Starting phenix.real_space_refine on Thu Mar 5 17:19:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lyl_23594/03_2026/7lyl_23594.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lyl_23594/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7lyl_23594/03_2026/7lyl_23594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lyl_23594/03_2026/7lyl_23594.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lyl_23594/03_2026/7lyl_23594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lyl_23594/03_2026/7lyl_23594.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 24 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 dihedrals: 33 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.08, per 1000 atoms: 0.26 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: 2.02 Conformation dependent library (CDL) restraints added in 938.7 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: 1.31 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: 6.28 Time building geometry restraints manager: 2.68 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: 13755 17.66 - 35.33: 875 35.33 - 52.99: 138 52.99 - 70.66: 53 70.66 - 88.32: 30 Dihedral angle restraints: 14851 sinusoidal: 6127 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 14848 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.270 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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 : 13.015 88.323 9121 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 covalent geometry : bond 0.01287 (24348) covalent geometry : angle 1.70390 (33116) SS BOND : bond 0.01190 ( 38) SS BOND : angle 1.74974 ( 76) hydrogen bonds : bond 0.15595 ( 1046) hydrogen bonds : angle 8.47028 ( 2847) link_NAG-ASN : bond 0.01332 ( 28) link_NAG-ASN : angle 4.51823 ( 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 : 0.917 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: 0.1738 time to fit residues: 67.2159 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 : 0.839 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 282 ASN 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 = 0.3664 r_free = 0.3664 target = 0.093123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.066321 restraints weight = 72462.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.068649 restraints weight = 34925.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.069569 restraints weight = 19226.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.069725 restraints weight = 15504.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.069881 restraints weight = 14834.808| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24414 Z= 0.176 Angle : 0.691 11.891 33276 Z= 0.361 Chirality : 0.048 0.266 3863 Planarity : 0.004 0.043 4243 Dihedral : 7.243 57.997 3804 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.42 % Rotamer: Outliers : 1.18 % Allowed : 5.46 % Favored : 93.35 % 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: -0.11 (0.15), residues: 2949 helix: 1.08 (0.20), residues: 686 sheet: -0.04 (0.19), residues: 676 loop : -0.55 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 237 TYR 0.024 0.002 TYR B 495 PHE 0.017 0.002 PHE A 220 TRP 0.031 0.002 TRP A 353 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00392 (24348) covalent geometry : angle 0.66725 (33116) SS BOND : bond 0.01020 ( 38) SS BOND : angle 1.44001 ( 76) hydrogen bonds : bond 0.05140 ( 1046) hydrogen bonds : angle 6.36401 ( 2847) link_NAG-ASN : bond 0.00415 ( 28) link_NAG-ASN : angle 3.43553 ( 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 164 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.930 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: 0.7870 (OUTLIER) cc_final: 0.7243 (t) REVERT: A 129 LYS cc_start: 0.8455 (mmtm) cc_final: 0.8007 (pttt) REVERT: A 238 PHE cc_start: 0.7361 (p90) cc_final: 0.6977 (p90) REVERT: A 269 TYR cc_start: 0.7937 (m-80) cc_final: 0.7047 (m-80) REVERT: A 353 TRP cc_start: 0.8784 (p-90) cc_final: 0.8016 (p90) REVERT: A 731 MET cc_start: 0.8981 (ptt) cc_final: 0.8621 (ptt) REVERT: B 347 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7732 (t80) REVERT: C 314 GLN cc_start: 0.8401 (tp40) cc_final: 0.8077 (tp40) REVERT: C 317 ASN cc_start: 0.5484 (OUTLIER) cc_final: 0.5279 (t0) REVERT: C 384 PRO cc_start: 0.8843 (Cg_endo) cc_final: 0.8595 (Cg_exo) REVERT: C 400 PHE cc_start: 0.7597 (p90) cc_final: 0.6934 (p90) REVERT: C 501 TYR cc_start: 0.2342 (OUTLIER) cc_final: 0.2141 (m-80) outliers start: 31 outliers final: 13 residues processed: 157 average time/residue: 0.1551 time to fit residues: 39.3390 Evaluate side-chains 115 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL 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 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 317 ASN 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: 5.9990 chunk 248 optimal weight: 6.9990 chunk 295 optimal weight: 0.7980 chunk 212 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 167 optimal weight: 0.0170 chunk 294 optimal weight: 0.5980 chunk 232 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 291 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.4620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN C 317 ASN C 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.093289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.066565 restraints weight = 72676.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.068806 restraints weight = 34948.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.069702 restraints weight = 19193.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.069924 restraints weight = 16297.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.070075 restraints weight = 14877.689| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24414 Z= 0.134 Angle : 0.594 11.705 33276 Z= 0.308 Chirality : 0.045 0.190 3863 Planarity : 0.004 0.040 4243 Dihedral : 6.513 55.608 3802 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.22 % Allowed : 6.95 % Favored : 91.82 % 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: 0.15 (0.15), residues: 2949 helix: 1.52 (0.20), residues: 679 sheet: -0.06 (0.19), residues: 673 loop : -0.40 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1107 TYR 0.030 0.001 TYR B 904 PHE 0.018 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 covalent geometry : bond 0.00292 (24348) covalent geometry : angle 0.57680 (33116) SS BOND : bond 0.00795 ( 38) SS BOND : angle 0.87095 ( 76) hydrogen bonds : bond 0.04256 ( 1046) hydrogen bonds : angle 5.83861 ( 2847) link_NAG-ASN : bond 0.00359 ( 28) link_NAG-ASN : angle 2.82327 ( 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 148 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.767 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: 0.7899 (OUTLIER) cc_final: 0.7391 (t) REVERT: A 238 PHE cc_start: 0.7301 (p90) cc_final: 0.6927 (p90) REVERT: A 269 TYR cc_start: 0.8002 (m-80) cc_final: 0.7171 (m-80) REVERT: A 347 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.6946 (m-80) REVERT: B 347 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.7753 (t80) REVERT: B 780 GLU cc_start: 0.8678 (tp30) cc_final: 0.8469 (tp30) REVERT: C 400 PHE cc_start: 0.7682 (p90) cc_final: 0.6754 (p90) outliers start: 32 outliers final: 20 residues processed: 143 average time/residue: 0.1386 time to fit residues: 33.8493 Evaluate side-chains 119 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 675 GLN 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 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: 0.8980 chunk 137 optimal weight: 8.9990 chunk 231 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 259 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 220 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS C 314 GLN C 317 ASN C 394 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 = 0.3642 r_free = 0.3642 target = 0.091875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.064838 restraints weight = 72933.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.067088 restraints weight = 35639.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.068043 restraints weight = 19457.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.068183 restraints weight = 16658.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.068322 restraints weight = 15313.452| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 24414 Z= 0.196 Angle : 0.602 11.464 33276 Z= 0.308 Chirality : 0.045 0.187 3863 Planarity : 0.004 0.043 4243 Dihedral : 6.335 54.643 3802 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.80 % Allowed : 7.64 % Favored : 90.56 % 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: 0.15 (0.15), residues: 2949 helix: 1.57 (0.21), residues: 682 sheet: -0.13 (0.19), residues: 679 loop : -0.40 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 357 TYR 0.023 0.001 TYR B 904 PHE 0.019 0.001 PHE A 92 TRP 0.017 0.001 TRP C 436 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00454 (24348) covalent geometry : angle 0.58661 (33116) SS BOND : bond 0.00428 ( 38) SS BOND : angle 0.87758 ( 76) hydrogen bonds : bond 0.04190 ( 1046) hydrogen bonds : angle 5.75788 ( 2847) link_NAG-ASN : bond 0.00351 ( 28) link_NAG-ASN : angle 2.68273 ( 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 155 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 108 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7366 (p90) cc_final: 0.6975 (p90) REVERT: A 269 TYR cc_start: 0.8039 (m-80) cc_final: 0.7311 (m-80) REVERT: A 353 TRP cc_start: 0.8830 (p-90) cc_final: 0.7922 (p90) REVERT: A 731 MET cc_start: 0.8896 (ptt) cc_final: 0.8605 (ptt) REVERT: A 1041 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7880 (t0) REVERT: B 313 TYR cc_start: 0.8518 (m-80) cc_final: 0.8217 (m-80) REVERT: B 347 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.7848 (t80) REVERT: B 979 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8332 (m-30) REVERT: C 387 LEU cc_start: 0.9091 (mt) cc_final: 0.8651 (mt) REVERT: C 400 PHE cc_start: 0.7841 (p90) cc_final: 0.7172 (p90) REVERT: C 468 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7861 (mm) REVERT: C 1029 MET cc_start: 0.9074 (tpp) cc_final: 0.8811 (ttm) outliers start: 47 outliers final: 28 residues processed: 149 average time/residue: 0.1306 time to fit residues: 34.0992 Evaluate side-chains 123 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 415 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 768 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 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 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 314 GLN Chi-restraints excluded: chain C residue 315 THR 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: 10.0000 chunk 174 optimal weight: 4.9990 chunk 99 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 267 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN C 762 GLN C1142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.091690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.064711 restraints weight = 72374.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.066985 restraints weight = 35238.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.067738 restraints weight = 19257.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.067954 restraints weight = 16701.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.068043 restraints weight = 15648.064| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24414 Z= 0.192 Angle : 0.587 11.509 33276 Z= 0.301 Chirality : 0.045 0.195 3863 Planarity : 0.003 0.044 4243 Dihedral : 6.137 54.285 3798 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.83 % Allowed : 8.25 % Favored : 89.91 % 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: 0.13 (0.15), residues: 2949 helix: 1.62 (0.21), residues: 683 sheet: -0.13 (0.20), residues: 650 loop : -0.45 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 995 TYR 0.020 0.001 TYR A 904 PHE 0.019 0.001 PHE C 559 TRP 0.015 0.001 TRP C 436 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00442 (24348) covalent geometry : angle 0.57108 (33116) SS BOND : bond 0.00429 ( 38) SS BOND : angle 1.18059 ( 76) hydrogen bonds : bond 0.04053 ( 1046) hydrogen bonds : angle 5.70775 ( 2847) link_NAG-ASN : bond 0.00345 ( 28) link_NAG-ASN : angle 2.60205 ( 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 149 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 101 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7359 (p90) cc_final: 0.6966 (p90) REVERT: A 269 TYR cc_start: 0.8097 (m-80) cc_final: 0.7412 (m-80) REVERT: A 979 ASP cc_start: 0.8336 (m-30) cc_final: 0.7945 (t70) REVERT: A 1041 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7920 (t0) REVERT: B 313 TYR cc_start: 0.8525 (m-80) cc_final: 0.8270 (m-80) REVERT: B 347 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.7876 (t80) REVERT: B 403 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7901 (ptm160) REVERT: B 912 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8252 (p) REVERT: B 979 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8334 (m-30) REVERT: C 387 LEU cc_start: 0.9093 (mt) cc_final: 0.8645 (mt) REVERT: C 400 PHE cc_start: 0.7747 (p90) cc_final: 0.6996 (p90) outliers start: 48 outliers final: 34 residues processed: 143 average time/residue: 0.1481 time to fit residues: 35.8635 Evaluate side-chains 130 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP 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 511 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 768 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 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 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 315 THR 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 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: 4.9990 chunk 82 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 219 optimal weight: 8.9990 chunk 286 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 195 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS B 115 GLN C 314 GLN C 762 GLN C1142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.092413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.064306 restraints weight = 72562.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.066491 restraints weight = 34663.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.067849 restraints weight = 21775.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.068775 restraints weight = 16276.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.069288 restraints weight = 13527.800| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24414 Z= 0.122 Angle : 0.537 11.711 33276 Z= 0.275 Chirality : 0.044 0.205 3863 Planarity : 0.003 0.043 4243 Dihedral : 5.845 55.677 3798 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.57 % Allowed : 9.21 % Favored : 89.22 % 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: 0.31 (0.15), residues: 2949 helix: 1.78 (0.21), residues: 691 sheet: 0.02 (0.20), residues: 649 loop : -0.37 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1107 TYR 0.018 0.001 TYR C 369 PHE 0.021 0.001 PHE A 92 TRP 0.018 0.001 TRP C 436 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00274 (24348) covalent geometry : angle 0.52191 (33116) SS BOND : bond 0.00364 ( 38) SS BOND : angle 0.92826 ( 76) hydrogen bonds : bond 0.03692 ( 1046) hydrogen bonds : angle 5.48366 ( 2847) link_NAG-ASN : bond 0.00336 ( 28) link_NAG-ASN : angle 2.45626 ( 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 151 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7223 (p90) cc_final: 0.6901 (p90) REVERT: A 269 TYR cc_start: 0.8056 (m-80) cc_final: 0.7517 (m-80) REVERT: A 353 TRP cc_start: 0.8727 (p-90) cc_final: 0.7978 (p90) REVERT: A 979 ASP cc_start: 0.8317 (m-30) cc_final: 0.7789 (t0) REVERT: A 1041 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7795 (t0) REVERT: B 347 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.7909 (t80) REVERT: B 979 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8504 (t0) REVERT: C 338 PHE cc_start: 0.8145 (m-10) cc_final: 0.7870 (m-10) REVERT: C 342 PHE cc_start: 0.6315 (OUTLIER) cc_final: 0.5883 (m-80) REVERT: C 400 PHE cc_start: 0.7731 (p90) cc_final: 0.6869 (p90) REVERT: C 468 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7807 (mm) outliers start: 41 outliers final: 27 residues processed: 142 average time/residue: 0.1381 time to fit residues: 33.0059 Evaluate side-chains 124 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP 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 441 LEU Chi-restraints excluded: chain A residue 519 HIS 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 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 651 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU 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 189 LEU 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 468 ILE 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: 0.9990 chunk 89 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 276 optimal weight: 0.7980 chunk 212 optimal weight: 8.9990 chunk 120 optimal weight: 0.5980 chunk 170 optimal weight: 8.9990 chunk 55 optimal weight: 0.0870 chunk 185 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS C 762 GLN C1142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.092815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.065306 restraints weight = 72154.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.068306 restraints weight = 35783.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.068743 restraints weight = 19286.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.069096 restraints weight = 15802.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.069208 restraints weight = 14522.452| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24414 Z= 0.106 Angle : 0.525 11.790 33276 Z= 0.269 Chirality : 0.043 0.212 3863 Planarity : 0.003 0.043 4243 Dihedral : 5.685 56.075 3798 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.72 % Allowed : 9.32 % Favored : 88.96 % 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: 0.45 (0.15), residues: 2949 helix: 1.97 (0.21), residues: 679 sheet: 0.13 (0.20), residues: 640 loop : -0.31 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 403 TYR 0.034 0.001 TYR B 369 PHE 0.019 0.001 PHE C 592 TRP 0.018 0.001 TRP C 436 HIS 0.024 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00232 (24348) covalent geometry : angle 0.51101 (33116) SS BOND : bond 0.00330 ( 38) SS BOND : angle 0.83281 ( 76) hydrogen bonds : bond 0.03560 ( 1046) hydrogen bonds : angle 5.37801 ( 2847) link_NAG-ASN : bond 0.00352 ( 28) link_NAG-ASN : angle 2.39407 ( 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 147 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 102 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7298 (p90) cc_final: 0.6936 (p90) REVERT: A 269 TYR cc_start: 0.8098 (m-80) cc_final: 0.7500 (m-80) REVERT: A 353 TRP cc_start: 0.8747 (p-90) cc_final: 0.7942 (p90) REVERT: A 979 ASP cc_start: 0.8296 (m-30) cc_final: 0.7798 (t0) REVERT: A 1041 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7780 (t0) REVERT: B 118 LEU cc_start: 0.9047 (tt) cc_final: 0.8575 (mt) REVERT: B 347 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.7851 (t80) REVERT: B 776 LYS cc_start: 0.9056 (tppt) cc_final: 0.8791 (tptp) REVERT: B 912 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8200 (p) REVERT: B 979 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8348 (m-30) REVERT: C 400 PHE cc_start: 0.7640 (p90) cc_final: 0.7025 (p90) REVERT: C 1029 MET cc_start: 0.9107 (tpp) cc_final: 0.8740 (ttm) outliers start: 45 outliers final: 30 residues processed: 139 average time/residue: 0.1314 time to fit residues: 31.4836 Evaluate side-chains 126 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP 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 675 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1037 SER 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 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 578 ASP 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 869 MET Chi-restraints excluded: chain B residue 912 THR 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 240 THR 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 1032 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 61 optimal weight: 9.9990 chunk 274 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 167 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.089504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.061661 restraints weight = 72321.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.064411 restraints weight = 37652.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.064897 restraints weight = 20306.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.065218 restraints weight = 16498.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.065261 restraints weight = 15345.877| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 24414 Z= 0.253 Angle : 0.630 12.944 33276 Z= 0.320 Chirality : 0.047 0.745 3863 Planarity : 0.004 0.045 4243 Dihedral : 6.012 54.925 3796 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.80 % Allowed : 9.78 % 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: 0.22 (0.15), residues: 2949 helix: 1.70 (0.21), residues: 675 sheet: -0.02 (0.20), residues: 659 loop : -0.41 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 403 TYR 0.023 0.001 TYR A 904 PHE 0.022 0.002 PHE C 592 TRP 0.010 0.001 TRP A 104 HIS 0.008 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00587 (24348) covalent geometry : angle 0.61479 (33116) SS BOND : bond 0.00463 ( 38) SS BOND : angle 0.99891 ( 76) hydrogen bonds : bond 0.04098 ( 1046) hydrogen bonds : angle 5.65197 ( 2847) link_NAG-ASN : bond 0.00389 ( 28) link_NAG-ASN : angle 2.70641 ( 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 : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7317 (p90) cc_final: 0.6940 (p90) REVERT: A 269 TYR cc_start: 0.8058 (m-80) cc_final: 0.7516 (m-80) REVERT: A 979 ASP cc_start: 0.8372 (m-30) cc_final: 0.7891 (t0) REVERT: A 1041 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7958 (t0) REVERT: B 912 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8286 (p) REVERT: B 979 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8298 (m-30) REVERT: C 400 PHE cc_start: 0.7717 (p90) cc_final: 0.6978 (p90) outliers start: 47 outliers final: 36 residues processed: 132 average time/residue: 0.1398 time to fit residues: 31.7530 Evaluate side-chains 128 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 89 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP 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 483 VAL 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 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 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 578 ASP 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 781 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 912 THR 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 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: 5.9990 chunk 278 optimal weight: 0.8980 chunk 238 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 167 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.090940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.062696 restraints weight = 72309.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.064765 restraints weight = 35344.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.066087 restraints weight = 22490.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.066946 restraints weight = 16877.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.067476 restraints weight = 14106.917| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24414 Z= 0.138 Angle : 0.573 11.750 33276 Z= 0.291 Chirality : 0.046 0.843 3863 Planarity : 0.003 0.044 4243 Dihedral : 5.804 55.461 3794 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.34 % Allowed : 10.43 % 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: 0.35 (0.16), residues: 2949 helix: 1.87 (0.21), residues: 681 sheet: 0.09 (0.21), residues: 613 loop : -0.37 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 403 TYR 0.032 0.001 TYR B 369 PHE 0.020 0.001 PHE C 592 TRP 0.014 0.001 TRP A 104 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00315 (24348) covalent geometry : angle 0.55492 (33116) SS BOND : bond 0.00366 ( 38) SS BOND : angle 1.23969 ( 76) hydrogen bonds : bond 0.03730 ( 1046) hydrogen bonds : angle 5.44546 ( 2847) link_NAG-ASN : bond 0.00352 ( 28) link_NAG-ASN : angle 2.70734 ( 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 130 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7284 (p90) cc_final: 0.7044 (p90) REVERT: A 979 ASP cc_start: 0.8367 (m-30) cc_final: 0.7866 (t0) REVERT: A 1041 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7904 (t0) REVERT: B 912 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8205 (p) REVERT: B 979 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8642 (t0) REVERT: C 400 PHE cc_start: 0.7784 (p90) cc_final: 0.7116 (p90) REVERT: C 1029 MET cc_start: 0.9205 (tpp) cc_final: 0.8754 (ttm) outliers start: 35 outliers final: 30 residues processed: 124 average time/residue: 0.1372 time to fit residues: 29.4051 Evaluate side-chains 126 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP 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 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 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 578 ASP 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 869 MET Chi-restraints excluded: chain B residue 912 THR 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 240 THR 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 294 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 288 optimal weight: 0.7980 chunk 227 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 258 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 223 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.090374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.061999 restraints weight = 72580.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.064049 restraints weight = 35850.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.065348 restraints weight = 22905.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.066215 restraints weight = 17236.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066662 restraints weight = 14428.926| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24414 Z= 0.178 Angle : 0.586 11.938 33276 Z= 0.297 Chirality : 0.046 0.819 3863 Planarity : 0.003 0.044 4243 Dihedral : 5.751 54.952 3794 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.38 % Allowed : 10.55 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.32 (0.16), residues: 2949 helix: 1.79 (0.21), residues: 688 sheet: 0.07 (0.21), residues: 614 loop : -0.38 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 403 TYR 0.024 0.001 TYR A 904 PHE 0.023 0.001 PHE A 92 TRP 0.039 0.002 TRP A 353 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00413 (24348) covalent geometry : angle 0.56718 (33116) SS BOND : bond 0.00394 ( 38) SS BOND : angle 1.16710 ( 76) hydrogen bonds : bond 0.03842 ( 1046) hydrogen bonds : angle 5.49049 ( 2847) link_NAG-ASN : bond 0.00435 ( 28) link_NAG-ASN : angle 2.80692 ( 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 132 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7240 (p90) cc_final: 0.6999 (p90) REVERT: A 1041 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7943 (t0) REVERT: B 912 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8229 (p) REVERT: B 979 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8671 (t0) REVERT: C 400 PHE cc_start: 0.7701 (p90) cc_final: 0.6974 (p90) outliers start: 36 outliers final: 31 residues processed: 126 average time/residue: 0.1387 time to fit residues: 30.1042 Evaluate side-chains 125 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP 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 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 1037 SER Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 578 ASP 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 869 MET Chi-restraints excluded: chain B residue 912 THR 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 240 THR 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: 3.9990 chunk 68 optimal weight: 0.3980 chunk 98 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 chunk 271 optimal weight: 0.0370 chunk 77 optimal weight: 0.5980 chunk 277 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.091401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.063146 restraints weight = 71881.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.065247 restraints weight = 35245.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066600 restraints weight = 22417.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.067475 restraints weight = 16782.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067903 restraints weight = 14015.291| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 24414 Z= 0.122 Angle : 0.563 12.018 33276 Z= 0.284 Chirality : 0.045 0.684 3863 Planarity : 0.003 0.045 4243 Dihedral : 5.589 56.471 3794 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.34 % Allowed : 10.74 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.16), residues: 2949 helix: 1.88 (0.21), residues: 689 sheet: 0.16 (0.21), residues: 614 loop : -0.32 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1039 TYR 0.032 0.001 TYR B 369 PHE 0.021 0.001 PHE C 592 TRP 0.055 0.002 TRP C 436 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00278 (24348) covalent geometry : angle 0.54399 (33116) SS BOND : bond 0.00421 ( 38) SS BOND : angle 1.39090 ( 76) hydrogen bonds : bond 0.03632 ( 1046) hydrogen bonds : angle 5.39351 ( 2847) link_NAG-ASN : bond 0.00369 ( 28) link_NAG-ASN : angle 2.65694 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3447.51 seconds wall clock time: 60 minutes 44.38 seconds (3644.38 seconds total)