Starting phenix.real_space_refine on Sat Jul 4 23:40:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7od3_12818/07_2026/7od3_12818.cif Found real_map, /net/cci-nas-00/data/ceres_data/7od3_12818/07_2026/7od3_12818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7od3_12818/07_2026/7od3_12818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7od3_12818/07_2026/7od3_12818.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7od3_12818/07_2026/7od3_12818.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7od3_12818/07_2026/7od3_12818.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7od3_12818/07_2026/7od3_12818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7od3_12818/07_2026/7od3_12818.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 111 5.16 5 C 15459 2.51 5 N 3975 2.21 5 O 4677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24222 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7900 Classifications: {'peptide': 1012} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 45, 'TRANS': 966} Chain breaks: 10 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7900 Classifications: {'peptide': 1012} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 45, 'TRANS': 966} Chain breaks: 10 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7900 Classifications: {'peptide': 1012} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 45, 'TRANS': 966} Chain breaks: 10 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 174 Unusual residues: {'EIC': 1, 'NAG': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 174 Unusual residues: {'EIC': 1, 'NAG': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 174 Unusual residues: {'EIC': 1, 'NAG': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.29, per 1000 atoms: 0.22 Number of scatterers: 24222 At special positions: 0 Unit cell: (120.75, 124.95, 170.1, 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 111 16.00 O 4677 8.00 N 3975 7.00 C 15459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 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=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 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 NAG-ASN " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 717 " " NAG A1308 " - " ASN A 801 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 343 " " NAG B1301 " - " ASN B 343 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 717 " " NAG B1309 " - " ASN B 801 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B1098 " " NAG B1312 " - " ASN B1134 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 717 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C1134 " " NAG C1312 " - " ASN C 343 " Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 995.1 milliseconds 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5676 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 47 sheets defined 25.8% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.512A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.613A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.772A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.466A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 758 removed outlier: 6.458A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.828A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 842 through 847 removed outlier: 3.697A pdb=" N ARG A 847 " --> pdb=" O ILE A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.589A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.658A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.552A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.084A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 938 removed outlier: 3.537A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.977A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.637A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.056A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.548A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.795A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.378A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 758 removed outlier: 6.404A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.834A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.525A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 847 removed outlier: 3.684A pdb=" N ARG B 847 " --> pdb=" O ILE B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.622A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.513A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.131A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 938 removed outlier: 3.600A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 965 removed outlier: 4.064A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (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 removed outlier: 3.737A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.099A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.572A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.592A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.726A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.468A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 758 removed outlier: 6.380A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 783 removed outlier: 3.845A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.539A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 847 removed outlier: 3.704A pdb=" N ARG C 847 " --> pdb=" O ILE C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 855 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.519A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.628A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 938 Processing helix chain 'C' and resid 946 through 965 removed outlier: 4.069A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.687A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.153A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.253A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.997A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.671A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 140 removed outlier: 6.714A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N CYS A 136 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.266A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.477A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.596A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.636A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.636A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.556A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.912A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1121 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.568A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.065A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.740A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 133 through 140 removed outlier: 6.691A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N CYS B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.200A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.583A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.528A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.593A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.542A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.623A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.623A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.528A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1121 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.336A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.983A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.718A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 133 through 140 removed outlier: 6.700A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.245A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.674A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 538 through 543 removed outlier: 5.503A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.548A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.660A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.660A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.594A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1121 through 1122 998 hydrogen bonds defined for protein. 2709 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.73 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7726 1.35 - 1.47: 6179 1.47 - 1.59: 10698 1.59 - 1.71: 0 1.71 - 1.83: 135 Bond restraints: 24738 Sorted by residual: bond pdb=" C13 EIC A1301 " pdb=" C14 EIC A1301 " ideal model delta sigma weight residual 1.496 1.530 -0.034 2.00e-02 2.50e+03 2.82e+00 bond pdb=" C8 EIC B1302 " pdb=" C9 EIC B1302 " ideal model delta sigma weight residual 1.496 1.529 -0.033 2.00e-02 2.50e+03 2.76e+00 bond pdb=" C13 EIC C1301 " pdb=" C14 EIC C1301 " ideal model delta sigma weight residual 1.496 1.529 -0.033 2.00e-02 2.50e+03 2.68e+00 bond pdb=" C8 EIC C1301 " pdb=" C9 EIC C1301 " ideal model delta sigma weight residual 1.496 1.528 -0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" C13 EIC B1302 " pdb=" C14 EIC B1302 " ideal model delta sigma weight residual 1.496 1.528 -0.032 2.00e-02 2.50e+03 2.57e+00 ... (remaining 24733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 32239 1.33 - 2.67: 1100 2.67 - 4.00: 232 4.00 - 5.33: 27 5.33 - 6.67: 11 Bond angle restraints: 33609 Sorted by residual: angle pdb=" C GLU B1092 " pdb=" N GLY B1093 " pdb=" CA GLY B1093 " ideal model delta sigma weight residual 121.01 115.98 5.03 1.86e+00 2.89e-01 7.31e+00 angle pdb=" CA CYS B 851 " pdb=" CB CYS B 851 " pdb=" SG CYS B 851 " ideal model delta sigma weight residual 114.40 119.78 -5.38 2.30e+00 1.89e-01 5.47e+00 angle pdb=" N LYS A 986 " pdb=" CA LYS A 986 " pdb=" C LYS A 986 " ideal model delta sigma weight residual 111.02 113.80 -2.78 1.22e+00 6.72e-01 5.18e+00 angle pdb=" N GLY C 842 " pdb=" CA GLY C 842 " pdb=" C GLY C 842 " ideal model delta sigma weight residual 111.21 113.57 -2.36 1.04e+00 9.25e-01 5.15e+00 angle pdb=" CA CYS C 851 " pdb=" CB CYS C 851 " pdb=" SG CYS C 851 " ideal model delta sigma weight residual 114.40 119.57 -5.17 2.30e+00 1.89e-01 5.05e+00 ... (remaining 33604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 13019 17.78 - 35.56: 1155 35.56 - 53.34: 163 53.34 - 71.12: 63 71.12 - 88.90: 24 Dihedral angle restraints: 14424 sinusoidal: 5607 harmonic: 8817 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 174.83 -81.83 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 174.72 -81.72 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 170.86 -77.86 1 1.00e+01 1.00e-02 7.58e+01 ... (remaining 14421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2841 0.044 - 0.087: 722 0.087 - 0.131: 305 0.131 - 0.174: 41 0.174 - 0.218: 3 Chirality restraints: 3912 Sorted by residual: chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C1 NAG C1310 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG C1310 " pdb=" O5 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C1 NAG B1311 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1311 " pdb=" O5 NAG B1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.81e-01 ... (remaining 3909 not shown) Planarity restraints: 4335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 347 " 0.021 2.00e-02 2.50e+03 1.92e-02 6.42e+00 pdb=" CG PHE C 347 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE C 347 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 347 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 347 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 347 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 347 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 560 " -0.041 5.00e-02 4.00e+02 6.26e-02 6.26e+00 pdb=" N PRO B 561 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 411 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO A 412 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " -0.028 5.00e-02 4.00e+02 ... (remaining 4332 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 102 2.54 - 3.13: 17521 3.13 - 3.72: 32873 3.72 - 4.31: 50418 4.31 - 4.90: 86157 Nonbonded interactions: 187071 Sorted by model distance: nonbonded pdb=" O3 NAG C1305 " pdb=" O7 NAG C1305 " model vdw 1.953 3.040 nonbonded pdb=" O3 NAG B1306 " pdb=" O7 NAG B1306 " model vdw 1.953 3.040 nonbonded pdb=" O3 NAG A1305 " pdb=" O7 NAG A1305 " model vdw 1.954 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" OD2 ASP A 53 " model vdw 1.997 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" O TYR C1138 " model vdw 2.024 3.040 ... (remaining 187066 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 1139 or resid 1303 through 1312)) selection = (chain 'B' and (resid 27 through 1139 or resid 1303 through 1312)) selection = (chain 'C' and (resid 27 through 1139 or resid 1303 through 1312)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.280 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 : 0.004 0.049 24804 Z= 0.185 Angle : 0.626 6.666 33774 Z= 0.321 Chirality : 0.046 0.218 3912 Planarity : 0.004 0.063 4302 Dihedral : 14.001 88.895 8649 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.23 % Allowed : 0.19 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 2970 helix: 0.61 (0.21), residues: 660 sheet: 0.86 (0.21), residues: 612 loop : -1.95 (0.13), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 34 TYR 0.029 0.002 TYR A 266 PHE 0.044 0.002 PHE C 347 TRP 0.020 0.002 TRP C 886 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (24738) covalent geometry : angle 0.60615 / 0.32 (33609) SS BOND : bond 0.00573 / 0.35 ( 33) SS BOND : angle 1.28859 / 0.78 ( 66) hydrogen bonds : bond 0.17567 / 11.64 ( 962) hydrogen bonds : angle 7.33955 / 5.20 ( 2709) link_NAG-ASN : bond 0.00246 / 0.15 ( 33) link_NAG-ASN : angle 2.81474 / 1.81 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 283 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7229 (tt0) cc_final: 0.6967 (tt0) REVERT: A 820 ASP cc_start: 0.6982 (m-30) cc_final: 0.6738 (m-30) REVERT: A 957 GLN cc_start: 0.8203 (tt0) cc_final: 0.7884 (tt0) REVERT: C 820 ASP cc_start: 0.7220 (m-30) cc_final: 0.6950 (m-30) REVERT: C 921 LYS cc_start: 0.7956 (mtmm) cc_final: 0.7484 (mppt) REVERT: C 1017 GLU cc_start: 0.7373 (tt0) cc_final: 0.7099 (tt0) outliers start: 6 outliers final: 6 residues processed: 289 average time/residue: 0.5801 time to fit residues: 193.0069 Evaluate side-chains 214 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 208 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 331 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN A1058 HIS B 334 ASN B 448 ASN B 474 GLN B 613 GLN B 779 GLN B 957 GLN C 334 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 613 GLN C 804 GLN C 907 ASN C 955 ASN C1010 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.136438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.109793 restraints weight = 26374.566| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.88 r_work: 0.2878 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 24804 Z= 0.263 Angle : 0.792 10.644 33774 Z= 0.415 Chirality : 0.054 0.240 3912 Planarity : 0.006 0.066 4302 Dihedral : 6.962 83.349 3297 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.82 % Allowed : 7.25 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 2970 helix: 0.48 (0.21), residues: 663 sheet: 1.00 (0.21), residues: 630 loop : -1.98 (0.13), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 273 TYR 0.031 0.003 TYR C 756 PHE 0.046 0.003 PHE C 347 TRP 0.014 0.002 TRP B 64 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.26 (24738) covalent geometry : angle 0.76404 / 0.41 (33609) SS BOND : bond 0.00882 / 0.52 ( 33) SS BOND : angle 1.91914 / 1.16 ( 66) hydrogen bonds : bond 0.09016 / 5.94 ( 962) hydrogen bonds : angle 5.96826 / 4.19 ( 2709) link_NAG-ASN : bond 0.00627 / 0.39 ( 33) link_NAG-ASN : angle 3.61982 / 2.40 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 654 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6908 (tm-30) REVERT: A 957 GLN cc_start: 0.8792 (tt0) cc_final: 0.8561 (tt0) REVERT: B 309 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7694 (mm-30) REVERT: C 190 ARG cc_start: 0.8136 (mtt-85) cc_final: 0.7770 (mtt-85) REVERT: C 207 HIS cc_start: 0.6448 (m90) cc_final: 0.5648 (m90) REVERT: C 762 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7762 (mt0) REVERT: C 779 GLN cc_start: 0.8496 (tp40) cc_final: 0.8238 (tp-100) REVERT: C 814 LYS cc_start: 0.8151 (mptt) cc_final: 0.7717 (mptt) REVERT: C 820 ASP cc_start: 0.7953 (m-30) cc_final: 0.7617 (m-30) REVERT: C 881 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8886 (m) REVERT: C 921 LYS cc_start: 0.8317 (mtmm) cc_final: 0.7566 (mppt) REVERT: C 1002 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: C 1017 GLU cc_start: 0.8734 (tt0) cc_final: 0.8490 (tt0) REVERT: C 1111 GLU cc_start: 0.7956 (tt0) cc_final: 0.7232 (tt0) outliers start: 48 outliers final: 19 residues processed: 247 average time/residue: 0.5652 time to fit residues: 160.8959 Evaluate side-chains 232 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1002 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 297 optimal weight: 3.9990 chunk 258 optimal weight: 0.9980 chunk 273 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 223 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 172 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN B 52 GLN B 334 ASN B 474 GLN B 779 GLN B 955 ASN B 957 GLN C 474 GLN C1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.138771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.111893 restraints weight = 26260.590| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.95 r_work: 0.3007 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24804 Z= 0.156 Angle : 0.641 11.832 33774 Z= 0.335 Chirality : 0.047 0.182 3912 Planarity : 0.005 0.056 4302 Dihedral : 6.573 87.608 3297 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.86 % Allowed : 9.91 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.15), residues: 2970 helix: 0.78 (0.21), residues: 660 sheet: 1.22 (0.21), residues: 606 loop : -1.85 (0.13), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.021 0.002 TYR C 380 PHE 0.018 0.002 PHE A 133 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (24738) covalent geometry : angle 0.61029 / 0.33 (33609) SS BOND : bond 0.00515 / 0.31 ( 33) SS BOND : angle 1.35922 / 0.81 ( 66) hydrogen bonds : bond 0.07148 / 4.71 ( 962) hydrogen bonds : angle 5.60603 / 3.94 ( 2709) link_NAG-ASN : bond 0.00514 / 0.31 ( 33) link_NAG-ASN : angle 3.56391 / 2.38 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 ASN cc_start: 0.7441 (OUTLIER) cc_final: 0.7231 (m110) REVERT: A 357 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8195 (ttm170) REVERT: A 654 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6879 (tm-30) REVERT: A 779 GLN cc_start: 0.8638 (tp40) cc_final: 0.8377 (tp-100) REVERT: A 869 MET cc_start: 0.8856 (mtt) cc_final: 0.8609 (mtp) REVERT: A 957 GLN cc_start: 0.8798 (tt0) cc_final: 0.8568 (tt0) REVERT: B 309 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7775 (mm-30) REVERT: C 779 GLN cc_start: 0.8367 (tp40) cc_final: 0.8094 (tp-100) REVERT: C 820 ASP cc_start: 0.7818 (m-30) cc_final: 0.7509 (m-30) REVERT: C 921 LYS cc_start: 0.8232 (mtmm) cc_final: 0.7530 (mppt) REVERT: C 1002 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8290 (tm-30) REVERT: C 1017 GLU cc_start: 0.8565 (tt0) cc_final: 0.8314 (tt0) outliers start: 49 outliers final: 23 residues processed: 231 average time/residue: 0.5765 time to fit residues: 153.8688 Evaluate side-chains 222 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 63 optimal weight: 6.9990 chunk 272 optimal weight: 9.9990 chunk 273 optimal weight: 2.9990 chunk 229 optimal weight: 0.9990 chunk 204 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 240 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 GLN B 334 ASN B 474 GLN B 954 GLN B 957 GLN C 207 HIS C 474 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.137259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.110592 restraints weight = 26269.629| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.92 r_work: 0.2935 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24804 Z= 0.176 Angle : 0.664 11.831 33774 Z= 0.346 Chirality : 0.049 0.333 3912 Planarity : 0.005 0.057 4302 Dihedral : 6.575 88.783 3295 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.28 % Allowed : 11.01 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.15), residues: 2970 helix: 0.81 (0.21), residues: 660 sheet: 1.24 (0.21), residues: 621 loop : -1.87 (0.13), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.024 0.002 TYR C 380 PHE 0.019 0.002 PHE B 86 TRP 0.007 0.001 TRP B 64 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (24738) covalent geometry : angle 0.63347 / 0.34 (33609) SS BOND : bond 0.00598 / 0.35 ( 33) SS BOND : angle 1.48192 / 0.88 ( 66) hydrogen bonds : bond 0.07483 / 4.93 ( 962) hydrogen bonds : angle 5.56882 / 3.91 ( 2709) link_NAG-ASN : bond 0.00458 / 0.28 ( 33) link_NAG-ASN : angle 3.59488 / 2.39 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 200 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7225 (OUTLIER) cc_final: 0.6866 (mt) REVERT: A 334 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.7265 (m-40) REVERT: A 357 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8385 (ttm170) REVERT: A 654 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: A 779 GLN cc_start: 0.8627 (tp40) cc_final: 0.8375 (tp-100) REVERT: A 869 MET cc_start: 0.8846 (mtt) cc_final: 0.8627 (mtp) REVERT: A 957 GLN cc_start: 0.8765 (tt0) cc_final: 0.8526 (tt0) REVERT: A 1114 ILE cc_start: 0.7635 (mm) cc_final: 0.7358 (mp) REVERT: B 309 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7707 (mm-30) REVERT: B 703 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8300 (t0) REVERT: C 190 ARG cc_start: 0.8171 (mtt-85) cc_final: 0.7664 (mtt-85) REVERT: C 207 HIS cc_start: 0.6349 (m-70) cc_final: 0.5474 (m90) REVERT: C 779 GLN cc_start: 0.8361 (tp40) cc_final: 0.8086 (tp-100) REVERT: C 820 ASP cc_start: 0.7804 (m-30) cc_final: 0.7493 (m-30) REVERT: C 921 LYS cc_start: 0.8232 (mtmm) cc_final: 0.7528 (mppt) REVERT: C 1002 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: C 1017 GLU cc_start: 0.8558 (tt0) cc_final: 0.8298 (tt0) outliers start: 60 outliers final: 35 residues processed: 241 average time/residue: 0.5114 time to fit residues: 143.2122 Evaluate side-chains 236 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 133 optimal weight: 0.6980 chunk 129 optimal weight: 20.0000 chunk 234 optimal weight: 7.9990 chunk 256 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 284 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 474 GLN B 954 GLN B 957 GLN C 334 ASN C 474 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.141449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.115011 restraints weight = 26376.309| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.85 r_work: 0.2961 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24804 Z= 0.132 Angle : 0.596 11.768 33774 Z= 0.309 Chirality : 0.046 0.382 3912 Planarity : 0.004 0.053 4302 Dihedral : 6.274 86.480 3295 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.13 % Allowed : 12.07 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.15), residues: 2970 helix: 1.10 (0.21), residues: 648 sheet: 1.41 (0.21), residues: 597 loop : -1.78 (0.13), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 815 TYR 0.018 0.001 TYR B 660 PHE 0.016 0.001 PHE C 133 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (24738) covalent geometry : angle 0.56535 / 0.30 (33609) SS BOND : bond 0.00425 / 0.26 ( 33) SS BOND : angle 1.18858 / 0.70 ( 66) hydrogen bonds : bond 0.06406 / 4.22 ( 962) hydrogen bonds : angle 5.36710 / 3.77 ( 2709) link_NAG-ASN : bond 0.00448 / 0.28 ( 33) link_NAG-ASN : angle 3.39944 / 2.29 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 211 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7609 (pt0) REVERT: A 334 ASN cc_start: 0.7503 (OUTLIER) cc_final: 0.7260 (m-40) REVERT: A 357 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8158 (ttm170) REVERT: A 654 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6788 (tm-30) REVERT: A 779 GLN cc_start: 0.8594 (tp40) cc_final: 0.8307 (tp-100) REVERT: A 957 GLN cc_start: 0.8733 (tt0) cc_final: 0.8494 (tt0) REVERT: A 1114 ILE cc_start: 0.7603 (mm) cc_final: 0.7336 (mp) REVERT: B 100 ILE cc_start: 0.7174 (mm) cc_final: 0.6893 (mp) REVERT: B 309 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7678 (mm-30) REVERT: C 169 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7104 (tp30) REVERT: C 190 ARG cc_start: 0.8121 (mtt-85) cc_final: 0.7473 (mtt-85) REVERT: C 207 HIS cc_start: 0.6370 (m-70) cc_final: 0.5426 (m90) REVERT: C 389 ASP cc_start: 0.8532 (m-30) cc_final: 0.8291 (m-30) REVERT: C 574 ASP cc_start: 0.8155 (m-30) cc_final: 0.7924 (p0) REVERT: C 820 ASP cc_start: 0.7748 (m-30) cc_final: 0.7446 (m-30) REVERT: C 921 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7508 (mppt) REVERT: C 1002 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: C 1017 GLU cc_start: 0.8489 (tt0) cc_final: 0.8232 (tt0) outliers start: 56 outliers final: 31 residues processed: 254 average time/residue: 0.5378 time to fit residues: 158.4520 Evaluate side-chains 233 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 142 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 254 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 237 optimal weight: 0.0170 chunk 172 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 overall best weight: 3.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 334 ASN B 474 GLN B 954 GLN B 957 GLN C 334 ASN C 474 GLN C 779 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.141521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.115442 restraints weight = 26306.231| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.80 r_work: 0.2912 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24804 Z= 0.174 Angle : 0.659 12.114 33774 Z= 0.342 Chirality : 0.049 0.515 3912 Planarity : 0.005 0.054 4302 Dihedral : 6.420 87.447 3293 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.47 % Allowed : 12.98 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 2970 helix: 0.93 (0.21), residues: 660 sheet: 1.35 (0.21), residues: 636 loop : -1.82 (0.13), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 102 TYR 0.023 0.002 TYR C 380 PHE 0.019 0.002 PHE B 86 TRP 0.007 0.001 TRP B 64 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (24738) covalent geometry : angle 0.62749 / 0.33 (33609) SS BOND : bond 0.00600 / 0.35 ( 33) SS BOND : angle 1.47251 / 0.87 ( 66) hydrogen bonds : bond 0.07379 / 4.86 ( 962) hydrogen bonds : angle 5.48288 / 3.85 ( 2709) link_NAG-ASN : bond 0.00444 / 0.29 ( 33) link_NAG-ASN : angle 3.61883 / 2.39 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 202 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6791 (mt) REVERT: A 334 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.7289 (m-40) REVERT: A 357 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8395 (ttm170) REVERT: A 646 ARG cc_start: 0.7864 (mtp180) cc_final: 0.7628 (mtm110) REVERT: A 654 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.6931 (tm-30) REVERT: A 779 GLN cc_start: 0.8663 (tp40) cc_final: 0.8400 (tp-100) REVERT: A 957 GLN cc_start: 0.8773 (tt0) cc_final: 0.8539 (tt0) REVERT: A 1114 ILE cc_start: 0.7600 (mm) cc_final: 0.7331 (mp) REVERT: B 100 ILE cc_start: 0.7113 (OUTLIER) cc_final: 0.6842 (mp) REVERT: B 309 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7738 (mm-30) REVERT: B 703 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8310 (t0) REVERT: C 169 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7211 (tp30) REVERT: C 190 ARG cc_start: 0.8157 (mtt-85) cc_final: 0.7488 (mtt-85) REVERT: C 207 HIS cc_start: 0.6351 (m-70) cc_final: 0.5517 (m90) REVERT: C 332 ILE cc_start: 0.6840 (OUTLIER) cc_final: 0.6608 (mt) REVERT: C 574 ASP cc_start: 0.8175 (m-30) cc_final: 0.7899 (p0) REVERT: C 748 GLU cc_start: 0.8020 (mp0) cc_final: 0.7793 (mp0) REVERT: C 820 ASP cc_start: 0.7844 (m-30) cc_final: 0.7517 (m-30) REVERT: C 921 LYS cc_start: 0.8282 (mtmm) cc_final: 0.7534 (mppt) REVERT: C 1002 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8181 (tm-30) REVERT: C 1017 GLU cc_start: 0.8605 (tt0) cc_final: 0.8357 (tt0) outliers start: 65 outliers final: 37 residues processed: 250 average time/residue: 0.5342 time to fit residues: 154.7240 Evaluate side-chains 239 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 126 optimal weight: 6.9990 chunk 292 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 chunk 279 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 253 optimal weight: 0.4980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 474 GLN B 954 GLN B 957 GLN C 99 ASN C 334 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.141657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.116218 restraints weight = 26119.432| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.73 r_work: 0.2945 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24804 Z= 0.170 Angle : 0.655 12.070 33774 Z= 0.339 Chirality : 0.049 0.497 3912 Planarity : 0.005 0.054 4302 Dihedral : 6.423 86.315 3293 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.62 % Allowed : 13.21 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.15), residues: 2970 helix: 0.97 (0.21), residues: 657 sheet: 1.37 (0.21), residues: 636 loop : -1.83 (0.13), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 765 TYR 0.022 0.002 TYR C 380 PHE 0.019 0.002 PHE A 86 TRP 0.008 0.001 TRP B 64 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (24738) covalent geometry : angle 0.62252 / 0.33 (33609) SS BOND : bond 0.00571 / 0.34 ( 33) SS BOND : angle 1.43634 / 0.85 ( 66) hydrogen bonds : bond 0.07265 / 4.78 ( 962) hydrogen bonds : angle 5.46467 / 3.84 ( 2709) link_NAG-ASN : bond 0.00525 / 0.29 ( 33) link_NAG-ASN : angle 3.64890 / 2.46 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 200 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7097 (OUTLIER) cc_final: 0.6750 (mt) REVERT: A 334 ASN cc_start: 0.7537 (OUTLIER) cc_final: 0.7291 (m-40) REVERT: A 357 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8379 (ttm170) REVERT: A 654 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6938 (tm-30) REVERT: A 779 GLN cc_start: 0.8677 (tp40) cc_final: 0.8411 (tp-100) REVERT: A 957 GLN cc_start: 0.8778 (tt0) cc_final: 0.8544 (tt0) REVERT: A 1114 ILE cc_start: 0.7589 (mm) cc_final: 0.7314 (mp) REVERT: B 100 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6923 (mp) REVERT: B 223 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8823 (mp) REVERT: B 309 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7783 (mm-30) REVERT: B 703 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8314 (t0) REVERT: B 814 LYS cc_start: 0.8197 (mptt) cc_final: 0.7855 (mptt) REVERT: C 169 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7214 (tp30) REVERT: C 190 ARG cc_start: 0.8168 (mtt-85) cc_final: 0.7512 (mtt-85) REVERT: C 207 HIS cc_start: 0.6389 (m-70) cc_final: 0.5580 (m90) REVERT: C 574 ASP cc_start: 0.8155 (m-30) cc_final: 0.7906 (p0) REVERT: C 748 GLU cc_start: 0.8033 (mp0) cc_final: 0.7751 (mp0) REVERT: C 820 ASP cc_start: 0.7809 (m-30) cc_final: 0.7517 (m-30) REVERT: C 921 LYS cc_start: 0.8279 (mtmm) cc_final: 0.7636 (mppt) REVERT: C 1002 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8202 (tm-30) REVERT: C 1017 GLU cc_start: 0.8593 (tt0) cc_final: 0.8347 (tt0) outliers start: 69 outliers final: 39 residues processed: 253 average time/residue: 0.5869 time to fit residues: 171.7653 Evaluate side-chains 245 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 196 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 126 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 289 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 234 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 334 ASN B 474 GLN B 779 GLN B 954 GLN C 334 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.140143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.113740 restraints weight = 26219.829| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.80 r_work: 0.2954 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24804 Z= 0.167 Angle : 0.652 12.486 33774 Z= 0.337 Chirality : 0.048 0.381 3912 Planarity : 0.005 0.054 4302 Dihedral : 6.384 85.633 3291 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.47 % Allowed : 13.52 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.15), residues: 2970 helix: 0.99 (0.21), residues: 657 sheet: 1.37 (0.21), residues: 636 loop : -1.81 (0.13), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 765 TYR 0.022 0.002 TYR C 380 PHE 0.018 0.002 PHE B 86 TRP 0.007 0.001 TRP B 64 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (24738) covalent geometry : angle 0.61809 / 0.33 (33609) SS BOND : bond 0.00564 / 0.33 ( 33) SS BOND : angle 1.42203 / 0.84 ( 66) hydrogen bonds : bond 0.07232 / 4.76 ( 962) hydrogen bonds : angle 5.45107 / 3.83 ( 2709) link_NAG-ASN : bond 0.00547 / 0.34 ( 33) link_NAG-ASN : angle 3.73550 / 2.52 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6744 (mt) REVERT: A 357 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8391 (ttm170) REVERT: A 654 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.6927 (tm-30) REVERT: A 779 GLN cc_start: 0.8658 (tp40) cc_final: 0.8393 (tp-100) REVERT: A 957 GLN cc_start: 0.8762 (tt0) cc_final: 0.8524 (tt0) REVERT: A 1114 ILE cc_start: 0.7583 (mm) cc_final: 0.7311 (mp) REVERT: B 100 ILE cc_start: 0.7212 (mm) cc_final: 0.6899 (mp) REVERT: B 223 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8812 (mp) REVERT: B 309 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7757 (mm-30) REVERT: B 703 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8311 (t0) REVERT: B 814 LYS cc_start: 0.8190 (mptt) cc_final: 0.7846 (mptt) REVERT: C 100 ILE cc_start: 0.7176 (mm) cc_final: 0.6842 (mp) REVERT: C 169 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7198 (tp30) REVERT: C 207 HIS cc_start: 0.6401 (m-70) cc_final: 0.5453 (m90) REVERT: C 748 GLU cc_start: 0.8007 (mp0) cc_final: 0.7719 (mp0) REVERT: C 820 ASP cc_start: 0.7819 (m-30) cc_final: 0.7526 (m-30) REVERT: C 921 LYS cc_start: 0.8272 (mtmm) cc_final: 0.7607 (mppt) REVERT: C 1002 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: C 1017 GLU cc_start: 0.8583 (tt0) cc_final: 0.8337 (tt0) outliers start: 65 outliers final: 40 residues processed: 244 average time/residue: 0.5958 time to fit residues: 168.0747 Evaluate side-chains 242 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 79 optimal weight: 7.9990 chunk 285 optimal weight: 4.9990 chunk 141 optimal weight: 0.0170 chunk 187 optimal weight: 9.9990 chunk 245 optimal weight: 6.9990 chunk 216 optimal weight: 0.0980 chunk 103 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 100 optimal weight: 0.0870 chunk 111 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 overall best weight: 2.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 474 GLN B 954 GLN C 334 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.142570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.116794 restraints weight = 26204.657| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.74 r_work: 0.2949 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24804 Z= 0.147 Angle : 0.621 12.285 33774 Z= 0.321 Chirality : 0.047 0.333 3912 Planarity : 0.005 0.054 4302 Dihedral : 6.251 85.846 3291 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.20 % Allowed : 13.82 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.15), residues: 2970 helix: 1.12 (0.21), residues: 648 sheet: 1.54 (0.21), residues: 606 loop : -1.75 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 765 TYR 0.019 0.002 TYR C 380 PHE 0.017 0.002 PHE A 592 TRP 0.008 0.001 TRP B 64 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (24738) covalent geometry : angle 0.58908 / 0.31 (33609) SS BOND : bond 0.00486 / 0.29 ( 33) SS BOND : angle 1.29872 / 0.76 ( 66) hydrogen bonds : bond 0.06758 / 4.45 ( 962) hydrogen bonds : angle 5.37301 / 3.77 ( 2709) link_NAG-ASN : bond 0.00503 / 0.29 ( 33) link_NAG-ASN : angle 3.52407 / 2.37 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 200 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7130 (OUTLIER) cc_final: 0.6772 (mt) REVERT: A 357 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8175 (ttm170) REVERT: A 654 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: A 779 GLN cc_start: 0.8601 (tp40) cc_final: 0.8337 (tp-100) REVERT: A 957 GLN cc_start: 0.8747 (tt0) cc_final: 0.8507 (tt0) REVERT: A 1114 ILE cc_start: 0.7564 (mm) cc_final: 0.7283 (mp) REVERT: B 100 ILE cc_start: 0.7182 (mm) cc_final: 0.6858 (mp) REVERT: B 223 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8802 (mp) REVERT: B 309 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7732 (mm-30) REVERT: B 703 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8307 (t0) REVERT: B 921 LYS cc_start: 0.8022 (mttp) cc_final: 0.7436 (mppt) REVERT: C 100 ILE cc_start: 0.7147 (mm) cc_final: 0.6812 (mp) REVERT: C 169 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7181 (tp30) REVERT: C 748 GLU cc_start: 0.8007 (mp0) cc_final: 0.7733 (mp0) REVERT: C 820 ASP cc_start: 0.7791 (m-30) cc_final: 0.7488 (m-30) REVERT: C 921 LYS cc_start: 0.8256 (mtmm) cc_final: 0.7595 (mppt) REVERT: C 1002 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8147 (tm-30) REVERT: C 1017 GLU cc_start: 0.8518 (tt0) cc_final: 0.8267 (tt0) outliers start: 58 outliers final: 43 residues processed: 246 average time/residue: 0.5942 time to fit residues: 169.3693 Evaluate side-chains 247 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.1254 > 50: distance: 27 - 162: 18.881 distance: 79 - 83: 9.425 distance: 83 - 84: 8.920 distance: 84 - 85: 18.179 distance: 84 - 87: 12.342 distance: 85 - 86: 11.204 distance: 85 - 95: 24.777 distance: 87 - 88: 7.534 distance: 88 - 89: 10.355 distance: 88 - 90: 9.526 distance: 89 - 91: 12.966 distance: 90 - 92: 9.174 distance: 91 - 93: 5.681 distance: 92 - 93: 4.486 distance: 93 - 94: 7.008 distance: 95 - 96: 25.137 distance: 96 - 97: 40.651 distance: 96 - 99: 20.510 distance: 97 - 104: 46.347 distance: 99 - 100: 21.517 distance: 100 - 101: 23.345 distance: 101 - 102: 25.878 distance: 102 - 103: 33.050 distance: 104 - 105: 22.470 distance: 105 - 106: 38.459 distance: 105 - 108: 19.679 distance: 106 - 107: 35.476 distance: 106 - 112: 7.541 distance: 108 - 109: 28.499 distance: 109 - 110: 42.980 distance: 109 - 111: 56.283 distance: 112 - 113: 20.803 distance: 112 - 118: 15.256 distance: 113 - 114: 27.261 distance: 113 - 116: 43.078 distance: 114 - 115: 32.013 distance: 114 - 119: 29.351 distance: 116 - 117: 49.230 distance: 117 - 118: 35.914 distance: 119 - 120: 18.456 distance: 120 - 121: 14.484 distance: 120 - 123: 11.801 distance: 121 - 122: 9.765 distance: 121 - 127: 14.943 distance: 123 - 124: 21.173 distance: 124 - 125: 9.195 distance: 124 - 126: 12.594 distance: 127 - 128: 19.214 distance: 128 - 129: 35.754 distance: 128 - 131: 21.430 distance: 129 - 130: 23.706 distance: 129 - 135: 41.174 distance: 131 - 132: 15.301 distance: 132 - 133: 20.117 distance: 132 - 134: 23.336 distance: 135 - 136: 7.292 distance: 136 - 137: 20.182 distance: 136 - 139: 36.784 distance: 137 - 138: 33.043 distance: 137 - 146: 23.899 distance: 139 - 140: 14.293 distance: 140 - 141: 21.186 distance: 140 - 142: 34.128 distance: 141 - 143: 12.433 distance: 142 - 144: 7.569 distance: 143 - 145: 15.312 distance: 144 - 145: 14.730 distance: 146 - 147: 6.645 distance: 147 - 148: 19.538 distance: 147 - 150: 17.915 distance: 148 - 149: 32.849 distance: 148 - 153: 33.025 distance: 150 - 151: 18.624 distance: 150 - 152: 15.903 distance: 153 - 154: 29.539 distance: 154 - 155: 20.711 distance: 155 - 156: 27.274 distance: 155 - 157: 30.971 distance: 157 - 158: 15.439 distance: 157 - 206: 32.033 distance: 158 - 159: 40.856 distance: 158 - 161: 33.043 distance: 159 - 160: 13.794 distance: 159 - 163: 18.559 distance: 160 - 203: 17.924 distance: 161 - 162: 12.946