Starting phenix.real_space_refine on Sat Jun 21 00:33:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r16_14232/06_2025/7r16_14232.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r16_14232/06_2025/7r16_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7r16_14232/06_2025/7r16_14232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r16_14232/06_2025/7r16_14232.map" model { file = "/net/cci-nas-00/data/ceres_data/7r16_14232/06_2025/7r16_14232.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r16_14232/06_2025/7r16_14232.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.64, per 1000 atoms: 0.73 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: 5.92 Conformation dependent library (CDL) restraints added in 2.9 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: 3.33 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: 9.43 Time building geometry restraints manager: 7.04 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 1146 or resid 1301 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 1146 or resid 1301 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 1146 or resid 1301 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: 0.000 Normalize map: mean=0, sd=1: 16.140 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: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 58.760 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.700 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.001 TRP B 886 HIS 0.004 0.001 HIS A 655 PHE 0.041 0.001 PHE A 906 TYR 0.016 0.001 TYR C 873 ARG 0.005 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00787 ( 34) link_NAG-ASN : angle 3.95672 ( 102) link_BETA1-4 : bond 0.00322 ( 6) link_BETA1-4 : angle 1.31565 ( 18) hydrogen bonds : bond 0.23321 ( 843) hydrogen bonds : angle 8.30442 ( 2355) SS BOND : bond 0.00337 ( 39) SS BOND : angle 1.23524 ( 78) covalent geometry : bond 0.00471 (24567) covalent geometry : angle 0.60561 (33417) *********************** 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 : 2.631 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: 0.7557 (m-40) outliers start: 5 outliers final: 1 residues processed: 267 average time/residue: 0.3280 time to fit residues: 141.4729 Evaluate side-chains 186 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 2.780 ------------------------------------------------------------------------------- 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 252 optimal weight: 0.0010 chunk 226 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 234 optimal weight: 7.9990 chunk 90 optimal weight: 0.0970 chunk 142 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 271 optimal weight: 4.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN A1106 GLN B 965 GLN B1071 GLN C 978 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.145151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.104249 restraints weight = 42589.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103697 restraints weight = 28753.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104519 restraints weight = 21252.572| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24646 Z= 0.127 Angle : 0.595 19.990 33615 Z= 0.299 Chirality : 0.045 0.357 3914 Planarity : 0.004 0.042 4270 Dihedral : 6.651 59.753 4047 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.65 % Allowed : 6.74 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 2938 helix: 2.11 (0.21), residues: 665 sheet: -0.14 (0.20), residues: 655 loop : -1.18 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 353 HIS 0.003 0.001 HIS A1083 PHE 0.027 0.001 PHE A 392 TYR 0.020 0.001 TYR B1067 ARG 0.003 0.000 ARG B 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00764 ( 34) link_NAG-ASN : angle 3.80551 ( 102) link_BETA1-4 : bond 0.00435 ( 6) link_BETA1-4 : angle 1.06294 ( 18) hydrogen bonds : bond 0.05295 ( 843) hydrogen bonds : angle 6.03243 ( 2355) SS BOND : bond 0.00321 ( 39) SS BOND : angle 1.89631 ( 78) covalent geometry : bond 0.00280 (24567) covalent geometry : angle 0.54998 (33417) *********************** 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 237 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 2.398 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: 0.8032 (m-80) cc_final: 0.7738 (m-80) REVERT: B 52 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7759 (pp30) REVERT: B 902 MET cc_start: 0.8503 (tpt) cc_final: 0.8141 (tpt) REVERT: C 392 PHE cc_start: 0.7771 (m-80) cc_final: 0.6790 (m-10) REVERT: C 394 ASN cc_start: 0.7962 (m110) cc_final: 0.7681 (m-40) REVERT: C 400 PHE cc_start: 0.7762 (p90) cc_final: 0.7518 (p90) outliers start: 17 outliers final: 11 residues processed: 229 average time/residue: 0.3148 time to fit residues: 119.3123 Evaluate side-chains 195 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 2.324 ------------------------------------------------------------------------------- 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 780 GLU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 342 PHE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 248 optimal weight: 0.2980 chunk 117 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 245 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 235 optimal weight: 9.9990 chunk 81 optimal weight: 0.4980 chunk 283 optimal weight: 5.9990 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 B1071 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.144453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.098723 restraints weight = 42481.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102409 restraints weight = 24481.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.104771 restraints weight = 14781.099| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1317 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= 0.132 Angle : 0.569 19.803 33615 Z= 0.283 Chirality : 0.044 0.372 3914 Planarity : 0.004 0.044 4270 Dihedral : 6.151 59.167 4047 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.29 % Allowed : 9.29 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 2938 helix: 2.08 (0.21), residues: 660 sheet: -0.04 (0.20), residues: 654 loop : -1.18 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 353 HIS 0.003 0.001 HIS C1064 PHE 0.018 0.001 PHE A 140 TYR 0.017 0.001 TYR B1067 ARG 0.011 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00720 ( 34) link_NAG-ASN : angle 3.68283 ( 102) link_BETA1-4 : bond 0.00315 ( 6) link_BETA1-4 : angle 1.06264 ( 18) hydrogen bonds : bond 0.05003 ( 843) hydrogen bonds : angle 5.54898 ( 2355) SS BOND : bond 0.00407 ( 39) SS BOND : angle 1.97166 ( 78) covalent geometry : bond 0.00308 (24567) covalent geometry : angle 0.52450 (33417) *********************** 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 224 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.7525 (mmm160) cc_final: 0.7305 (mmm160) REVERT: B 52 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7776 (pp30) REVERT: C 392 PHE cc_start: 0.7784 (m-80) cc_final: 0.6935 (m-10) outliers start: 34 outliers final: 22 residues processed: 211 average time/residue: 0.3229 time to fit residues: 113.9556 Evaluate side-chains 193 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 120 VAL 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 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 1120 THR 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 604 THR 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 524 VAL Chi-restraints excluded: chain C residue 922 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 274 optimal weight: 1.9990 chunk 285 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 113 optimal weight: 0.2980 chunk 147 optimal weight: 0.6980 chunk 283 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 171 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 244 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.144686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.103665 restraints weight = 42859.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.103484 restraints weight = 27961.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104210 restraints weight = 21045.547| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24646 Z= 0.119 Angle : 0.552 19.658 33615 Z= 0.273 Chirality : 0.044 0.380 3914 Planarity : 0.003 0.047 4270 Dihedral : 5.895 59.959 4047 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.33 % Allowed : 10.93 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 2938 helix: 2.19 (0.21), residues: 654 sheet: -0.01 (0.20), residues: 653 loop : -1.17 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 353 HIS 0.003 0.001 HIS C1064 PHE 0.018 0.001 PHE A 140 TYR 0.017 0.001 TYR B1067 ARG 0.004 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00714 ( 34) link_NAG-ASN : angle 3.59418 ( 102) link_BETA1-4 : bond 0.00280 ( 6) link_BETA1-4 : angle 1.04711 ( 18) hydrogen bonds : bond 0.04662 ( 843) hydrogen bonds : angle 5.31115 ( 2355) SS BOND : bond 0.00363 ( 39) SS BOND : angle 1.81509 ( 78) covalent geometry : bond 0.00274 (24567) covalent geometry : angle 0.50918 (33417) *********************** 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 213 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.7483 (mmm160) cc_final: 0.7277 (mmm160) REVERT: B 52 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7824 (pp30) REVERT: C 353 TRP cc_start: 0.7416 (p-90) cc_final: 0.7026 (p-90) REVERT: C 392 PHE cc_start: 0.7825 (m-80) cc_final: 0.7179 (m-10) outliers start: 35 outliers final: 27 residues processed: 195 average time/residue: 0.3074 time to fit residues: 100.7471 Evaluate side-chains 192 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 342 PHE 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 975 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 342 PHE 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 619 GLU Chi-restraints excluded: chain C residue 884 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 177 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 277 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 275 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN C 965 GLN 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 = 0.144357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.098578 restraints weight = 42649.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.101776 restraints weight = 22607.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.103836 restraints weight = 15279.316| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24646 Z= 0.127 Angle : 0.549 19.591 33615 Z= 0.270 Chirality : 0.044 0.384 3914 Planarity : 0.003 0.047 4270 Dihedral : 5.687 57.262 4047 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.79 % Allowed : 11.61 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 2938 helix: 2.20 (0.21), residues: 654 sheet: 0.03 (0.20), residues: 651 loop : -1.19 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 353 HIS 0.003 0.001 HIS C1064 PHE 0.019 0.001 PHE A 140 TYR 0.017 0.001 TYR B1067 ARG 0.003 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00702 ( 34) link_NAG-ASN : angle 3.53547 ( 102) link_BETA1-4 : bond 0.00287 ( 6) link_BETA1-4 : angle 1.04030 ( 18) hydrogen bonds : bond 0.04620 ( 843) hydrogen bonds : angle 5.15901 ( 2355) SS BOND : bond 0.00355 ( 39) SS BOND : angle 1.75786 ( 78) covalent geometry : bond 0.00296 (24567) covalent geometry : angle 0.50724 (33417) *********************** 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 225 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 178 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7433 (p90) REVERT: A 1068 VAL cc_start: 0.8763 (OUTLIER) cc_final: 0.8515 (m) REVERT: B 52 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7855 (pp30) outliers start: 47 outliers final: 31 residues processed: 208 average time/residue: 0.3050 time to fit residues: 107.0833 Evaluate side-chains 194 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL 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 392 PHE 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 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 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 524 VAL Chi-restraints excluded: chain C residue 697 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 114 optimal weight: 0.3980 chunk 181 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 239 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 288 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.143996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098229 restraints weight = 42522.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101426 restraints weight = 22428.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.103465 restraints weight = 15123.427| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24646 Z= 0.132 Angle : 0.554 19.505 33615 Z= 0.273 Chirality : 0.044 0.386 3914 Planarity : 0.003 0.047 4270 Dihedral : 5.565 56.105 4047 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.87 % Allowed : 12.87 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 2938 helix: 2.19 (0.21), residues: 654 sheet: 0.11 (0.20), residues: 620 loop : -1.20 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 353 HIS 0.003 0.001 HIS C1064 PHE 0.024 0.001 PHE B 347 TYR 0.016 0.001 TYR B1067 ARG 0.004 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00690 ( 34) link_NAG-ASN : angle 3.49473 ( 102) link_BETA1-4 : bond 0.00292 ( 6) link_BETA1-4 : angle 1.04342 ( 18) hydrogen bonds : bond 0.04657 ( 843) hydrogen bonds : angle 5.04474 ( 2355) SS BOND : bond 0.00320 ( 39) SS BOND : angle 1.74260 ( 78) covalent geometry : bond 0.00312 (24567) covalent geometry : angle 0.51384 (33417) *********************** 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 225 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1068 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8518 (m) REVERT: B 52 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7846 (pp30) REVERT: B 452 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9166 (mm) REVERT: C 823 PHE cc_start: 0.8399 (m-80) cc_final: 0.8158 (m-80) outliers start: 49 outliers final: 36 residues processed: 204 average time/residue: 0.2946 time to fit residues: 100.9507 Evaluate side-chains 206 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL 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 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR 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 1068 VAL 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 452 LEU 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 697 MET 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 187 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 285 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 216 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.143774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.097938 restraints weight = 42727.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.101076 restraints weight = 22669.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.103120 restraints weight = 15368.977| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24646 Z= 0.137 Angle : 0.554 19.489 33615 Z= 0.274 Chirality : 0.044 0.385 3914 Planarity : 0.003 0.047 4270 Dihedral : 5.500 55.146 4047 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.71 % Allowed : 13.82 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 2938 helix: 2.18 (0.21), residues: 654 sheet: 0.10 (0.20), residues: 619 loop : -1.20 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 353 HIS 0.003 0.001 HIS C1064 PHE 0.021 0.001 PHE A 140 TYR 0.016 0.001 TYR B1067 ARG 0.004 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00688 ( 34) link_NAG-ASN : angle 3.47073 ( 102) link_BETA1-4 : bond 0.00275 ( 6) link_BETA1-4 : angle 1.05680 ( 18) hydrogen bonds : bond 0.04681 ( 843) hydrogen bonds : angle 5.00072 ( 2355) SS BOND : bond 0.00316 ( 39) SS BOND : angle 1.75110 ( 78) covalent geometry : bond 0.00324 (24567) covalent geometry : angle 0.51383 (33417) *********************** 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 223 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 2.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1068 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8524 (m) REVERT: B 52 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7889 (pp30) REVERT: B 421 TYR cc_start: 0.7877 (m-10) cc_final: 0.7389 (m-10) REVERT: B 759 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.6981 (t80) REVERT: C 354 ASN cc_start: 0.8097 (t0) cc_final: 0.7561 (p0) REVERT: C 823 PHE cc_start: 0.8397 (m-80) cc_final: 0.8161 (m-80) outliers start: 45 outliers final: 40 residues processed: 203 average time/residue: 0.3241 time to fit residues: 110.0927 Evaluate side-chains 210 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 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 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 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 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 360 ASN 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 191 GLU 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 697 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 273 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 292 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.143250 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 = 42607.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.100549 restraints weight = 22526.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.102562 restraints weight = 15220.852| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24646 Z= 0.153 Angle : 0.573 19.489 33615 Z= 0.283 Chirality : 0.044 0.385 3914 Planarity : 0.004 0.048 4270 Dihedral : 5.497 54.803 4046 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.79 % Allowed : 14.13 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 2938 helix: 2.16 (0.21), residues: 653 sheet: 0.08 (0.20), residues: 618 loop : -1.22 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 353 HIS 0.003 0.001 HIS C1064 PHE 0.023 0.001 PHE A 140 TYR 0.021 0.001 TYR A 473 ARG 0.004 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00681 ( 34) link_NAG-ASN : angle 3.45787 ( 102) link_BETA1-4 : bond 0.00267 ( 6) link_BETA1-4 : angle 1.04431 ( 18) hydrogen bonds : bond 0.04871 ( 843) hydrogen bonds : angle 4.99416 ( 2355) SS BOND : bond 0.00346 ( 39) SS BOND : angle 1.73081 ( 78) covalent geometry : bond 0.00366 (24567) covalent geometry : angle 0.53545 (33417) *********************** 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 227 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.7286 (pttt) cc_final: 0.6286 (mtmt) REVERT: A 347 PHE cc_start: 0.7967 (m-80) cc_final: 0.7426 (m-80) REVERT: B 52 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7971 (pp30) REVERT: B 421 TYR cc_start: 0.7871 (m-10) cc_final: 0.7383 (m-10) REVERT: B 452 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9097 (mm) REVERT: B 759 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7029 (t80) REVERT: C 354 ASN cc_start: 0.8045 (t0) cc_final: 0.7532 (p0) REVERT: C 823 PHE cc_start: 0.8384 (m-80) cc_final: 0.8154 (m-80) outliers start: 47 outliers final: 43 residues processed: 209 average time/residue: 0.3222 time to fit residues: 112.9468 Evaluate side-chains 217 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 LEU 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 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 560 LEU 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 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 289 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 452 LEU 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 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 884 SER 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 82 optimal weight: 1.9990 chunk 298 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 259 optimal weight: 0.6980 chunk 185 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 179 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 254 optimal weight: 0.0060 chunk 140 optimal weight: 4.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.144143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.098368 restraints weight = 42698.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101587 restraints weight = 22478.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103642 restraints weight = 15102.286| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24646 Z= 0.117 Angle : 0.554 19.408 33615 Z= 0.271 Chirality : 0.044 0.378 3914 Planarity : 0.003 0.047 4270 Dihedral : 5.338 54.329 4046 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.87 % Allowed : 14.39 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 2938 helix: 2.23 (0.21), residues: 653 sheet: 0.08 (0.20), residues: 632 loop : -1.15 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 353 HIS 0.003 0.001 HIS A1083 PHE 0.023 0.001 PHE A 140 TYR 0.018 0.001 TYR A 160 ARG 0.003 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00692 ( 34) link_NAG-ASN : angle 3.41281 ( 102) link_BETA1-4 : bond 0.00305 ( 6) link_BETA1-4 : angle 1.04337 ( 18) hydrogen bonds : bond 0.04412 ( 843) hydrogen bonds : angle 4.85841 ( 2355) SS BOND : bond 0.00303 ( 39) SS BOND : angle 1.66347 ( 78) covalent geometry : bond 0.00271 (24567) covalent geometry : angle 0.51536 (33417) *********************** 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 232 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 183 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.7544 (t80) cc_final: 0.7322 (t80) REVERT: A 195 LYS cc_start: 0.7279 (pttt) cc_final: 0.6366 (mtmt) REVERT: A 347 PHE cc_start: 0.7856 (m-80) cc_final: 0.7291 (m-80) REVERT: A 389 ASP cc_start: 0.8168 (m-30) cc_final: 0.7890 (p0) REVERT: A 1068 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8523 (m) REVERT: B 40 ASP cc_start: 0.7934 (t70) cc_final: 0.7248 (p0) REVERT: B 52 GLN cc_start: 0.8269 (tm-30) cc_final: 0.8062 (pp30) REVERT: B 421 TYR cc_start: 0.7861 (m-10) cc_final: 0.7412 (m-10) REVERT: B 759 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.7060 (t80) REVERT: C 354 ASN cc_start: 0.8132 (t0) cc_final: 0.7640 (p0) REVERT: C 374 PHE cc_start: 0.8831 (m-80) cc_final: 0.8604 (m-80) REVERT: C 823 PHE cc_start: 0.8374 (m-80) cc_final: 0.8138 (m-80) outliers start: 49 outliers final: 41 residues processed: 213 average time/residue: 0.3355 time to fit residues: 117.7198 Evaluate side-chains 210 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 LEU 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 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 560 LEU 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 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 289 VAL Chi-restraints excluded: chain B residue 342 PHE 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 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 884 SER 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 211 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 259 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 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 = 0.3835 r_free = 0.3835 target = 0.141849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.095736 restraints weight = 42642.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098852 restraints weight = 22778.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.100836 restraints weight = 15474.970| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24646 Z= 0.201 Angle : 0.616 19.588 33615 Z= 0.305 Chirality : 0.046 0.393 3914 Planarity : 0.004 0.047 4270 Dihedral : 5.602 55.423 4046 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.60 % Allowed : 14.81 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 2938 helix: 1.94 (0.21), residues: 659 sheet: -0.01 (0.20), residues: 639 loop : -1.27 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 353 HIS 0.005 0.001 HIS C1064 PHE 0.025 0.002 PHE A 140 TYR 0.016 0.001 TYR C1067 ARG 0.008 0.000 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00685 ( 34) link_NAG-ASN : angle 3.47609 ( 102) link_BETA1-4 : bond 0.00259 ( 6) link_BETA1-4 : angle 1.09648 ( 18) hydrogen bonds : bond 0.05462 ( 843) hydrogen bonds : angle 5.05743 ( 2355) SS BOND : bond 0.00357 ( 39) SS BOND : angle 1.81935 ( 78) covalent geometry : bond 0.00488 (24567) covalent geometry : angle 0.57992 (33417) ********************** 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 219 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.7408 (pttt) cc_final: 0.6432 (mtmt) REVERT: A 347 PHE cc_start: 0.7984 (m-80) cc_final: 0.7419 (m-80) REVERT: B 52 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7973 (pp30) REVERT: B 421 TYR cc_start: 0.7883 (m-10) cc_final: 0.7446 (m-10) REVERT: B 759 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7162 (t80) REVERT: C 354 ASN cc_start: 0.8151 (t0) cc_final: 0.7639 (p0) REVERT: C 823 PHE cc_start: 0.8409 (m-80) cc_final: 0.8187 (m-80) outliers start: 42 outliers final: 39 residues processed: 205 average time/residue: 0.3032 time to fit residues: 103.4214 Evaluate side-chains 208 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 159 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 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 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 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 360 ASN 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 524 VAL Chi-restraints excluded: chain C residue 697 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 57 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 133 optimal weight: 20.0000 chunk 200 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.141778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.095800 restraints weight = 42613.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.098896 restraints weight = 22679.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.100903 restraints weight = 15398.834| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.194 24646 Z= 0.279 Angle : 0.765 59.173 33615 Z= 0.417 Chirality : 0.046 0.393 3914 Planarity : 0.004 0.083 4270 Dihedral : 5.619 55.566 4046 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.24 % Favored : 94.72 % Rotamer: Outliers : 1.71 % Allowed : 14.81 % Favored : 83.47 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 2938 helix: 1.92 (0.21), residues: 659 sheet: -0.03 (0.20), residues: 639 loop : -1.28 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 353 HIS 0.006 0.001 HIS C1064 PHE 0.054 0.002 PHE A 133 TYR 0.121 0.002 TYR A 160 ARG 0.022 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 34) link_NAG-ASN : angle 3.47674 ( 102) link_BETA1-4 : bond 0.00259 ( 6) link_BETA1-4 : angle 1.09191 ( 18) hydrogen bonds : bond 0.05571 ( 843) hydrogen bonds : angle 5.06036 ( 2355) SS BOND : bond 0.00415 ( 39) SS BOND : angle 1.85187 ( 78) covalent geometry : bond 0.00638 (24567) covalent geometry : angle 0.73649 (33417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7694.31 seconds wall clock time: 134 minutes 2.49 seconds (8042.49 seconds total)