Starting phenix.real_space_refine on Sat Jul 4 09:33:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f0g_28756/07_2026/8f0g_28756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f0g_28756/07_2026/8f0g_28756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f0g_28756/07_2026/8f0g_28756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f0g_28756/07_2026/8f0g_28756.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f0g_28756/07_2026/8f0g_28756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f0g_28756/07_2026/8f0g_28756.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8f0g_28756/07_2026/8f0g_28756.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f0g_28756/07_2026/8f0g_28756.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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 96 5.16 5 C 12483 2.51 5 N 3246 2.21 5 O 3810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19635 Number of models: 1 Model: "" Number of chains: 11 Chain: "X" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 888 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain breaks: 1 Chain: "Y" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 744 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 91} Chain breaks: 1 Chain: "A" Number of atoms: 6684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 860, 6684 Classifications: {'peptide': 860} Link IDs: {'PTRANS': 45, 'TRANS': 814} Chain breaks: 12 Chain: "B" Number of atoms: 4740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4740 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 32, 'TRANS': 584} Chain breaks: 4 Chain: "C" Number of atoms: 6243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6243 Classifications: {'peptide': 803} Link IDs: {'PTRANS': 42, 'TRANS': 760} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.16, per 1000 atoms: 0.21 Number of scatterers: 19635 At special positions: 0 Unit cell: (108.24, 118.8, 194.04, 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 96 16.00 O 3810 8.00 N 3246 7.00 C 12483 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 24 " - pdb=" SG CYS Y 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " 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 A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " 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 B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG B1301 " - " ASN B 801 " " NAG B1302 " - " ASN B 717 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B1098 " " NAG B1305 " - " ASN B1134 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C 717 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN C 801 " Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 807.4 milliseconds 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4666 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 41 sheets defined 28.1% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'X' and resid 101 through 105 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.616A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 630 through 636 removed outlier: 3.900A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.758A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.612A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.538A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 856 removed outlier: 3.624A pdb=" N PHE A 855 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 906 Processing helix chain 'A' and resid 907 through 910 removed outlier: 3.520A pdb=" N GLY A 910 " --> pdb=" O ASN A 907 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 907 through 910' Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.329A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.555A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.906A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.615A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.755A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 4.275A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.872A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.816A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.528A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.708A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.585A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 957 " --> pdb=" O ASN B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.531A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.608A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.470A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.777A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.644A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 827 removed outlier: 3.830A pdb=" N THR C 827 " --> pdb=" O PHE C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 856 removed outlier: 4.062A pdb=" N LYS C 854 " --> pdb=" O CYS C 851 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 855 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.179A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.823A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.304A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.522A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.936A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.675A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'X' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'X' and resid 59 through 60 removed outlier: 6.684A pdb=" N TRP X 36 " --> pdb=" O VAL X 48 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN X 39 " --> pdb=" O LEU X 93 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU X 93 " --> pdb=" O GLN X 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 5 through 7 removed outlier: 3.755A pdb=" N THR Y 6 " --> pdb=" O ARG Y 25 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG Y 25 " --> pdb=" O THR Y 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'Y' and resid 20 through 22 Processing sheet with id=AA5, first strand: chain 'Y' and resid 45 through 49 removed outlier: 6.565A pdb=" N TRP Y 36 " --> pdb=" O LEU Y 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.058A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.897A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.498A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 316 removed outlier: 3.969A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.932A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.564A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.523A pdb=" N PHE A 392 " --> pdb=" O VAL A 524 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.721A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.839A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 725 through 727 removed outlier: 4.616A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.543A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.668A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1086 through 1087 Processing sheet with id=AC1, first strand: chain 'B' and resid 275 through 279 removed outlier: 4.546A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.532A pdb=" N ILE B 598 " --> pdb=" O ALA B 609 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 326 through 328 removed outlier: 3.750A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.582A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AC7, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.486A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.486A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.716A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 278 through 279 removed outlier: 4.085A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.329A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.219A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.620A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.219A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.620A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.712A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.647A pdb=" N ARG C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD9, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.593A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 660 removed outlier: 3.622A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.573A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 717 through 728 removed outlier: 5.977A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.484A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.970A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) 759 hydrogen bonds defined for protein. 2091 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6067 1.33 - 1.45: 3662 1.45 - 1.58: 10196 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 20048 Sorted by residual: bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.65e+00 bond pdb=" CA SER C 884 " pdb=" CB SER C 884 " ideal model delta sigma weight residual 1.534 1.484 0.050 2.33e-02 1.84e+03 4.60e+00 bond pdb=" CB ASN A 914 " pdb=" CG ASN A 914 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.94e+00 bond pdb=" CB ASN B 914 " pdb=" CG ASN B 914 " ideal model delta sigma weight residual 1.516 1.468 0.048 2.50e-02 1.60e+03 3.63e+00 ... (remaining 20043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 26837 1.99 - 3.98: 373 3.98 - 5.97: 38 5.97 - 7.95: 13 7.95 - 9.94: 3 Bond angle restraints: 27264 Sorted by residual: angle pdb=" CA ILE B 285 " pdb=" CB ILE B 285 " pdb=" CG1 ILE B 285 " ideal model delta sigma weight residual 110.40 116.18 -5.78 1.70e+00 3.46e-01 1.16e+01 angle pdb=" N ASN A 234 " pdb=" CA ASN A 234 " pdb=" CB ASN A 234 " ideal model delta sigma weight residual 109.48 114.67 -5.19 1.55e+00 4.16e-01 1.12e+01 angle pdb=" C2 NAG A1307 " pdb=" N2 NAG A1307 " pdb=" C7 NAG A1307 " ideal model delta sigma weight residual 124.56 134.50 -9.94 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CB ILE B 285 " pdb=" CG1 ILE B 285 " pdb=" CD1 ILE B 285 " ideal model delta sigma weight residual 113.80 120.66 -6.86 2.10e+00 2.27e-01 1.07e+01 angle pdb=" C ASN A 61 " pdb=" CA ASN A 61 " pdb=" CB ASN A 61 " ideal model delta sigma weight residual 109.70 115.14 -5.44 1.81e+00 3.05e-01 9.03e+00 ... (remaining 27259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.15: 10671 18.15 - 36.29: 931 36.29 - 54.44: 190 54.44 - 72.58: 41 72.58 - 90.73: 6 Dihedral angle restraints: 11839 sinusoidal: 4608 harmonic: 7231 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 150.07 -57.07 1 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -138.01 52.01 1 1.00e+01 1.00e-02 3.69e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -135.05 49.05 1 1.00e+01 1.00e-02 3.31e+01 ... (remaining 11836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 3112 0.118 - 0.235: 92 0.235 - 0.353: 6 0.353 - 0.470: 1 0.470 - 0.588: 1 Chirality restraints: 3212 Sorted by residual: chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.65e+00 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 717 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 3209 not shown) Planarity restraints: 3502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " -0.175 2.00e-02 2.50e+03 1.71e-01 3.67e+02 pdb=" C7 NAG A1307 " -0.090 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " 0.018 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " 0.320 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1308 " -0.100 2.00e-02 2.50e+03 8.81e-02 9.70e+01 pdb=" C7 NAG A1308 " -0.024 2.00e-02 2.50e+03 pdb=" C8 NAG A1308 " -0.059 2.00e-02 2.50e+03 pdb=" N2 NAG A1308 " 0.155 2.00e-02 2.50e+03 pdb=" O7 NAG A1308 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.004 2.00e-02 2.50e+03 3.92e-02 1.92e+01 pdb=" CG ASN A 61 " -0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " 0.048 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.034 2.00e-02 2.50e+03 ... (remaining 3499 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4229 2.77 - 3.30: 18874 3.30 - 3.84: 32182 3.84 - 4.37: 36827 4.37 - 4.90: 63885 Nonbonded interactions: 155997 Sorted by model distance: nonbonded pdb=" O SER B 708 " pdb=" OG SER B 711 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR A1076 " pdb=" OG SER A1097 " model vdw 2.245 3.040 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.276 3.040 nonbonded pdb=" OG SER A 383 " pdb=" OD1 ASP B 985 " model vdw 2.298 3.040 ... (remaining 155992 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: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 5.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.950 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 : 0.011 0.069 20103 Z= 0.479 Angle : 0.672 18.370 27398 Z= 0.354 Chirality : 0.058 0.588 3212 Planarity : 0.005 0.171 3481 Dihedral : 14.003 90.725 7080 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.14 % Allowed : 16.61 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2438 helix: 1.61 (0.21), residues: 612 sheet: -0.44 (0.24), residues: 478 loop : -0.83 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C1107 TYR 0.025 0.002 TYR A 904 PHE 0.021 0.003 PHE A 86 TRP 0.013 0.003 TRP B 886 HIS 0.008 0.002 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.01097 / 0.48 (20048) covalent geometry : angle 0.63353 / 0.35 (27264) SS BOND : bond 0.00372 / 0.24 ( 31) SS BOND : angle 0.87117 / 0.50 ( 62) hydrogen bonds : bond 0.25352 / 17.52 ( 747) hydrogen bonds : angle 8.66644 / 5.96 ( 2091) link_BETA1-4 : bond 0.00461 / 0.22 ( 3) link_BETA1-4 : angle 2.07365 / 1.08 ( 9) link_NAG-ASN : bond 0.00626 / 0.40 ( 21) link_NAG-ASN : angle 4.59728 / 2.36 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 30 ASP cc_start: 0.8511 (m-30) cc_final: 0.8193 (t0) REVERT: X 60 TYR cc_start: 0.7931 (m-80) cc_final: 0.7489 (m-80) REVERT: X 84 ASN cc_start: 0.8485 (p0) cc_final: 0.8106 (m110) REVERT: Y 40 LYS cc_start: 0.8633 (mptm) cc_final: 0.8172 (mmmt) REVERT: Y 48 LEU cc_start: 0.8804 (mt) cc_final: 0.8459 (mp) REVERT: Y 56 GLU cc_start: 0.8410 (tp30) cc_final: 0.7103 (mp0) REVERT: Y 97 LEU cc_start: 0.8480 (mm) cc_final: 0.8261 (mm) outliers start: 3 outliers final: 2 residues processed: 102 average time/residue: 0.1619 time to fit residues: 25.6121 Evaluate side-chains 84 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain C residue 488 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.3980 chunk 107 optimal weight: 0.0370 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN A 955 ASN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN C 641 ASN C 751 ASN C1011 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.076290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.056685 restraints weight = 68295.232| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.79 r_work: 0.2922 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20103 Z= 0.123 Angle : 0.553 11.650 27398 Z= 0.280 Chirality : 0.044 0.366 3212 Planarity : 0.004 0.054 3481 Dihedral : 3.624 58.951 2648 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.75 % Allowed : 14.94 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.17), residues: 2438 helix: 2.08 (0.21), residues: 615 sheet: -0.19 (0.23), residues: 469 loop : -0.84 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 19 TYR 0.021 0.001 TYR B1067 PHE 0.013 0.001 PHE B 759 TRP 0.010 0.001 TRP A 886 HIS 0.003 0.001 HIS X 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (20048) covalent geometry : angle 0.53750 / 0.28 (27264) SS BOND : bond 0.00244 / 0.14 ( 31) SS BOND : angle 0.76680 / 0.46 ( 62) hydrogen bonds : bond 0.05562 / 3.75 ( 747) hydrogen bonds : angle 5.94551 / 4.06 ( 2091) link_BETA1-4 : bond 0.00251 / 0.13 ( 3) link_BETA1-4 : angle 1.62861 / 0.99 ( 9) link_NAG-ASN : bond 0.00383 / 0.26 ( 21) link_NAG-ASN : angle 2.63875 / 1.51 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 93 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 30 ASP cc_start: 0.8546 (m-30) cc_final: 0.8203 (t0) REVERT: X 31 ASP cc_start: 0.8485 (m-30) cc_final: 0.8141 (m-30) REVERT: X 43 LYS cc_start: 0.9297 (mmmm) cc_final: 0.9087 (tmtt) REVERT: X 60 TYR cc_start: 0.8038 (m-80) cc_final: 0.7602 (m-80) REVERT: X 116 TRP cc_start: 0.8325 (m100) cc_final: 0.7818 (m100) REVERT: Y 56 GLU cc_start: 0.8515 (tp30) cc_final: 0.7342 (mp0) REVERT: Y 76 ILE cc_start: 0.6230 (OUTLIER) cc_final: 0.5972 (tp) REVERT: A 906 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.7948 (m-10) REVERT: C 375 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7401 (m-10) REVERT: C 984 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7624 (tp) outliers start: 38 outliers final: 12 residues processed: 124 average time/residue: 0.1417 time to fit residues: 28.3355 Evaluate side-chains 97 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 751 ASN Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 100 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 168 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 80 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.074696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.055091 restraints weight = 69440.519| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.78 r_work: 0.2886 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20103 Z= 0.165 Angle : 0.544 11.233 27398 Z= 0.273 Chirality : 0.044 0.382 3212 Planarity : 0.004 0.046 3481 Dihedral : 3.603 41.302 2648 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.71 % Allowed : 15.22 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2438 helix: 2.14 (0.21), residues: 613 sheet: -0.17 (0.23), residues: 473 loop : -0.82 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 67 TYR 0.022 0.001 TYR B1067 PHE 0.012 0.001 PHE A 643 TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (20048) covalent geometry : angle 0.53018 / 0.27 (27264) SS BOND : bond 0.00518 / 0.38 ( 31) SS BOND : angle 0.91459 / 0.50 ( 62) hydrogen bonds : bond 0.05153 / 3.50 ( 747) hydrogen bonds : angle 5.52576 / 3.76 ( 2091) link_BETA1-4 : bond 0.00207 / 0.10 ( 3) link_BETA1-4 : angle 1.46837 / 0.93 ( 9) link_NAG-ASN : bond 0.00342 / 0.25 ( 21) link_NAG-ASN : angle 2.39532 / 1.34 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 30 ASP cc_start: 0.8601 (m-30) cc_final: 0.8243 (t0) REVERT: X 31 ASP cc_start: 0.8501 (m-30) cc_final: 0.8198 (m-30) REVERT: X 34 MET cc_start: 0.8679 (mpm) cc_final: 0.8342 (mpm) REVERT: X 60 TYR cc_start: 0.8257 (m-80) cc_final: 0.7920 (m-80) REVERT: X 81 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6952 (tt) REVERT: X 86 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7953 (mt) REVERT: Y 48 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8057 (mm) REVERT: Y 56 GLU cc_start: 0.8550 (tp30) cc_final: 0.7386 (mp0) REVERT: A 392 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.6524 (p90) REVERT: A 906 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8060 (m-10) REVERT: C 375 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7571 (m-80) REVERT: C 984 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7800 (tp) REVERT: C 1095 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7820 (m-10) outliers start: 37 outliers final: 16 residues processed: 122 average time/residue: 0.1494 time to fit residues: 29.1316 Evaluate side-chains 104 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain Y residue 48 LEU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1095 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 16 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 241 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 242 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN C 751 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.074359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.054781 restraints weight = 69337.693| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.75 r_work: 0.2878 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20103 Z= 0.163 Angle : 0.538 10.450 27398 Z= 0.269 Chirality : 0.044 0.382 3212 Planarity : 0.004 0.091 3481 Dihedral : 3.575 42.116 2646 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.21 % Allowed : 15.36 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.17), residues: 2438 helix: 2.15 (0.21), residues: 613 sheet: -0.22 (0.23), residues: 479 loop : -0.82 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 19 TYR 0.021 0.001 TYR B1067 PHE 0.013 0.001 PHE B 559 TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (20048) covalent geometry : angle 0.52463 / 0.27 (27264) SS BOND : bond 0.00322 / 0.23 ( 31) SS BOND : angle 1.01238 / 0.52 ( 62) hydrogen bonds : bond 0.04708 / 3.19 ( 747) hydrogen bonds : angle 5.27173 / 3.58 ( 2091) link_BETA1-4 : bond 0.00207 / 0.10 ( 3) link_BETA1-4 : angle 1.51605 / 1.01 ( 9) link_NAG-ASN : bond 0.00319 / 0.24 ( 21) link_NAG-ASN : angle 2.32637 / 1.28 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 81 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 30 ASP cc_start: 0.8669 (m-30) cc_final: 0.8396 (t0) REVERT: X 31 ASP cc_start: 0.8518 (m-30) cc_final: 0.8306 (m-30) REVERT: X 34 MET cc_start: 0.8738 (mpm) cc_final: 0.8398 (mpm) REVERT: X 83 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6257 (tpp) REVERT: X 93 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7497 (tm) REVERT: Y 48 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8073 (mm) REVERT: Y 56 GLU cc_start: 0.8560 (tp30) cc_final: 0.7444 (mp0) REVERT: Y 84 PHE cc_start: 0.8445 (t80) cc_final: 0.8240 (t80) REVERT: A 392 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.6495 (p90) REVERT: A 906 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.8115 (m-10) REVERT: C 375 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7620 (m-80) REVERT: C 517 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6922 (tm) REVERT: C 984 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.7831 (tp) REVERT: C 1095 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7823 (m-10) outliers start: 48 outliers final: 21 residues processed: 121 average time/residue: 0.1388 time to fit residues: 27.5356 Evaluate side-chains 106 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 83 MET Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 48 LEU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1095 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 105 optimal weight: 7.9990 chunk 204 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.067659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.049556 restraints weight = 72726.543| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.48 r_work: 0.2825 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20103 Z= 0.237 Angle : 0.590 10.311 27398 Z= 0.296 Chirality : 0.046 0.386 3212 Planarity : 0.004 0.057 3481 Dihedral : 3.863 42.426 2646 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.21 % Allowed : 15.73 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.17), residues: 2438 helix: 2.00 (0.21), residues: 614 sheet: -0.30 (0.23), residues: 481 loop : -0.91 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG X 16 TYR 0.023 0.001 TYR B1067 PHE 0.014 0.002 PHE B 898 TRP 0.013 0.002 TRP C 436 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.24 (20048) covalent geometry : angle 0.57733 / 0.29 (27264) SS BOND : bond 0.00264 / 0.17 ( 31) SS BOND : angle 0.98899 / 0.53 ( 62) hydrogen bonds : bond 0.04929 / 3.33 ( 747) hydrogen bonds : angle 5.27695 / 3.58 ( 2091) link_BETA1-4 : bond 0.00181 / 0.09 ( 3) link_BETA1-4 : angle 1.56323 / 1.06 ( 9) link_NAG-ASN : bond 0.00356 / 0.26 ( 21) link_NAG-ASN : angle 2.41454 / 1.32 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 80 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 16 ARG cc_start: 0.8268 (mmm160) cc_final: 0.7844 (tpp80) REVERT: X 30 ASP cc_start: 0.8679 (m-30) cc_final: 0.8393 (t0) REVERT: X 31 ASP cc_start: 0.8597 (m-30) cc_final: 0.8349 (m-30) REVERT: X 34 MET cc_start: 0.8809 (mpm) cc_final: 0.8273 (mmt) REVERT: X 93 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7521 (tm) REVERT: Y 32 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8377 (p) REVERT: Y 48 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8052 (mm) REVERT: Y 56 GLU cc_start: 0.8710 (tp30) cc_final: 0.7529 (mp0) REVERT: A 906 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.7953 (m-10) REVERT: C 375 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: C 501 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7904 (m-10) REVERT: C 517 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6841 (tm) REVERT: C 984 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.7822 (tp) REVERT: C 1095 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.8076 (m-10) outliers start: 48 outliers final: 22 residues processed: 123 average time/residue: 0.1448 time to fit residues: 28.9745 Evaluate side-chains 106 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 32 SER Chi-restraints excluded: chain Y residue 48 LEU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1095 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 158 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 30 optimal weight: 0.3980 chunk 163 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.068146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.050093 restraints weight = 71982.000| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.49 r_work: 0.2838 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20103 Z= 0.172 Angle : 0.553 10.297 27398 Z= 0.277 Chirality : 0.045 0.380 3212 Planarity : 0.004 0.064 3481 Dihedral : 3.798 42.411 2646 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.21 % Allowed : 16.19 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.17), residues: 2438 helix: 2.10 (0.21), residues: 614 sheet: -0.29 (0.23), residues: 491 loop : -0.91 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 67 TYR 0.021 0.001 TYR B1067 PHE 0.013 0.001 PHE Y 84 TRP 0.014 0.001 TRP C 436 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (20048) covalent geometry : angle 0.53840 / 0.27 (27264) SS BOND : bond 0.00222 / 0.14 ( 31) SS BOND : angle 1.36918 / 0.63 ( 62) hydrogen bonds : bond 0.04491 / 3.04 ( 747) hydrogen bonds : angle 5.10106 / 3.47 ( 2091) link_BETA1-4 : bond 0.00251 / 0.13 ( 3) link_BETA1-4 : angle 1.50706 / 1.01 ( 9) link_NAG-ASN : bond 0.00294 / 0.22 ( 21) link_NAG-ASN : angle 2.28307 / 1.25 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 82 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 30 ASP cc_start: 0.8624 (m-30) cc_final: 0.8256 (t0) REVERT: X 31 ASP cc_start: 0.8575 (m-30) cc_final: 0.8246 (m-30) REVERT: X 34 MET cc_start: 0.8787 (mpm) cc_final: 0.8145 (mmt) REVERT: X 93 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7572 (tm) REVERT: X 118 GLN cc_start: 0.7385 (mp10) cc_final: 0.7138 (mp10) REVERT: Y 32 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8396 (p) REVERT: Y 48 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8066 (mp) REVERT: Y 56 GLU cc_start: 0.8708 (tp30) cc_final: 0.7560 (mp0) REVERT: Y 84 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.8158 (t80) REVERT: A 392 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.6525 (p90) REVERT: A 906 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.7969 (m-10) REVERT: C 375 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: C 408 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8208 (ptt90) REVERT: C 501 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7842 (m-10) REVERT: C 517 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6867 (tm) REVERT: C 619 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: C 984 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7800 (tp) outliers start: 48 outliers final: 24 residues processed: 124 average time/residue: 0.1550 time to fit residues: 30.8585 Evaluate side-chains 110 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 32 SER Chi-restraints excluded: chain Y residue 48 LEU Chi-restraints excluded: chain Y residue 84 PHE Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 204 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 194 optimal weight: 7.9990 chunk 166 optimal weight: 8.9990 chunk 217 optimal weight: 0.9980 chunk 195 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 215 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 901 GLN B 913 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.068802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.050802 restraints weight = 72319.656| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.51 r_work: 0.2859 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20103 Z= 0.117 Angle : 0.525 10.174 27398 Z= 0.260 Chirality : 0.044 0.378 3212 Planarity : 0.004 0.051 3481 Dihedral : 3.648 41.994 2646 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.89 % Allowed : 16.65 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.17), residues: 2438 helix: 2.29 (0.21), residues: 614 sheet: -0.18 (0.23), residues: 478 loop : -0.84 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 67 TYR 0.019 0.001 TYR B1067 PHE 0.012 0.001 PHE Y 84 TRP 0.012 0.001 TRP A 886 HIS 0.002 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (20048) covalent geometry : angle 0.51224 / 0.26 (27264) SS BOND : bond 0.00205 / 0.13 ( 31) SS BOND : angle 1.11028 / 0.54 ( 62) hydrogen bonds : bond 0.04074 / 2.74 ( 747) hydrogen bonds : angle 4.90465 / 3.34 ( 2091) link_BETA1-4 : bond 0.00308 / 0.15 ( 3) link_BETA1-4 : angle 1.42624 / 0.94 ( 9) link_NAG-ASN : bond 0.00303 / 0.23 ( 21) link_NAG-ASN : angle 2.20121 / 1.21 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 83 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 30 ASP cc_start: 0.8717 (m-30) cc_final: 0.8406 (t0) REVERT: X 31 ASP cc_start: 0.8582 (m-30) cc_final: 0.8217 (m-30) REVERT: X 34 MET cc_start: 0.8741 (mpm) cc_final: 0.8030 (mmt) REVERT: X 93 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7439 (tm) REVERT: Y 32 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8369 (p) REVERT: Y 48 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8121 (mp) REVERT: Y 56 GLU cc_start: 0.8673 (tp30) cc_final: 0.7555 (mp0) REVERT: Y 84 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.8118 (t80) REVERT: A 357 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7910 (ppp80) REVERT: A 906 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.7841 (m-10) REVERT: C 501 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7860 (m-10) REVERT: C 517 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6855 (tm) REVERT: C 619 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: C 984 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7891 (tp) outliers start: 41 outliers final: 20 residues processed: 118 average time/residue: 0.1582 time to fit residues: 29.6239 Evaluate side-chains 104 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 32 SER Chi-restraints excluded: chain Y residue 48 LEU Chi-restraints excluded: chain Y residue 84 PHE Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 217 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 205 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 957 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.067878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.050134 restraints weight = 72551.055| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.38 r_work: 0.2846 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20103 Z= 0.208 Angle : 0.574 10.066 27398 Z= 0.286 Chirality : 0.045 0.379 3212 Planarity : 0.004 0.048 3481 Dihedral : 3.824 41.377 2646 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.94 % Allowed : 16.79 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.17), residues: 2438 helix: 2.13 (0.21), residues: 614 sheet: -0.23 (0.23), residues: 480 loop : -0.90 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 67 TYR 0.021 0.001 TYR B1067 PHE 0.028 0.001 PHE X 68 TRP 0.013 0.001 TRP C 436 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (20048) covalent geometry : angle 0.56178 / 0.28 (27264) SS BOND : bond 0.00233 / 0.15 ( 31) SS BOND : angle 1.07701 / 0.54 ( 62) hydrogen bonds : bond 0.04494 / 3.03 ( 747) hydrogen bonds : angle 5.00606 / 3.41 ( 2091) link_BETA1-4 : bond 0.00197 / 0.10 ( 3) link_BETA1-4 : angle 1.49746 / 1.02 ( 9) link_NAG-ASN : bond 0.00313 / 0.23 ( 21) link_NAG-ASN : angle 2.29741 / 1.25 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 78 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 30 ASP cc_start: 0.8616 (m-30) cc_final: 0.8278 (t0) REVERT: X 31 ASP cc_start: 0.8656 (m-30) cc_final: 0.8313 (m-30) REVERT: X 34 MET cc_start: 0.8897 (mpm) cc_final: 0.8628 (mmt) REVERT: X 93 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7648 (tm) REVERT: Y 32 SER cc_start: 0.9018 (OUTLIER) cc_final: 0.8553 (p) REVERT: Y 48 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8375 (mm) REVERT: Y 56 GLU cc_start: 0.8751 (tp30) cc_final: 0.7708 (mp0) REVERT: Y 84 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7973 (t80) REVERT: A 357 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8152 (ppp80) REVERT: A 906 PHE cc_start: 0.9396 (OUTLIER) cc_final: 0.8105 (m-10) REVERT: B 754 LEU cc_start: 0.9667 (pt) cc_final: 0.9462 (pt) REVERT: C 501 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7849 (m-10) REVERT: C 517 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6743 (tm) REVERT: C 619 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: C 984 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.7935 (tp) REVERT: C 1095 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7968 (m-10) outliers start: 42 outliers final: 24 residues processed: 114 average time/residue: 0.1408 time to fit residues: 25.4517 Evaluate side-chains 111 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 32 SER Chi-restraints excluded: chain Y residue 48 LEU Chi-restraints excluded: chain Y residue 84 PHE Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1095 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 133 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 1 optimal weight: 30.0000 chunk 5 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 154 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.068142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.050546 restraints weight = 71864.303| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.36 r_work: 0.2856 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20103 Z= 0.163 Angle : 0.551 10.079 27398 Z= 0.273 Chirality : 0.044 0.375 3212 Planarity : 0.004 0.048 3481 Dihedral : 3.768 40.996 2646 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.85 % Allowed : 16.84 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.17), residues: 2438 helix: 2.19 (0.21), residues: 614 sheet: -0.32 (0.23), residues: 492 loop : -0.91 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 67 TYR 0.040 0.001 TYR C 508 PHE 0.028 0.001 PHE X 27 TRP 0.012 0.001 TRP C 436 HIS 0.003 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (20048) covalent geometry : angle 0.53853 / 0.27 (27264) SS BOND : bond 0.00221 / 0.14 ( 31) SS BOND : angle 0.98751 / 0.51 ( 62) hydrogen bonds : bond 0.04256 / 2.87 ( 747) hydrogen bonds : angle 4.91647 / 3.35 ( 2091) link_BETA1-4 : bond 0.00236 / 0.12 ( 3) link_BETA1-4 : angle 1.45815 / 0.98 ( 9) link_NAG-ASN : bond 0.00285 / 0.22 ( 21) link_NAG-ASN : angle 2.24709 / 1.23 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 79 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 16 ARG cc_start: 0.7682 (ttm110) cc_final: 0.6570 (ttm110) REVERT: X 30 ASP cc_start: 0.8635 (m-30) cc_final: 0.8292 (t0) REVERT: X 31 ASP cc_start: 0.8629 (m-30) cc_final: 0.8267 (m-30) REVERT: X 34 MET cc_start: 0.8852 (mpm) cc_final: 0.8582 (mmt) REVERT: X 93 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7533 (tm) REVERT: Y 32 SER cc_start: 0.9023 (OUTLIER) cc_final: 0.8550 (p) REVERT: Y 48 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8410 (mm) REVERT: Y 56 GLU cc_start: 0.8725 (tp30) cc_final: 0.7686 (mp0) REVERT: Y 84 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7899 (t80) REVERT: A 392 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.6792 (p90) REVERT: A 906 PHE cc_start: 0.9390 (OUTLIER) cc_final: 0.7993 (m-10) REVERT: B 754 LEU cc_start: 0.9668 (pt) cc_final: 0.9465 (pt) REVERT: C 501 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7772 (m-10) REVERT: C 517 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6745 (tm) REVERT: C 619 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: C 984 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.7941 (tp) outliers start: 40 outliers final: 26 residues processed: 113 average time/residue: 0.1445 time to fit residues: 26.0767 Evaluate side-chains 110 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 32 SER Chi-restraints excluded: chain Y residue 48 LEU Chi-restraints excluded: chain Y residue 84 PHE Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 4 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 242 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.067487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.049760 restraints weight = 72769.337| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.34 r_work: 0.2838 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20103 Z= 0.213 Angle : 0.587 9.994 27398 Z= 0.293 Chirality : 0.045 0.372 3212 Planarity : 0.004 0.048 3481 Dihedral : 3.906 40.627 2646 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.89 % Allowed : 16.93 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.17), residues: 2438 helix: 2.08 (0.21), residues: 614 sheet: -0.31 (0.23), residues: 485 loop : -0.97 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 19 TYR 0.031 0.001 TYR C 508 PHE 0.023 0.001 PHE X 27 TRP 0.013 0.001 TRP C 436 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (20048) covalent geometry : angle 0.57551 / 0.29 (27264) SS BOND : bond 0.00237 / 0.15 ( 31) SS BOND : angle 1.01110 / 0.53 ( 62) hydrogen bonds : bond 0.04513 / 3.05 ( 747) hydrogen bonds : angle 4.99147 / 3.40 ( 2091) link_BETA1-4 : bond 0.00179 / 0.09 ( 3) link_BETA1-4 : angle 1.50594 / 1.03 ( 9) link_NAG-ASN : bond 0.00305 / 0.23 ( 21) link_NAG-ASN : angle 2.32526 / 1.27 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 76 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 30 ASP cc_start: 0.8664 (m-30) cc_final: 0.8294 (t0) REVERT: X 31 ASP cc_start: 0.8640 (m-30) cc_final: 0.8286 (m-30) REVERT: X 34 MET cc_start: 0.8937 (mpm) cc_final: 0.8652 (mmt) REVERT: X 93 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7683 (tm) REVERT: Y 32 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8564 (p) REVERT: Y 48 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8412 (mm) REVERT: Y 56 GLU cc_start: 0.8804 (tp30) cc_final: 0.7702 (mp0) REVERT: Y 84 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7808 (t80) REVERT: A 357 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8127 (ppp80) REVERT: A 906 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.8001 (m-10) REVERT: B 754 LEU cc_start: 0.9670 (pt) cc_final: 0.9469 (pt) REVERT: C 501 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7785 (m-10) REVERT: C 508 TYR cc_start: 0.7294 (OUTLIER) cc_final: 0.6150 (m-10) REVERT: C 517 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6700 (tm) REVERT: C 619 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: C 984 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8048 (tp) outliers start: 41 outliers final: 28 residues processed: 111 average time/residue: 0.1499 time to fit residues: 26.7079 Evaluate side-chains 114 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 75 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 32 SER Chi-restraints excluded: chain Y residue 48 LEU Chi-restraints excluded: chain Y residue 84 PHE Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 65 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 241 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 243 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 165 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 82 GLN B 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.073723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054968 restraints weight = 68413.983| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.53 r_work: 0.2863 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20103 Z= 0.123 Angle : 0.540 9.970 27398 Z= 0.268 Chirality : 0.044 0.370 3212 Planarity : 0.004 0.048 3481 Dihedral : 3.734 40.037 2646 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.80 % Allowed : 17.07 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.17), residues: 2438 helix: 2.28 (0.21), residues: 614 sheet: -0.25 (0.23), residues: 487 loop : -0.91 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG X 16 TYR 0.023 0.001 TYR C 508 PHE 0.024 0.001 PHE X 27 TRP 0.012 0.001 TRP A 886 HIS 0.002 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (20048) covalent geometry : angle 0.52878 / 0.27 (27264) SS BOND : bond 0.00209 / 0.13 ( 31) SS BOND : angle 0.92222 / 0.50 ( 62) hydrogen bonds : bond 0.04021 / 2.71 ( 747) hydrogen bonds : angle 4.80537 / 3.28 ( 2091) link_BETA1-4 : bond 0.00304 / 0.15 ( 3) link_BETA1-4 : angle 1.43841 / 0.96 ( 9) link_NAG-ASN : bond 0.00296 / 0.22 ( 21) link_NAG-ASN : angle 2.19439 / 1.20 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4032.60 seconds wall clock time: 70 minutes 29.59 seconds (4229.59 seconds total)