle 1.33211 ( 48) covalent geometry : bond 0.00227 (23538) covalent geometry : angle 0.53813 (32001) *********************** 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 248 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 193 time to evaluate : 2.510 Fit side-chains revert: symmetry clash REVERT: A 229 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6524 (tt) REVERT: A 542 ASN cc_start: 0.8441 (t0) cc_final: 0.8238 (t0) REVERT: A 756 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.7239 (t80) REVERT: A 795 LYS cc_start: 0.6398 (tptt) cc_final: 0.5413 (mmmt) REVERT: A 855 PHE cc_start: 0.8325 (m-80) cc_final: 0.8055 (m-80) REVERT: A 1050 MET cc_start: 0.8350 (ptm) cc_final: 0.8112 (ptm) REVERT: B 65 PHE cc_start: 0.6721 (m-80) cc_final: 0.6422 (m-80) REVERT: B 92 PHE cc_start: 0.6833 (t80) cc_final: 0.6453 (t80) REVERT: B 290 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7677 (t70) REVERT: B 347 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8974 (m-10) REVERT: B 420 ASP cc_start: 0.8313 (m-30) cc_final: 0.7778 (t0) REVERT: B 756 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.7054 (t80) REVERT: B 795 LYS cc_start: 0.6468 (tptt) cc_final: 0.5556 (mmmt) REVERT: B 855 PHE cc_start: 0.8270 (m-80) cc_final: 0.8050 (m-80) REVERT: B 887 THR cc_start: 0.9363 (p) cc_final: 0.9005 (t) REVERT: B 994 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8046 (t0) REVERT: D 347 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8991 (m-10) REVERT: D 795 LYS cc_start: 0.6385 (tptt) cc_final: 0.5298 (mmmt) REVERT: D 855 PHE cc_start: 0.8143 (m-80) cc_final: 0.7912 (m-80) outliers start: 55 outliers final: 46 residues processed: 235 average time/residue: 0.3057 time to fit residues: 120.2433 Evaluate side-chains 224 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 171 time to evaluate : 2.849 ------------------------------------------------------------------------------- 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 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 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 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 290 ASP 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 425 LEU 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 425 LEU Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 705 VAL 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 132 optimal weight: 0.1980 chunk 99 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 254 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 240 optimal weight: 8.9990 chunk 268 optimal weight: 2.9990 chunk 222 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 460 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 = 0.3859 r_free = 0.3859 target = 0.134141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.099637 restraints weight = 42067.050| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.06 r_work: 0.3156 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23589 Z= 0.125 Angle : 0.563 15.148 32130 Z= 0.280 Chirality : 0.047 0.934 3741 Planarity : 0.004 0.052 4089 Dihedral : 6.165 88.597 3675 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.38 % Allowed : 15.77 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.15), residues: 2814 helix: 0.10 (0.21), residues: 717 sheet: -1.27 (0.20), residues: 561 loop : -1.69 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 104 HIS 0.002 0.000 HIS D 207 PHE 0.016 0.001 PHE D 562 TYR 0.017 0.001 TYR B 473 ARG 0.006 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00627 ( 27) link_NAG-ASN : angle 2.64019 ( 81) hydrogen bonds : bond 0.03374 ( 715) hydrogen bonds : angle 4.95403 ( 1884) SS BOND : bond 0.00290 ( 24) SS BOND : angle 1.40278 ( 48) covalent geometry : bond 0.00301 (23538) covalent geometry : angle 0.54597 (32001) ********************** 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 238 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 178 time to evaluate : 2.627 Fit side-chains REVERT: A 229 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6513 (tt) REVERT: A 756 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.7248 (t80) REVERT: A 855 PHE cc_start: 0.8346 (m-80) cc_final: 0.8084 (m-80) REVERT: B 65 PHE cc_start: 0.6752 (m-80) cc_final: 0.6448 (m-80) REVERT: B 92 PHE cc_start: 0.6807 (t80) cc_final: 0.6488 (t80) REVERT: B 290 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7698 (t70) REVERT: B 347 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.9039 (m-10) REVERT: B 405 ASP cc_start: 0.7836 (m-30) cc_final: 0.7406 (m-30) REVERT: B 420 ASP cc_start: 0.8358 (m-30) cc_final: 0.7834 (t0) REVERT: B 462 LYS cc_start: 0.8478 (mmmm) cc_final: 0.8098 (mmtm) REVERT: B 756 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.7170 (t80) REVERT: B 795 LYS cc_start: 0.6385 (tptt) cc_final: 0.5487 (mmmt) REVERT: B 855 PHE cc_start: 0.8302 (m-80) cc_final: 0.8089 (m-80) REVERT: B 887 THR cc_start: 0.9345 (p) cc_final: 0.8990 (t) REVERT: B 994 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8089 (t0) REVERT: D 347 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.9046 (m-10) REVERT: D 420 ASP cc_start: 0.8364 (t70) cc_final: 0.8061 (t0) REVERT: D 460 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7415 (t0) REVERT: D 756 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.7375 (t80) REVERT: D 795 LYS cc_start: 0.6468 (tptt) cc_final: 0.5498 (mmmt) REVERT: D 855 PHE cc_start: 0.8146 (m-80) cc_final: 0.7920 (m-80) outliers start: 60 outliers final: 46 residues processed: 224 average time/residue: 0.2926 time to fit residues: 111.0296 Evaluate side-chains 232 residues out of total 2535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 177 time to evaluate : 2.572 ------------------------------------------------------------------------------- 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 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 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 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 290 ASP 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 425 LEU 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 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 460 ASN 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 235 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 107 optimal weight: 0.0470 chunk 115 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 286 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.134511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.099885 restraints weight = 41960.908| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.08 r_work: 0.3151 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 23589 Z= 0.172 Angle : 0.704 59.200 32130 Z= 0.388 Chirality : 0.050 0.918 3741 Planarity : 0.004 0.071 4089 Dihedral : 6.184 88.534 3675 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.86 % Favored : 94.10 % Rotamer: Outliers : 2.30 % Allowed : 16.09 % Favored : 81.61 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.15), residues: 2814 helix: 0.09 (0.20), residues: 717 sheet: -1.27 (0.20), residues: 561 loop : -1.69 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 104 HIS 0.002 0.000 HIS A1088 PHE 0.011 0.001 PHE B1121 TYR 0.019 0.001 TYR D 904 ARG 0.010 0.000 ARG D 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00625 ( 27) link_NAG-ASN : angle 2.65393 ( 81) hydrogen bonds : bond 0.03439 ( 715) hydrogen bonds : angle 4.95506 ( 1884) SS BOND : bond 0.00288 ( 24) SS BOND : angle 1.40315 ( 48) covalent geometry : bond 0.00390 (23538) covalent geometry : angle 0.69103 (32001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10338.21 seconds wall clock time: 182 minutes 2.64 seconds (10922.64 seconds total)