Starting phenix.real_space_refine on Tue Apr 7 02:15:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r16_14232/04_2026/7r16_14232.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r16_14232/04_2026/7r16_14232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r16_14232/04_2026/7r16_14232.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r16_14232/04_2026/7r16_14232.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r16_14232/04_2026/7r16_14232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r16_14232/04_2026/7r16_14232.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.088 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 104 5.16 5 C 15334 2.51 5 N 3940 2.21 5 O 4656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24034 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7874 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 52, 'TRANS': 953} Chain breaks: 10 Chain: "B" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7823 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 53, 'TRANS': 947} Chain breaks: 10 Chain: "C" Number of atoms: 7777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7777 Classifications: {'peptide': 995} Link IDs: {'PTRANS': 50, 'TRANS': 944} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.14, per 1000 atoms: 0.26 Number of scatterers: 24034 At special positions: 0 Unit cell: (135.875, 135.875, 197.834, 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 104 16.00 O 4656 8.00 N 3940 7.00 C 15334 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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 131 " - pdb=" SG CYS C 166 " 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=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.03 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 282 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1134 " " NAG B1309 " - " ASN B 282 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 717 " " NAG C1309 " - " ASN C 657 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN C 801 " Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.2 seconds 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5620 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 51 sheets defined 25.0% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.285A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.685A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.920A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.775A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.934A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.544A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.666A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.331A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.804A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.681A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.552A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.772A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 371 removed outlier: 4.121A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 371' Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.057A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.936A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.801A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.658A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 852 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.062A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.578A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.657A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.686A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.453A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.156A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.594A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 337 through 342' Processing helix chain 'C' and resid 366 through 372 removed outlier: 4.154A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.636A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (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 747 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.849A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.590A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.548A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.967A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.696A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.624A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.989A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.710A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR C1009 " --> pdb=" O GLN C1005 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLN C1011 " --> pdb=" O TYR C1007 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.091A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1140 through 1146' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.041A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.828A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 4.005A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 118 through 120 removed outlier: 3.506A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 4.038A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.760A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.648A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB3, first strand: chain 'A' and resid 575 through 577 removed outlier: 3.536A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.352A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 672 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 703 removed outlier: 3.724A pdb=" N ASN A 703 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.413A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.413A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.061A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.796A pdb=" N VAL A1133 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC3, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.689A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.563A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.657A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.570A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.730A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.613A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.806A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.163A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.580A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.807A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B1052 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.677A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1080 through 1082 Processing sheet with id=AE2, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AE3, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AE4, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.296A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 9.410A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.918A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.880A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.781A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.673A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.304A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 712 through 722 removed outlier: 6.316A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.812A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.515A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.525A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 859 hydrogen bonds defined for protein. 2355 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.24 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7629 1.34 - 1.46: 6024 1.46 - 1.59: 10785 1.59 - 1.71: 0 1.71 - 1.84: 129 Bond restraints: 24567 Sorted by residual: bond pdb=" N ILE A1132 " pdb=" CA ILE A1132 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.14e-02 7.69e+03 1.00e+01 bond pdb=" N ILE C 742 " pdb=" CA ILE C 742 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.61e+00 bond pdb=" N ASP A1041 " pdb=" CA ASP A1041 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.15e-02 7.56e+03 9.32e+00 bond pdb=" N VAL A1133 " pdb=" CA VAL A1133 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.24e-02 6.50e+03 9.10e+00 bond pdb=" N SER A 162 " pdb=" CA SER A 162 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.16e-02 7.43e+03 8.98e+00 ... (remaining 24562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 32561 1.83 - 3.65: 799 3.65 - 5.48: 51 5.48 - 7.30: 5 7.30 - 9.13: 1 Bond angle restraints: 33417 Sorted by residual: angle pdb=" CA VAL A1133 " pdb=" C VAL A1133 " pdb=" O VAL A1133 " ideal model delta sigma weight residual 121.64 118.13 3.51 9.80e-01 1.04e+00 1.28e+01 angle pdb=" C CYS A1082 " pdb=" CA CYS A1082 " pdb=" CB CYS A1082 " ideal model delta sigma weight residual 109.72 115.60 -5.88 1.73e+00 3.34e-01 1.15e+01 angle pdb=" CA PHE A 515 " pdb=" C PHE A 515 " pdb=" O PHE A 515 " ideal model delta sigma weight residual 121.31 117.70 3.61 1.07e+00 8.73e-01 1.14e+01 angle pdb=" N PRO B 499 " pdb=" CA PRO B 499 " pdb=" C PRO B 499 " ideal model delta sigma weight residual 113.65 109.19 4.46 1.35e+00 5.49e-01 1.09e+01 angle pdb=" CA ALA A 163 " pdb=" C ALA A 163 " pdb=" O ALA A 163 " ideal model delta sigma weight residual 121.58 117.75 3.83 1.16e+00 7.43e-01 1.09e+01 ... (remaining 33412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 13687 17.33 - 34.66: 1153 34.66 - 51.99: 247 51.99 - 69.32: 41 69.32 - 86.65: 25 Dihedral angle restraints: 15153 sinusoidal: 6428 harmonic: 8725 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -164.25 78.25 1 1.00e+01 1.00e-02 7.65e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.75 71.75 1 1.00e+01 1.00e-02 6.59e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -154.88 68.88 1 1.00e+01 1.00e-02 6.14e+01 ... (remaining 15150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3349 0.068 - 0.137: 504 0.137 - 0.205: 42 0.205 - 0.274: 14 0.274 - 0.342: 5 Chirality restraints: 3914 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA ILE A1081 " pdb=" N ILE A1081 " pdb=" C ILE A1081 " pdb=" CB ILE A1081 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 3911 not shown) Planarity restraints: 4304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 514 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C SER A 514 " 0.049 2.00e-02 2.50e+03 pdb=" O SER A 514 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE A 515 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " -0.018 2.00e-02 2.50e+03 1.77e-02 5.51e+00 pdb=" CG PHE A 906 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A1078 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO A1079 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A1079 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1079 " 0.027 5.00e-02 4.00e+02 ... (remaining 4301 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4510 2.77 - 3.30: 22065 3.30 - 3.84: 36616 3.84 - 4.37: 41139 4.37 - 4.90: 73403 Nonbonded interactions: 177733 Sorted by model distance: nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.241 3.040 nonbonded pdb=" OE1 GLN B 965 " pdb=" OG SER C 758 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR A 645 " pdb=" O GLY A 648 " model vdw 2.255 3.040 nonbonded pdb=" OE2 GLU A 281 " pdb=" O6 NAG A1310 " model vdw 2.280 3.040 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.281 3.040 ... (remaining 177728 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 'A' and (resid 26 through 96 or resid 102 through 135 or resid 157 throug \ h 171 or resid 188 through 263 or resid 265 through 515 or resid 520 through 616 \ or (resid 617 and (name N or name CA or name C or name CB or name SG )) or resi \ d 618 through 1309)) selection = (chain 'B' and (resid 26 through 96 or resid 102 through 123 or resid 125 throug \ h 135 or resid 157 through 171 or resid 188 through 616 or (resid 617 and (name \ N or name CA or name C or name CB or name SG )) or resid 618 through 620 or resi \ d 641 through 827 or resid 855 through 1309)) selection = (chain 'C' and (resid 26 through 66 or resid 81 through 123 or resid 125 through \ 135 or resid 157 through 263 or resid 265 through 515 or resid 520 through 620 \ or resid 641 through 827 or resid 855 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.020 Find NCS groups from input model: 0.690 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: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 : 0.005 0.062 24646 Z= 0.257 Angle : 0.645 20.389 33615 Z= 0.352 Chirality : 0.050 0.342 3914 Planarity : 0.004 0.048 4270 Dihedral : 13.279 86.646 9416 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.19 % Allowed : 0.61 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.15), residues: 2938 helix: 2.01 (0.21), residues: 639 sheet: -0.33 (0.20), residues: 648 loop : -1.23 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.016 0.001 TYR C 873 PHE 0.041 0.001 PHE A 906 TRP 0.014 0.001 TRP B 886 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00471 (24567) covalent geometry : angle 0.60561 (33417) SS BOND : bond 0.00337 ( 39) SS BOND : angle 1.23524 ( 78) hydrogen bonds : bond 0.23321 ( 843) hydrogen bonds : angle 8.30442 ( 2355) link_BETA1-4 : bond 0.00322 ( 6) link_BETA1-4 : angle 1.31565 ( 18) link_NAG-ASN : bond 0.00787 ( 34) link_NAG-ASN : angle 3.95672 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 264 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 394 ASN cc_start: 0.7829 (m110) cc_final: 0.7556 (m-40) outliers start: 5 outliers final: 1 residues processed: 267 average time/residue: 0.1580 time to fit residues: 68.6896 Evaluate side-chains 184 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN C 978 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.144218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.098382 restraints weight = 42675.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101549 restraints weight = 22740.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.103610 restraints weight = 15401.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.104910 restraints weight = 12066.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.105681 restraints weight = 10354.593| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24646 Z= 0.148 Angle : 0.602 19.969 33615 Z= 0.303 Chirality : 0.045 0.365 3914 Planarity : 0.004 0.043 4270 Dihedral : 6.693 59.469 4047 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.76 % Allowed : 7.01 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.30 (0.15), residues: 2938 helix: 2.05 (0.21), residues: 660 sheet: -0.14 (0.20), residues: 649 loop : -1.22 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.020 0.001 TYR B1067 PHE 0.027 0.001 PHE A 392 TRP 0.022 0.001 TRP C 353 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00340 (24567) covalent geometry : angle 0.55713 (33417) SS BOND : bond 0.00326 ( 39) SS BOND : angle 1.96288 ( 78) hydrogen bonds : bond 0.05630 ( 843) hydrogen bonds : angle 6.05594 ( 2355) link_BETA1-4 : bond 0.00429 ( 6) link_BETA1-4 : angle 1.03733 ( 18) link_NAG-ASN : bond 0.00736 ( 34) link_NAG-ASN : angle 3.82419 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.8119 (m-80) cc_final: 0.7861 (m-80) REVERT: A 740 MET cc_start: 0.7761 (tpt) cc_final: 0.7498 (tpt) REVERT: B 52 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7718 (pp30) REVERT: C 353 TRP cc_start: 0.7302 (p-90) cc_final: 0.7002 (p-90) REVERT: C 392 PHE cc_start: 0.7820 (m-80) cc_final: 0.6852 (m-10) REVERT: C 394 ASN cc_start: 0.8004 (m110) cc_final: 0.7698 (m-40) REVERT: C 400 PHE cc_start: 0.7730 (p90) cc_final: 0.7433 (p90) outliers start: 20 outliers final: 14 residues processed: 221 average time/residue: 0.1455 time to fit residues: 53.6428 Evaluate side-chains 195 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 620 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 7 optimal weight: 4.9990 chunk 253 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 242 optimal weight: 6.9990 chunk 276 optimal weight: 0.0010 chunk 71 optimal weight: 0.0670 chunk 196 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 221 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN B 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.143998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.098087 restraints weight = 42757.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.101287 restraints weight = 22590.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.103340 restraints weight = 15214.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.104616 restraints weight = 11887.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.105285 restraints weight = 10191.391| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24646 Z= 0.135 Angle : 0.570 19.780 33615 Z= 0.283 Chirality : 0.044 0.374 3914 Planarity : 0.004 0.043 4270 Dihedral : 6.116 59.296 4047 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.29 % Allowed : 9.44 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.24 (0.15), residues: 2938 helix: 2.10 (0.21), residues: 654 sheet: 0.01 (0.20), residues: 642 loop : -1.22 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 214 TYR 0.019 0.001 TYR A 369 PHE 0.019 0.001 PHE A 140 TRP 0.013 0.001 TRP C 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00316 (24567) covalent geometry : angle 0.52577 (33417) SS BOND : bond 0.00406 ( 39) SS BOND : angle 1.91016 ( 78) hydrogen bonds : bond 0.05049 ( 843) hydrogen bonds : angle 5.50225 ( 2355) link_BETA1-4 : bond 0.00272 ( 6) link_BETA1-4 : angle 1.05013 ( 18) link_NAG-ASN : bond 0.00721 ( 34) link_NAG-ASN : angle 3.67957 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7828 (pp30) REVERT: C 392 PHE cc_start: 0.7889 (m-80) cc_final: 0.7073 (m-10) REVERT: C 394 ASN cc_start: 0.8006 (m110) cc_final: 0.7724 (m-40) outliers start: 34 outliers final: 24 residues processed: 213 average time/residue: 0.1472 time to fit residues: 52.2502 Evaluate side-chains 196 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 117 optimal weight: 3.9990 chunk 294 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 258 optimal weight: 0.0870 chunk 211 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 295 optimal weight: 0.5980 chunk 250 optimal weight: 0.8980 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN B 360 ASN C 895 GLN C 965 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.143379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.097370 restraints weight = 42901.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.100578 restraints weight = 22711.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.102642 restraints weight = 15285.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.103883 restraints weight = 11931.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.104690 restraints weight = 10260.371| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24646 Z= 0.142 Angle : 0.565 19.637 33615 Z= 0.280 Chirality : 0.044 0.384 3914 Planarity : 0.004 0.043 4270 Dihedral : 5.832 58.071 4047 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.79 % Allowed : 11.69 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.26 (0.15), residues: 2938 helix: 2.05 (0.21), residues: 660 sheet: 0.02 (0.20), residues: 644 loop : -1.24 (0.14), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.018 0.001 TYR B1067 PHE 0.020 0.001 PHE A 140 TRP 0.013 0.001 TRP C 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00335 (24567) covalent geometry : angle 0.52288 (33417) SS BOND : bond 0.00397 ( 39) SS BOND : angle 1.79617 ( 78) hydrogen bonds : bond 0.04933 ( 843) hydrogen bonds : angle 5.26441 ( 2355) link_BETA1-4 : bond 0.00281 ( 6) link_BETA1-4 : angle 1.04516 ( 18) link_NAG-ASN : bond 0.00699 ( 34) link_NAG-ASN : angle 3.59209 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 178 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7566 (p90) REVERT: B 52 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7895 (pp30) REVERT: C 392 PHE cc_start: 0.7925 (m-80) cc_final: 0.7268 (m-10) outliers start: 47 outliers final: 36 residues processed: 208 average time/residue: 0.1532 time to fit residues: 53.3958 Evaluate side-chains 203 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 264 optimal weight: 0.7980 chunk 222 optimal weight: 0.9990 chunk 198 optimal weight: 0.3980 chunk 58 optimal weight: 0.6980 chunk 224 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 286 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 271 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN C 394 ASN C 965 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.143650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.097728 restraints weight = 42601.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.100912 restraints weight = 22574.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.102953 restraints weight = 15237.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.104254 restraints weight = 11911.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.104920 restraints weight = 10227.633| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24646 Z= 0.128 Angle : 0.551 19.583 33615 Z= 0.273 Chirality : 0.044 0.382 3914 Planarity : 0.003 0.045 4270 Dihedral : 5.710 59.883 4047 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.90 % Allowed : 12.68 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.15), residues: 2938 helix: 2.18 (0.21), residues: 653 sheet: 0.08 (0.20), residues: 622 loop : -1.22 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.017 0.001 TYR B1067 PHE 0.020 0.001 PHE A 140 TRP 0.012 0.001 TRP C 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00301 (24567) covalent geometry : angle 0.50874 (33417) SS BOND : bond 0.00319 ( 39) SS BOND : angle 1.77334 ( 78) hydrogen bonds : bond 0.04704 ( 843) hydrogen bonds : angle 5.11854 ( 2355) link_BETA1-4 : bond 0.00274 ( 6) link_BETA1-4 : angle 1.04061 ( 18) link_NAG-ASN : bond 0.00698 ( 34) link_NAG-ASN : angle 3.54053 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1068 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8483 (m) REVERT: B 759 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.7063 (t80) REVERT: C 353 TRP cc_start: 0.7377 (p-90) cc_final: 0.7132 (p-90) REVERT: C 392 PHE cc_start: 0.8039 (m-80) cc_final: 0.7439 (m-80) REVERT: C 823 PHE cc_start: 0.8394 (m-80) cc_final: 0.8161 (m-80) outliers start: 50 outliers final: 37 residues processed: 206 average time/residue: 0.1488 time to fit residues: 51.2520 Evaluate side-chains 204 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 53 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 281 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN B 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.140398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.093961 restraints weight = 42730.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.097061 restraints weight = 23036.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.099061 restraints weight = 15717.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.100312 restraints weight = 12392.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.101031 restraints weight = 10683.373| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 24646 Z= 0.257 Angle : 0.651 19.713 33615 Z= 0.326 Chirality : 0.047 0.390 3914 Planarity : 0.004 0.048 4270 Dihedral : 5.989 59.851 4047 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.25 % Allowed : 13.59 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.51 (0.15), residues: 2938 helix: 1.77 (0.21), residues: 660 sheet: -0.17 (0.20), residues: 653 loop : -1.36 (0.14), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.018 0.002 TYR B 279 PHE 0.023 0.002 PHE B 347 TRP 0.014 0.001 TRP B 886 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00628 (24567) covalent geometry : angle 0.61372 (33417) SS BOND : bond 0.00398 ( 39) SS BOND : angle 1.96499 ( 78) hydrogen bonds : bond 0.06054 ( 843) hydrogen bonds : angle 5.36845 ( 2355) link_BETA1-4 : bond 0.00255 ( 6) link_BETA1-4 : angle 1.13531 ( 18) link_NAG-ASN : bond 0.00692 ( 34) link_NAG-ASN : angle 3.61797 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 169 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.8615 (tpp) cc_final: 0.8086 (ttp) REVERT: B 421 TYR cc_start: 0.7879 (m-10) cc_final: 0.7371 (m-10) REVERT: B 452 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9150 (mm) REVERT: B 759 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7185 (t80) REVERT: C 354 ASN cc_start: 0.8187 (t0) cc_final: 0.7584 (p0) REVERT: C 392 PHE cc_start: 0.8108 (m-80) cc_final: 0.7535 (m-10) REVERT: C 400 PHE cc_start: 0.7734 (p90) cc_final: 0.7472 (p90) outliers start: 59 outliers final: 47 residues processed: 209 average time/residue: 0.1450 time to fit residues: 51.0103 Evaluate side-chains 211 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 162 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 26 optimal weight: 3.9990 chunk 141 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 113 optimal weight: 0.3980 chunk 41 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 chunk 176 optimal weight: 0.4980 chunk 254 optimal weight: 0.6980 chunk 261 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.142719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.096805 restraints weight = 42637.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.099945 restraints weight = 22591.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101971 restraints weight = 15303.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.103253 restraints weight = 11990.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.103989 restraints weight = 10314.414| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24646 Z= 0.129 Angle : 0.569 19.555 33615 Z= 0.282 Chirality : 0.044 0.371 3914 Planarity : 0.004 0.047 4270 Dihedral : 5.638 54.671 4047 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.02 % Allowed : 14.09 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.35 (0.15), residues: 2938 helix: 1.99 (0.21), residues: 660 sheet: -0.01 (0.20), residues: 620 loop : -1.30 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.036 0.001 TYR A 473 PHE 0.023 0.001 PHE A 140 TRP 0.020 0.001 TRP C 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00300 (24567) covalent geometry : angle 0.52826 (33417) SS BOND : bond 0.00369 ( 39) SS BOND : angle 1.81311 ( 78) hydrogen bonds : bond 0.04910 ( 843) hydrogen bonds : angle 5.09391 ( 2355) link_BETA1-4 : bond 0.00291 ( 6) link_BETA1-4 : angle 1.03074 ( 18) link_NAG-ASN : bond 0.00701 ( 34) link_NAG-ASN : angle 3.52947 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 177 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8140 (m-30) cc_final: 0.7838 (p0) REVERT: B 421 TYR cc_start: 0.7860 (m-10) cc_final: 0.7372 (m-10) REVERT: B 452 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9151 (mm) REVERT: B 759 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7101 (t80) REVERT: C 354 ASN cc_start: 0.8129 (t0) cc_final: 0.7606 (p0) REVERT: C 392 PHE cc_start: 0.8198 (m-80) cc_final: 0.7407 (m-10) REVERT: C 400 PHE cc_start: 0.7658 (p90) cc_final: 0.7419 (p90) REVERT: C 823 PHE cc_start: 0.8477 (m-80) cc_final: 0.8270 (m-80) outliers start: 53 outliers final: 44 residues processed: 216 average time/residue: 0.1449 time to fit residues: 52.5923 Evaluate side-chains 215 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 133 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 272 optimal weight: 0.9980 chunk 242 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.096022 restraints weight = 42592.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.099154 restraints weight = 22659.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.101223 restraints weight = 15323.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.102449 restraints weight = 11984.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.103183 restraints weight = 10339.630| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24646 Z= 0.173 Angle : 0.595 19.564 33615 Z= 0.295 Chirality : 0.045 0.379 3914 Planarity : 0.004 0.046 4270 Dihedral : 5.613 54.896 4046 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.98 % Allowed : 14.70 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.42 (0.15), residues: 2938 helix: 1.91 (0.21), residues: 659 sheet: -0.06 (0.20), residues: 633 loop : -1.33 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.017 0.001 TYR C1067 PHE 0.024 0.001 PHE A 140 TRP 0.015 0.001 TRP C 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00416 (24567) covalent geometry : angle 0.55478 (33417) SS BOND : bond 0.00445 ( 39) SS BOND : angle 2.05472 ( 78) hydrogen bonds : bond 0.05172 ( 843) hydrogen bonds : angle 5.09597 ( 2355) link_BETA1-4 : bond 0.00279 ( 6) link_BETA1-4 : angle 1.07121 ( 18) link_NAG-ASN : bond 0.00682 ( 34) link_NAG-ASN : angle 3.51915 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.8002 (m-80) cc_final: 0.7426 (m-80) REVERT: B 421 TYR cc_start: 0.7856 (m-10) cc_final: 0.7381 (m-10) REVERT: B 452 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9132 (mm) REVERT: B 759 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.7140 (t80) REVERT: C 354 ASN cc_start: 0.8032 (t0) cc_final: 0.7557 (p0) outliers start: 52 outliers final: 43 residues processed: 212 average time/residue: 0.1470 time to fit residues: 51.7080 Evaluate side-chains 212 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 92 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 258 optimal weight: 0.8980 chunk 116 optimal weight: 0.0570 chunk 276 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.143251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.097561 restraints weight = 42609.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100721 restraints weight = 22421.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.102808 restraints weight = 15108.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.104080 restraints weight = 11773.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.104766 restraints weight = 10104.823| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24646 Z= 0.123 Angle : 0.564 19.504 33615 Z= 0.278 Chirality : 0.044 0.371 3914 Planarity : 0.003 0.047 4270 Dihedral : 5.392 54.368 4046 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.87 % Allowed : 14.93 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.30 (0.15), residues: 2938 helix: 2.04 (0.21), residues: 659 sheet: -0.03 (0.20), residues: 644 loop : -1.27 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.019 0.001 TYR A 473 PHE 0.024 0.001 PHE A 140 TRP 0.022 0.001 TRP C 353 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00285 (24567) covalent geometry : angle 0.52383 (33417) SS BOND : bond 0.00375 ( 39) SS BOND : angle 1.85925 ( 78) hydrogen bonds : bond 0.04554 ( 843) hydrogen bonds : angle 4.93693 ( 2355) link_BETA1-4 : bond 0.00327 ( 6) link_BETA1-4 : angle 1.04826 ( 18) link_NAG-ASN : bond 0.00694 ( 34) link_NAG-ASN : angle 3.46070 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.7441 (t80) cc_final: 0.7207 (t80) REVERT: A 347 PHE cc_start: 0.7998 (m-80) cc_final: 0.7429 (m-80) REVERT: A 646 ARG cc_start: 0.7398 (tpt170) cc_final: 0.7189 (tpt170) REVERT: A 1068 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8495 (m) REVERT: B 421 TYR cc_start: 0.7840 (m-10) cc_final: 0.7384 (m-10) REVERT: B 452 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9157 (mm) REVERT: B 759 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.7052 (t80) REVERT: C 354 ASN cc_start: 0.8073 (t0) cc_final: 0.7672 (p0) REVERT: C 357 ARG cc_start: 0.7876 (tpp80) cc_final: 0.7645 (tpp80) outliers start: 49 outliers final: 40 residues processed: 217 average time/residue: 0.1537 time to fit residues: 55.0091 Evaluate side-chains 212 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 204 optimal weight: 5.9990 chunk 166 optimal weight: 0.1980 chunk 233 optimal weight: 0.1980 chunk 232 optimal weight: 0.4980 chunk 40 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 169 optimal weight: 0.4980 chunk 158 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 284 optimal weight: 0.6980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.144663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.099094 restraints weight = 42764.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.102362 restraints weight = 22434.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.104428 restraints weight = 15011.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.105695 restraints weight = 11712.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.106516 restraints weight = 10036.907| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 24646 Z= 0.103 Angle : 0.550 19.408 33615 Z= 0.271 Chirality : 0.044 0.365 3914 Planarity : 0.003 0.046 4270 Dihedral : 5.186 53.964 4046 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.60 % Allowed : 15.31 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 2938 helix: 2.20 (0.22), residues: 646 sheet: 0.01 (0.20), residues: 653 loop : -1.18 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 357 TYR 0.016 0.001 TYR B1067 PHE 0.024 0.001 PHE A 140 TRP 0.019 0.001 TRP C 353 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00231 (24567) covalent geometry : angle 0.51022 (33417) SS BOND : bond 0.00286 ( 39) SS BOND : angle 1.84914 ( 78) hydrogen bonds : bond 0.04091 ( 843) hydrogen bonds : angle 4.81596 ( 2355) link_BETA1-4 : bond 0.00329 ( 6) link_BETA1-4 : angle 1.10357 ( 18) link_NAG-ASN : bond 0.00710 ( 34) link_NAG-ASN : angle 3.41132 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 190 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7958 (m-80) cc_final: 0.7440 (m-10) REVERT: A 1068 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8489 (m) REVERT: B 40 ASP cc_start: 0.8018 (t70) cc_final: 0.7365 (p0) REVERT: B 421 TYR cc_start: 0.7865 (m-10) cc_final: 0.7450 (m-10) REVERT: B 452 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9155 (mm) REVERT: B 515 PHE cc_start: 0.7922 (p90) cc_final: 0.7515 (p90) REVERT: B 759 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.7029 (t80) REVERT: C 354 ASN cc_start: 0.7971 (t0) cc_final: 0.7650 (p0) REVERT: C 374 PHE cc_start: 0.8742 (m-80) cc_final: 0.8533 (m-80) REVERT: C 392 PHE cc_start: 0.8470 (m-80) cc_final: 0.7837 (m-80) outliers start: 42 outliers final: 37 residues processed: 219 average time/residue: 0.1499 time to fit residues: 54.3438 Evaluate side-chains 214 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 267 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 296 optimal weight: 0.9990 chunk 120 optimal weight: 0.0470 chunk 240 optimal weight: 10.0000 chunk 220 optimal weight: 0.7980 chunk 287 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 292 optimal weight: 1.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN C 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.143150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.097389 restraints weight = 42823.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.100509 restraints weight = 22626.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.102542 restraints weight = 15324.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103794 restraints weight = 11980.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.104549 restraints weight = 10320.271| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24646 Z= 0.145 Angle : 0.573 19.607 33615 Z= 0.283 Chirality : 0.044 0.376 3914 Planarity : 0.004 0.064 4270 Dihedral : 5.257 54.611 4046 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.75 % Allowed : 15.58 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.27 (0.15), residues: 2938 helix: 1.98 (0.21), residues: 659 sheet: 0.03 (0.20), residues: 668 loop : -1.23 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 357 TYR 0.017 0.001 TYR A 160 PHE 0.025 0.001 PHE A 140 TRP 0.021 0.001 TRP C 353 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00347 (24567) covalent geometry : angle 0.53442 (33417) SS BOND : bond 0.00352 ( 39) SS BOND : angle 1.84798 ( 78) hydrogen bonds : bond 0.04614 ( 843) hydrogen bonds : angle 4.86926 ( 2355) link_BETA1-4 : bond 0.00285 ( 6) link_BETA1-4 : angle 1.06741 ( 18) link_NAG-ASN : bond 0.00687 ( 34) link_NAG-ASN : angle 3.41141 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4821.53 seconds wall clock time: 84 minutes 9.52 seconds (5049.52 seconds total)