Starting phenix.real_space_refine on Sat Jul 4 23:09:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lyl_23594/07_2026/7lyl_23594.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lyl_23594/07_2026/7lyl_23594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lyl_23594/07_2026/7lyl_23594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lyl_23594/07_2026/7lyl_23594.map" model { file = "/net/cci-nas-00/data/ceres_data/7lyl_23594/07_2026/7lyl_23594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lyl_23594/07_2026/7lyl_23594.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lyl_23594/07_2026/7lyl_23594.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lyl_23594/07_2026/7lyl_23594.cif" } resolution = 3.72 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= 0.050 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 103 5.16 5 C 15206 2.51 5 N 3928 2.21 5 O 4589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s 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: 23826 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7812 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 8 Chain: "B" Number of atoms: 7812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7812 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 8 Chain: "C" Number of atoms: 7810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7810 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 4.52, per 1000 atoms: 0.19 Number of scatterers: 23826 At special positions: 0 Unit cell: (129.349, 134.694, 175.316, 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 103 16.00 O 4589 8.00 N 3928 7.00 C 15206 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.06 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 801 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 784.0 milliseconds 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5616 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 49 sheets defined 27.5% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.659A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.908A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.249A 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 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.906A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.002A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.540A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.566A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (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: 3.771A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.364A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.788A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.796A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.658A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.849A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.017A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.709A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.553A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.053A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.854A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.258A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.954A 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 342 removed outlier: 3.656A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 337 through 342' Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.675A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.947A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.930A 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 616 through 620 removed outlier: 3.665A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.003A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.314A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.605A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.508A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.158A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.512A 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: 3.893A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.831A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.585A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.897A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.746A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.133A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.320A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.854A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.783A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.651A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.652A pdb=" N VAL A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LYS B 790 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.729A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.180A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.200A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.755A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.542A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.815A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.574A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.752A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.188A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.257A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.257A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.966A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.763A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.988A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.859A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.384A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.295A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.783A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE3, first strand: chain 'C' and resid 141 through 142 removed outlier: 6.370A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.351A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.865A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.990A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.653A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.582A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.999A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.643A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1054 hydrogen bonds defined for protein. 2847 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: 5.62 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6874 1.34 - 1.46: 4250 1.46 - 1.58: 13097 1.58 - 1.70: 0 1.70 - 1.82: 127 Bond restraints: 24348 Sorted by residual: bond pdb=" CA PRO A 792 " pdb=" C PRO A 792 " ideal model delta sigma weight residual 1.514 1.539 -0.024 5.50e-03 3.31e+04 1.98e+01 bond pdb=" C5 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C5 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C5 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 24343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 22687 1.68 - 3.36: 8791 3.36 - 5.03: 1481 5.03 - 6.71: 147 6.71 - 8.39: 10 Bond angle restraints: 33116 Sorted by residual: angle pdb=" CA GLY A 416 " pdb=" C GLY A 416 " pdb=" N ASN A 417 " ideal model delta sigma weight residual 114.23 119.87 -5.64 8.80e-01 1.29e+00 4.11e+01 angle pdb=" C LYS C 790 " pdb=" N THR C 791 " pdb=" CA THR C 791 " ideal model delta sigma weight residual 120.39 128.08 -7.69 1.39e+00 5.18e-01 3.06e+01 angle pdb=" N THR C 315 " pdb=" CA THR C 315 " pdb=" C THR C 315 " ideal model delta sigma weight residual 111.28 117.11 -5.83 1.09e+00 8.42e-01 2.86e+01 angle pdb=" CA PHE A 106 " pdb=" CB PHE A 106 " pdb=" CG PHE A 106 " ideal model delta sigma weight residual 113.80 118.92 -5.12 1.00e+00 1.00e+00 2.62e+01 angle pdb=" OE1 GLN B1106 " pdb=" CD GLN B1106 " pdb=" NE2 GLN B1106 " ideal model delta sigma weight residual 122.60 117.63 4.97 1.00e+00 1.00e+00 2.47e+01 ... (remaining 33111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 13221 17.66 - 35.33: 841 35.33 - 52.99: 119 52.99 - 70.66: 52 70.66 - 88.32: 30 Dihedral angle restraints: 14263 sinusoidal: 5539 harmonic: 8724 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -173.03 87.03 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -150.16 64.16 1 1.00e+01 1.00e-02 5.42e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -143.15 57.15 1 1.00e+01 1.00e-02 4.39e+01 ... (remaining 14260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2330 0.083 - 0.166: 1306 0.166 - 0.250: 193 0.250 - 0.333: 30 0.333 - 0.416: 4 Chirality restraints: 3863 Sorted by residual: chirality pdb=" CA ASN C 487 " pdb=" N ASN C 487 " pdb=" C ASN C 487 " pdb=" CB ASN C 487 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CG LEU B 229 " pdb=" CB LEU B 229 " pdb=" CD1 LEU B 229 " pdb=" CD2 LEU B 229 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA ASP B1041 " pdb=" N ASP B1041 " pdb=" C ASP B1041 " pdb=" CB ASP B1041 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 3860 not shown) Planarity restraints: 4271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 904 " 0.239 2.00e-02 2.50e+03 1.30e-01 3.40e+02 pdb=" CG TYR A 904 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR A 904 " -0.102 2.00e-02 2.50e+03 pdb=" CD2 TYR A 904 " -0.122 2.00e-02 2.50e+03 pdb=" CE1 TYR A 904 " -0.083 2.00e-02 2.50e+03 pdb=" CE2 TYR A 904 " -0.060 2.00e-02 2.50e+03 pdb=" CZ TYR A 904 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 904 " 0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " -0.142 2.00e-02 2.50e+03 1.51e-01 2.86e+02 pdb=" CG ASN B 331 " 0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " 0.231 2.00e-02 2.50e+03 pdb=" C1 NAG B1303 " -0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " 0.143 2.00e-02 2.50e+03 1.50e-01 2.80e+02 pdb=" CG ASN B 709 " -0.085 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " -0.226 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " 0.182 2.00e-02 2.50e+03 ... (remaining 4268 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 12916 3.01 - 3.48: 23493 3.48 - 3.96: 38983 3.96 - 4.43: 43190 4.43 - 4.90: 72424 Nonbonded interactions: 191006 Sorted by model distance: nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.538 3.040 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.540 3.040 nonbonded pdb=" OG SER B 813 " pdb=" OE1 GLU B 868 " model vdw 2.544 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.550 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.551 3.040 ... (remaining 191001 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 479 or (resid 480 and (name N or name CA or nam \ e C or name O or name CB )) or resid 481 through 487 or (resid 488 and (name N o \ r name CA or name C or name O or name CB )) or resid 489 through 1308)) selection = (chain 'B' and (resid 27 through 479 or (resid 480 and (name N or name CA or nam \ e C or name O or name CB )) or resid 481 through 487 or (resid 488 and (name N o \ r name CA or name C or name O or name CB )) or resid 489 through 1308)) selection = (chain 'C' and resid 27 through 1308) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.990 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.013 0.078 24414 Z= 0.734 Angle : 1.717 8.391 33276 Z= 1.139 Chirality : 0.093 0.416 3863 Planarity : 0.013 0.147 4243 Dihedral : 13.107 88.323 8533 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 0.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.70 % Favored : 94.20 % Rotamer: Outliers : 0.69 % Allowed : 2.37 % Favored : 96.94 % Cbeta Deviations : 0.07 % 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: -1.00 (0.14), residues: 2949 helix: -0.72 (0.17), residues: 688 sheet: 0.13 (0.20), residues: 560 loop : -0.88 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 457 TYR 0.239 0.019 TYR A 904 PHE 0.074 0.011 PHE B 927 TRP 0.108 0.024 TRP A 64 HIS 0.016 0.003 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01287 / 0.73 (24348) covalent geometry : angle 1.70390 / 1.14 (33116) SS BOND : bond 0.01190 / 0.69 ( 38) SS BOND : angle 1.74974 / 1.18 ( 76) hydrogen bonds : bond 0.15595 / 10.22 ( 1046) hydrogen bonds : angle 8.47028 / 5.84 ( 2847) link_NAG-ASN : bond 0.01332 / 0.86 ( 28) link_NAG-ASN : angle 4.51823 / 2.98 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 232 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7901 (p90) cc_final: 0.7374 (p90) REVERT: A 902 MET cc_start: 0.9358 (mmm) cc_final: 0.8996 (tpt) REVERT: A 1050 MET cc_start: 0.8765 (ttp) cc_final: 0.8531 (ttp) REVERT: B 111 ASP cc_start: 0.8003 (p0) cc_final: 0.7791 (p0) REVERT: B 290 ASP cc_start: 0.7668 (t0) cc_final: 0.6823 (t0) REVERT: B 347 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7434 (t80) REVERT: B 752 LEU cc_start: 0.9363 (mt) cc_final: 0.8740 (mm) REVERT: C 297 SER cc_start: 0.9155 (m) cc_final: 0.8513 (t) REVERT: C 400 PHE cc_start: 0.7614 (p90) cc_final: 0.6866 (p90) REVERT: C 408 ARG cc_start: 0.9022 (ptt90) cc_final: 0.8326 (mmp80) REVERT: C 596 SER cc_start: 0.9172 (t) cc_final: 0.8851 (m) REVERT: C 1029 MET cc_start: 0.9465 (tpp) cc_final: 0.9116 (tpp) REVERT: C 1047 TYR cc_start: 0.8937 (m-80) cc_final: 0.8695 (m-80) outliers start: 18 outliers final: 5 residues processed: 249 average time/residue: 0.1556 time to fit residues: 60.6368 Evaluate side-chains 118 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 HIS A 282 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 655 HIS C 317 ASN C 675 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.093101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.066288 restraints weight = 72543.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.068641 restraints weight = 34969.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.069589 restraints weight = 19162.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.069705 restraints weight = 15381.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.069856 restraints weight = 14891.624| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 24414 Z= 0.176 Angle : 0.694 12.041 33276 Z= 0.360 Chirality : 0.047 0.250 3863 Planarity : 0.004 0.043 4243 Dihedral : 6.459 58.016 3216 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.48 % Favored : 97.49 % Rotamer: Outliers : 1.18 % Allowed : 5.50 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 2949 helix: 1.09 (0.20), residues: 686 sheet: -0.05 (0.19), residues: 676 loop : -0.57 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 237 TYR 0.027 0.002 TYR B 495 PHE 0.017 0.002 PHE A 220 TRP 0.031 0.002 TRP A 353 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (24348) covalent geometry : angle 0.67133 / 0.36 (33116) SS BOND : bond 0.00576 / 0.40 ( 38) SS BOND : angle 1.44812 / 0.93 ( 76) hydrogen bonds : bond 0.05062 / 3.33 ( 1046) hydrogen bonds : angle 6.37561 / 4.45 ( 2847) link_NAG-ASN : bond 0.00435 / 0.30 ( 28) link_NAG-ASN : angle 3.37096 / 2.11 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.7652 (OUTLIER) cc_final: 0.7020 (t) REVERT: A 129 LYS cc_start: 0.8441 (mmtm) cc_final: 0.8009 (pttt) REVERT: A 238 PHE cc_start: 0.7335 (p90) cc_final: 0.6968 (p90) REVERT: A 269 TYR cc_start: 0.7933 (m-80) cc_final: 0.7028 (m-80) REVERT: A 353 TRP cc_start: 0.8758 (p-90) cc_final: 0.8014 (p90) REVERT: A 979 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8544 (m-30) REVERT: B 347 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7754 (t80) REVERT: C 314 GLN cc_start: 0.8405 (tp40) cc_final: 0.8082 (tp40) REVERT: C 384 PRO cc_start: 0.8848 (Cg_endo) cc_final: 0.8605 (Cg_exo) REVERT: C 400 PHE cc_start: 0.7593 (p90) cc_final: 0.6934 (p90) REVERT: C 501 TYR cc_start: 0.2336 (OUTLIER) cc_final: 0.2135 (m-80) outliers start: 31 outliers final: 12 residues processed: 158 average time/residue: 0.1472 time to fit residues: 37.8440 Evaluate side-chains 114 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 174 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 295 optimal weight: 0.8980 chunk 212 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 167 optimal weight: 0.2980 chunk 294 optimal weight: 0.9990 chunk 232 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 291 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.092832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.066008 restraints weight = 72847.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.068244 restraints weight = 35222.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.069152 restraints weight = 19317.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.069358 restraints weight = 16405.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.069513 restraints weight = 14992.665| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24414 Z= 0.154 Angle : 0.611 13.952 33276 Z= 0.315 Chirality : 0.045 0.204 3863 Planarity : 0.004 0.042 4243 Dihedral : 5.702 55.106 3214 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.38 % Allowed : 6.92 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.12 (0.15), residues: 2949 helix: 1.50 (0.20), residues: 676 sheet: -0.08 (0.19), residues: 673 loop : -0.42 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 346 TYR 0.029 0.001 TYR B 904 PHE 0.016 0.001 PHE C 592 TRP 0.016 0.001 TRP C 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (24348) covalent geometry : angle 0.59335 / 0.31 (33116) SS BOND : bond 0.00500 / 0.36 ( 38) SS BOND : angle 1.29554 / 0.80 ( 76) hydrogen bonds : bond 0.04336 / 2.85 ( 1046) hydrogen bonds : angle 5.87765 / 4.11 ( 2847) link_NAG-ASN : bond 0.00364 / 0.27 ( 28) link_NAG-ASN : angle 2.72212 / 1.72 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.8010 (OUTLIER) cc_final: 0.7522 (t) REVERT: A 238 PHE cc_start: 0.7297 (p90) cc_final: 0.6917 (p90) REVERT: A 269 TYR cc_start: 0.8013 (m-80) cc_final: 0.7188 (m-80) REVERT: A 347 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6984 (m-80) REVERT: A 979 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8373 (m-30) REVERT: B 347 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7811 (t80) REVERT: B 780 GLU cc_start: 0.8686 (tp30) cc_final: 0.8470 (tp30) REVERT: C 400 PHE cc_start: 0.7703 (p90) cc_final: 0.6766 (p90) outliers start: 36 outliers final: 19 residues processed: 146 average time/residue: 0.1296 time to fit residues: 32.4009 Evaluate side-chains 120 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 158 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 137 optimal weight: 8.9990 chunk 231 optimal weight: 20.0000 chunk 172 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 259 optimal weight: 2.9990 chunk 196 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 220 optimal weight: 0.0570 chunk 25 optimal weight: 2.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 388 ASN A1088 HIS C 314 GLN C 317 ASN C 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.093349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.065923 restraints weight = 72283.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.068949 restraints weight = 35237.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.069427 restraints weight = 18781.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.069826 restraints weight = 15493.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.069913 restraints weight = 14049.069| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24414 Z= 0.110 Angle : 0.557 14.470 33276 Z= 0.286 Chirality : 0.044 0.208 3863 Planarity : 0.003 0.040 4243 Dihedral : 5.270 53.870 3214 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.53 % Allowed : 7.76 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.31 (0.15), residues: 2949 helix: 1.74 (0.21), residues: 686 sheet: -0.08 (0.19), residues: 685 loop : -0.29 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 995 TYR 0.023 0.001 TYR B 904 PHE 0.024 0.001 PHE A 92 TRP 0.017 0.001 TRP C 436 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (24348) covalent geometry : angle 0.54060 / 0.28 (33116) SS BOND : bond 0.00279 / 0.20 ( 38) SS BOND : angle 1.31854 / 0.84 ( 76) hydrogen bonds : bond 0.03821 / 2.52 ( 1046) hydrogen bonds : angle 5.58000 / 3.91 ( 2847) link_NAG-ASN : bond 0.00359 / 0.27 ( 28) link_NAG-ASN : angle 2.49717 / 1.58 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 PHE cc_start: 0.7532 (m-80) cc_final: 0.7305 (m-80) REVERT: A 238 PHE cc_start: 0.7203 (p90) cc_final: 0.6820 (p90) REVERT: A 269 TYR cc_start: 0.8000 (m-80) cc_final: 0.7248 (m-80) REVERT: A 347 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6796 (m-80) REVERT: A 353 TRP cc_start: 0.8682 (p-90) cc_final: 0.7930 (p90) REVERT: A 979 ASP cc_start: 0.8644 (m-30) cc_final: 0.8211 (m-30) REVERT: A 1041 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7762 (t0) REVERT: B 347 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7830 (t80) REVERT: C 400 PHE cc_start: 0.7794 (p90) cc_final: 0.7146 (p90) REVERT: C 468 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7822 (mm) REVERT: C 1029 MET cc_start: 0.9059 (tpp) cc_final: 0.8743 (ttm) outliers start: 40 outliers final: 23 residues processed: 151 average time/residue: 0.1223 time to fit residues: 31.8389 Evaluate side-chains 126 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 54 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 70 optimal weight: 0.2980 chunk 152 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 207 HIS B 607 GLN C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.091576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.064563 restraints weight = 72435.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.066774 restraints weight = 35766.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.067736 restraints weight = 19427.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.067816 restraints weight = 16767.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.067911 restraints weight = 15448.940| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24414 Z= 0.218 Angle : 0.611 12.862 33276 Z= 0.312 Chirality : 0.045 0.206 3863 Planarity : 0.004 0.044 4243 Dihedral : 5.229 55.246 3212 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.06 % Allowed : 8.25 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.17 (0.15), residues: 2949 helix: 1.62 (0.21), residues: 686 sheet: -0.11 (0.20), residues: 650 loop : -0.40 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 995 TYR 0.024 0.001 TYR A 904 PHE 0.018 0.001 PHE C 592 TRP 0.015 0.001 TRP C 436 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 (24348) covalent geometry : angle 0.59389 / 0.31 (33116) SS BOND : bond 0.00522 / 0.34 ( 38) SS BOND : angle 1.64958 / 1.06 ( 76) hydrogen bonds : bond 0.04083 / 2.68 ( 1046) hydrogen bonds : angle 5.69205 / 3.98 ( 2847) link_NAG-ASN : bond 0.00369 / 0.26 ( 28) link_NAG-ASN : angle 2.50345 / 1.60 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 103 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7401 (p90) cc_final: 0.7006 (p90) REVERT: A 269 TYR cc_start: 0.8132 (m-80) cc_final: 0.7431 (m-80) REVERT: A 979 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8009 (t70) REVERT: A 1041 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7886 (t0) REVERT: B 347 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7897 (t80) REVERT: B 403 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7911 (ptm160) REVERT: B 912 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8248 (p) REVERT: B 979 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8363 (m-30) REVERT: C 387 LEU cc_start: 0.9087 (mt) cc_final: 0.8627 (mt) REVERT: C 400 PHE cc_start: 0.7752 (p90) cc_final: 0.6849 (p90) outliers start: 54 outliers final: 37 residues processed: 148 average time/residue: 0.1421 time to fit residues: 35.7653 Evaluate side-chains 136 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 93 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 284 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 219 optimal weight: 8.9990 chunk 286 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 195 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 764 ASN C 314 GLN C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.093590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.066373 restraints weight = 72444.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.069203 restraints weight = 35654.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.069740 restraints weight = 19897.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.070241 restraints weight = 16031.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.070327 restraints weight = 14005.272| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24414 Z= 0.103 Angle : 0.538 11.641 33276 Z= 0.274 Chirality : 0.044 0.221 3863 Planarity : 0.003 0.043 4243 Dihedral : 4.818 54.351 3210 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.57 % Allowed : 9.17 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.38 (0.15), residues: 2949 helix: 1.81 (0.21), residues: 691 sheet: 0.05 (0.20), residues: 649 loop : -0.29 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1107 TYR 0.019 0.001 TYR C 369 PHE 0.023 0.001 PHE A 92 TRP 0.020 0.001 TRP C 436 HIS 0.002 0.000 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (24348) covalent geometry : angle 0.52215 / 0.27 (33116) SS BOND : bond 0.00426 / 0.31 ( 38) SS BOND : angle 1.41463 / 0.92 ( 76) hydrogen bonds : bond 0.03577 / 2.36 ( 1046) hydrogen bonds : angle 5.40589 / 3.80 ( 2847) link_NAG-ASN : bond 0.00382 / 0.29 ( 28) link_NAG-ASN : angle 2.32169 / 1.47 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7256 (p90) cc_final: 0.6900 (p90) REVERT: A 269 TYR cc_start: 0.8081 (m-80) cc_final: 0.7476 (m-80) REVERT: A 353 TRP cc_start: 0.8703 (p-90) cc_final: 0.7897 (p90) REVERT: A 979 ASP cc_start: 0.8691 (m-30) cc_final: 0.7824 (t0) REVERT: B 347 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.7861 (t80) REVERT: B 776 LYS cc_start: 0.9050 (tppt) cc_final: 0.8796 (tptp) REVERT: B 979 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8359 (m-30) REVERT: C 338 PHE cc_start: 0.8155 (m-10) cc_final: 0.7869 (m-10) REVERT: C 342 PHE cc_start: 0.6388 (OUTLIER) cc_final: 0.6004 (m-80) REVERT: C 400 PHE cc_start: 0.7596 (p90) cc_final: 0.6975 (p90) REVERT: C 1029 MET cc_start: 0.9136 (tpp) cc_final: 0.8703 (ttm) outliers start: 41 outliers final: 27 residues processed: 143 average time/residue: 0.1334 time to fit residues: 32.1265 Evaluate side-chains 123 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 261 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 262 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 276 optimal weight: 0.7980 chunk 212 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 55 optimal weight: 0.0870 chunk 185 optimal weight: 3.9990 chunk 243 optimal weight: 0.6980 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN C 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.093628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.066332 restraints weight = 72334.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.069045 restraints weight = 36306.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.069709 restraints weight = 20569.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.070221 restraints weight = 16377.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.070241 restraints weight = 14128.871| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24414 Z= 0.106 Angle : 0.539 11.919 33276 Z= 0.273 Chirality : 0.045 0.572 3863 Planarity : 0.003 0.044 4243 Dihedral : 4.673 54.964 3210 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.53 % Allowed : 9.59 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 2949 helix: 1.99 (0.21), residues: 676 sheet: 0.18 (0.20), residues: 636 loop : -0.26 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 509 TYR 0.034 0.001 TYR B 369 PHE 0.020 0.001 PHE C 592 TRP 0.018 0.001 TRP C 436 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (24348) covalent geometry : angle 0.52281 / 0.27 (33116) SS BOND : bond 0.00250 / 0.17 ( 38) SS BOND : angle 1.34036 / 0.87 ( 76) hydrogen bonds : bond 0.03455 / 2.26 ( 1046) hydrogen bonds : angle 5.31981 / 3.75 ( 2847) link_NAG-ASN : bond 0.00511 / 0.32 ( 28) link_NAG-ASN : angle 2.38514 / 1.45 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7254 (p90) cc_final: 0.6893 (p90) REVERT: A 269 TYR cc_start: 0.8065 (m-80) cc_final: 0.7499 (m-80) REVERT: A 353 TRP cc_start: 0.8660 (p-90) cc_final: 0.7905 (p90) REVERT: A 886 TRP cc_start: 0.8533 (OUTLIER) cc_final: 0.7560 (p-90) REVERT: A 979 ASP cc_start: 0.8650 (m-30) cc_final: 0.7805 (t0) REVERT: A 1107 ARG cc_start: 0.8001 (mpt-90) cc_final: 0.7741 (mpt-90) REVERT: B 347 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.7901 (t80) REVERT: B 776 LYS cc_start: 0.9023 (tppt) cc_final: 0.8790 (tptp) REVERT: B 979 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8330 (m-30) REVERT: C 400 PHE cc_start: 0.7774 (p90) cc_final: 0.7130 (p90) REVERT: C 542 ASN cc_start: 0.7174 (t0) cc_final: 0.6266 (m-40) REVERT: C 1029 MET cc_start: 0.9147 (tpp) cc_final: 0.8715 (ttm) outliers start: 40 outliers final: 25 residues processed: 133 average time/residue: 0.1275 time to fit residues: 29.0174 Evaluate side-chains 124 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 61 optimal weight: 7.9990 chunk 274 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.090597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.062831 restraints weight = 72346.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.065791 restraints weight = 36713.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.066182 restraints weight = 19798.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.066457 restraints weight = 16320.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066511 restraints weight = 15188.332| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 24414 Z= 0.279 Angle : 0.663 13.179 33276 Z= 0.336 Chirality : 0.049 0.877 3863 Planarity : 0.004 0.052 4243 Dihedral : 4.946 53.383 3208 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.80 % Allowed : 9.63 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 2949 helix: 1.58 (0.21), residues: 680 sheet: -0.03 (0.20), residues: 654 loop : -0.36 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 509 TYR 0.023 0.002 TYR A 904 PHE 0.021 0.002 PHE C 592 TRP 0.017 0.002 TRP C 436 HIS 0.009 0.002 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.28 (24348) covalent geometry : angle 0.64610 / 0.33 (33116) SS BOND : bond 0.00432 / 0.26 ( 38) SS BOND : angle 1.53982 / 0.98 ( 76) hydrogen bonds : bond 0.04213 / 2.73 ( 1046) hydrogen bonds : angle 5.71550 / 3.99 ( 2847) link_NAG-ASN : bond 0.00445 / 0.28 ( 28) link_NAG-ASN : angle 2.70586 / 1.60 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 93 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7332 (p90) cc_final: 0.6948 (p90) REVERT: A 269 TYR cc_start: 0.8088 (m-80) cc_final: 0.7545 (m-80) REVERT: A 979 ASP cc_start: 0.8609 (m-30) cc_final: 0.7835 (t0) REVERT: A 1041 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7975 (t0) REVERT: B 403 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7980 (ptm160) REVERT: B 979 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8278 (m-30) REVERT: C 400 PHE cc_start: 0.7744 (p90) cc_final: 0.7012 (p90) REVERT: C 1094 VAL cc_start: 0.8711 (t) cc_final: 0.8510 (m) outliers start: 47 outliers final: 32 residues processed: 132 average time/residue: 0.1315 time to fit residues: 29.1923 Evaluate side-chains 128 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 130 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 278 optimal weight: 0.7980 chunk 238 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 777 ASN C 762 GLN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.093194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.065345 restraints weight = 72197.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.067558 restraints weight = 34560.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.068965 restraints weight = 21647.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.069868 restraints weight = 16089.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.070339 restraints weight = 13385.167| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 24414 Z= 0.112 Angle : 0.558 11.685 33276 Z= 0.283 Chirality : 0.045 0.632 3863 Planarity : 0.003 0.045 4243 Dihedral : 4.599 56.400 3206 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.30 % Allowed : 10.16 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 2949 helix: 1.86 (0.21), residues: 678 sheet: 0.12 (0.20), residues: 624 loop : -0.32 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.031 0.001 TYR B 369 PHE 0.020 0.001 PHE C 592 TRP 0.020 0.001 TRP C 436 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (24348) covalent geometry : angle 0.54027 / 0.28 (33116) SS BOND : bond 0.00552 / 0.24 ( 38) SS BOND : angle 1.68039 / 1.04 ( 76) hydrogen bonds : bond 0.03572 / 2.32 ( 1046) hydrogen bonds : angle 5.37121 / 3.76 ( 2847) link_NAG-ASN : bond 0.00433 / 0.31 ( 28) link_NAG-ASN : angle 2.43471 / 1.46 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7238 (p90) cc_final: 0.6923 (p90) REVERT: A 979 ASP cc_start: 0.8536 (m-30) cc_final: 0.7750 (t0) REVERT: B 347 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7891 (t80) REVERT: B 979 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8632 (t0) REVERT: C 380 TYR cc_start: 0.7609 (m-80) cc_final: 0.7293 (m-80) REVERT: C 400 PHE cc_start: 0.7642 (p90) cc_final: 0.7023 (p90) REVERT: C 1029 MET cc_start: 0.9163 (tpp) cc_final: 0.8728 (ttm) outliers start: 34 outliers final: 27 residues processed: 126 average time/residue: 0.1250 time to fit residues: 26.7181 Evaluate side-chains 122 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 294 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 288 optimal weight: 0.6980 chunk 227 optimal weight: 0.8980 chunk 192 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 258 optimal weight: 6.9990 chunk 93 optimal weight: 0.3980 chunk 223 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.092349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.064345 restraints weight = 72438.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.066511 restraints weight = 35041.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.067895 restraints weight = 22071.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.068771 restraints weight = 16442.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.069281 restraints weight = 13711.393| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24414 Z= 0.148 Angle : 0.566 11.727 33276 Z= 0.286 Chirality : 0.045 0.549 3863 Planarity : 0.003 0.045 4243 Dihedral : 4.555 55.829 3206 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.41 % Allowed : 10.16 % Favored : 88.42 % 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: 0.44 (0.16), residues: 2949 helix: 1.88 (0.21), residues: 677 sheet: 0.13 (0.20), residues: 649 loop : -0.28 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.020 0.001 TYR A 904 PHE 0.023 0.001 PHE A 92 TRP 0.038 0.001 TRP A 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (24348) covalent geometry : angle 0.54905 / 0.28 (33116) SS BOND : bond 0.00290 / 0.18 ( 38) SS BOND : angle 1.61264 / 1.01 ( 76) hydrogen bonds : bond 0.03652 / 2.37 ( 1046) hydrogen bonds : angle 5.37902 / 3.77 ( 2847) link_NAG-ASN : bond 0.00380 / 0.27 ( 28) link_NAG-ASN : angle 2.39227 / 1.45 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7271 (p90) cc_final: 0.6944 (p90) REVERT: A 979 ASP cc_start: 0.8577 (m-30) cc_final: 0.7800 (t0) REVERT: B 979 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8625 (t0) REVERT: C 380 TYR cc_start: 0.7585 (m-80) cc_final: 0.7257 (m-80) REVERT: C 400 PHE cc_start: 0.7746 (p90) cc_final: 0.7122 (p90) REVERT: C 1029 MET cc_start: 0.9187 (tpp) cc_final: 0.8751 (ttm) outliers start: 37 outliers final: 33 residues processed: 128 average time/residue: 0.1281 time to fit residues: 28.2449 Evaluate side-chains 127 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 298 optimal weight: 0.0970 chunk 271 optimal weight: 0.0010 chunk 77 optimal weight: 0.3980 chunk 277 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.093633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.065652 restraints weight = 71867.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.067885 restraints weight = 34347.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.069325 restraints weight = 21540.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.070196 restraints weight = 15982.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.070774 restraints weight = 13348.113| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.098 24414 Z= 0.100 Angle : 0.543 11.877 33276 Z= 0.275 Chirality : 0.044 0.448 3863 Planarity : 0.003 0.045 4243 Dihedral : 4.381 57.935 3206 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.22 % Allowed : 10.55 % 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: 0.54 (0.16), residues: 2949 helix: 1.91 (0.21), residues: 685 sheet: 0.32 (0.21), residues: 609 loop : -0.25 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.030 0.001 TYR B 369 PHE 0.020 0.001 PHE C 592 TRP 0.039 0.001 TRP A 353 HIS 0.004 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (24348) covalent geometry : angle 0.52628 / 0.27 (33116) SS BOND : bond 0.00250 / 0.17 ( 38) SS BOND : angle 1.66321 / 1.06 ( 76) hydrogen bonds : bond 0.03401 / 2.20 ( 1046) hydrogen bonds : angle 5.24832 / 3.68 ( 2847) link_NAG-ASN : bond 0.00418 / 0.30 ( 28) link_NAG-ASN : angle 2.25975 / 1.38 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3278.00 seconds wall clock time: 57 minutes 50.97 seconds (3470.97 seconds total)