Starting phenix.real_space_refine on Sat Jul 4 22:18:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r17_14233/07_2026/7r17_14233.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r17_14233/07_2026/7r17_14233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r17_14233/07_2026/7r17_14233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r17_14233/07_2026/7r17_14233.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7r17_14233/07_2026/7r17_14233.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r17_14233/07_2026/7r17_14233.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r17_14233/07_2026/7r17_14233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r17_14233/07_2026/7r17_14233.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.070 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 107 5.16 5 C 15092 2.51 5 N 3886 2.21 5 O 4541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23626 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7790 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 51, 'TRANS': 942} Chain breaks: 9 Chain: "B" Number of atoms: 7821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7821 Classifications: {'peptide': 1000} Link IDs: {'PTRANS': 50, 'TRANS': 949} Chain breaks: 9 Chain: "C" Number of atoms: 7707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7707 Classifications: {'peptide': 987} Link IDs: {'PTRANS': 50, 'TRANS': 936} Chain breaks: 11 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 4.77, per 1000 atoms: 0.20 Number of scatterers: 23626 At special positions: 0 Unit cell: (146.745, 136.962, 196.747, 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 107 16.00 O 4541 8.00 N 3886 7.00 C 15092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1134 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B 717 " " NAG B1304 " - " ASN B 801 " " NAG B1305 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C 801 " " NAG C1306 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 804.8 milliseconds 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5572 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 49 sheets defined 23.9% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.553A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.692A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.912A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.769A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.037A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 953 " --> pdb=" O GLN A 949 " (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: 3.619A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.990A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.017A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.801A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 removed outlier: 4.274A pdb=" N ALA B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.541A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.063A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.595A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.655A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 947 through 966 removed outlier: 3.940A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.568A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.729A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 369 removed outlier: 3.987A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.438A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.716A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.787A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.638A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.504A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.547A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.039A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.903A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.595A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.676A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (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 133 through 135 removed outlier: 6.470A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 145 removed outlier: 7.242A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER A 155 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 removed outlier: 4.084A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 645 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.716A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE A 541 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.627A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 454 removed outlier: 8.384A pdb=" N ASN A 450 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 10.622A pdb=" N GLN A 493 " --> pdb=" O ASN A 450 " (cutoff:3.500A) 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: 5.886A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.751A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.647A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.540A 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 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.070A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.070A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.783A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.886A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 317 removed outlier: 4.037A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 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 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.314A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 703 through 704 removed outlier: 7.539A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.513A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.662A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.662A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.501A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.731A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.779A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.956A 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 removed outlier: 3.845A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.722A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.528A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.584A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.727A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.792A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AF1, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.586A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 899 hydrogen bonds defined for protein. 2457 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.94 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7525 1.34 - 1.46: 5521 1.46 - 1.58: 10982 1.58 - 1.70: 0 1.70 - 1.82: 134 Bond restraints: 24162 Sorted by residual: bond pdb=" N PHE A 329 " pdb=" CA PHE A 329 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.55e+01 bond pdb=" N ILE B 418 " pdb=" CA ILE B 418 " ideal model delta sigma weight residual 1.457 1.497 -0.041 1.07e-02 8.73e+03 1.45e+01 bond pdb=" N ILE B1132 " pdb=" CA ILE B1132 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.19e-02 7.06e+03 9.01e+00 bond pdb=" N VAL C 362 " pdb=" CA VAL C 362 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.71e+00 bond pdb=" N VAL C 524 " pdb=" CA VAL C 524 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.24e-02 6.50e+03 8.14e+00 ... (remaining 24157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 31526 1.16 - 2.31: 988 2.31 - 3.47: 300 3.47 - 4.63: 38 4.63 - 5.79: 10 Bond angle restraints: 32862 Sorted by residual: angle pdb=" N ILE B 418 " pdb=" CA ILE B 418 " pdb=" C ILE B 418 " ideal model delta sigma weight residual 113.10 109.54 3.56 9.70e-01 1.06e+00 1.35e+01 angle pdb=" CA ASN A 331 " pdb=" C ASN A 331 " pdb=" O ASN A 331 " ideal model delta sigma weight residual 122.64 118.08 4.56 1.25e+00 6.40e-01 1.33e+01 angle pdb=" CA GLN B 613 " pdb=" C GLN B 613 " pdb=" O GLN B 613 " ideal model delta sigma weight residual 120.42 116.55 3.87 1.06e+00 8.90e-01 1.33e+01 angle pdb=" CA GLN B 271 " pdb=" C GLN B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 118.16 121.99 -3.83 1.08e+00 8.57e-01 1.26e+01 angle pdb=" CA ASN B 422 " pdb=" C ASN B 422 " pdb=" N TYR B 423 " ideal model delta sigma weight residual 119.98 116.97 3.01 8.50e-01 1.38e+00 1.25e+01 ... (remaining 32857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 13064 17.98 - 35.95: 913 35.95 - 53.93: 168 53.93 - 71.90: 32 71.90 - 89.88: 20 Dihedral angle restraints: 14197 sinusoidal: 5539 harmonic: 8658 Sorted by residual: 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 -152.08 66.08 1 1.00e+01 1.00e-02 5.71e+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 -148.36 62.36 1 1.00e+01 1.00e-02 5.15e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -35.51 -50.49 1 1.00e+01 1.00e-02 3.49e+01 ... (remaining 14194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3316 0.071 - 0.141: 445 0.141 - 0.212: 20 0.212 - 0.283: 1 0.283 - 0.353: 1 Chirality restraints: 3783 Sorted by residual: chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 717 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.49e+00 chirality pdb=" CA VAL A 327 " pdb=" N VAL A 327 " pdb=" C VAL A 327 " pdb=" CB VAL A 327 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 3780 not shown) Planarity restraints: 4247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.301 2.00e-02 2.50e+03 2.53e-01 8.02e+02 pdb=" C7 NAG A1301 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.187 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.435 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 985 " -0.037 5.00e-02 4.00e+02 5.54e-02 4.90e+00 pdb=" N PRO B 986 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 986 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 986 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.034 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO A 295 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.028 5.00e-02 4.00e+02 ... (remaining 4244 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3190 2.76 - 3.29: 22467 3.29 - 3.83: 37410 3.83 - 4.36: 41524 4.36 - 4.90: 73076 Nonbonded interactions: 177667 Sorted by model distance: nonbonded pdb=" OG SER B 968 " pdb=" O GLN C 755 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASN A 969 " pdb=" OG SER A 975 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 94 " pdb=" O ALA A 264 " model vdw 2.260 3.040 nonbonded pdb=" O ASN A 448 " pdb=" OG SER A 494 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.274 3.040 ... (remaining 177662 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 65 or resid 81 through 94 or resid 103 through \ 143 or resid 153 through 175 or resid 188 through 209 or resid 215 through 263 o \ r resid 265 through 827 or resid 855 through 1305)) selection = (chain 'B' and (resid 26 through 94 or resid 103 through 119 or resid 132 throug \ h 143 or resid 153 through 175 or resid 188 through 209 or resid 215 through 130 \ 5)) selection = (chain 'C' and (resid 26 through 65 or resid 81 through 119 or resid 132 through \ 263 or resid 265 through 827 or resid 855 through 1305)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.980 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.270 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24222 Z= 0.202 Angle : 0.537 8.187 33004 Z= 0.304 Chirality : 0.045 0.353 3783 Planarity : 0.005 0.253 4226 Dihedral : 12.830 89.879 8511 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.50 % Allowed : 0.15 % Favored : 99.35 % 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: 0.37 (0.16), residues: 2917 helix: 2.68 (0.21), residues: 606 sheet: 0.49 (0.20), residues: 632 loop : -0.81 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.027 0.001 TYR C 873 PHE 0.025 0.001 PHE B 906 TRP 0.014 0.001 TRP B 353 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.20 (24162) covalent geometry : angle 0.52673 / 0.30 (32862) SS BOND : bond 0.00176 / 0.10 ( 38) SS BOND : angle 0.89211 / 0.67 ( 76) hydrogen bonds : bond 0.23125 / 14.80 ( 874) hydrogen bonds : angle 8.09062 / 5.66 ( 2457) link_BETA1-4 : bond 0.00020 / 0.01 ( 1) link_BETA1-4 : angle 1.23213 / 0.94 ( 3) link_NAG-ASN : bond 0.00439 / 0.28 ( 21) link_NAG-ASN : angle 2.31363 / 1.66 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 231 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8800 (t80) cc_final: 0.8272 (t80) REVERT: A 153 MET cc_start: 0.7721 (mmp) cc_final: 0.7514 (mmm) REVERT: A 198 ASP cc_start: 0.7772 (m-30) cc_final: 0.7433 (m-30) REVERT: A 396 TYR cc_start: 0.8391 (m-10) cc_final: 0.8118 (m-10) REVERT: A 774 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8363 (mm-40) REVERT: B 265 TYR cc_start: 0.8334 (p90) cc_final: 0.8030 (p90) REVERT: B 342 PHE cc_start: 0.7644 (m-80) cc_final: 0.6648 (m-80) REVERT: B 418 ILE cc_start: 0.2775 (OUTLIER) cc_final: 0.2528 (mp) REVERT: B 740 MET cc_start: 0.8671 (tpp) cc_final: 0.8435 (tpt) REVERT: B 759 PHE cc_start: 0.7819 (p90) cc_final: 0.7599 (p90) REVERT: C 237 ARG cc_start: 0.7285 (ttm110) cc_final: 0.7075 (ttm110) REVERT: C 421 TYR cc_start: 0.8486 (m-10) cc_final: 0.8223 (m-10) REVERT: C 979 ASP cc_start: 0.8914 (m-30) cc_final: 0.8574 (m-30) outliers start: 13 outliers final: 2 residues processed: 239 average time/residue: 0.1283 time to fit residues: 50.9132 Evaluate side-chains 155 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.0050 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 655 HIS C 563 GLN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.117120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.078224 restraints weight = 63329.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.081515 restraints weight = 34215.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.081907 restraints weight = 19563.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.082483 restraints weight = 15219.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.082649 restraints weight = 13439.009| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24222 Z= 0.118 Angle : 0.512 9.379 33004 Z= 0.269 Chirality : 0.043 0.304 3783 Planarity : 0.004 0.058 4226 Dihedral : 3.686 36.761 3187 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.58 % Allowed : 6.44 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.16), residues: 2917 helix: 2.79 (0.21), residues: 624 sheet: 0.54 (0.20), residues: 611 loop : -0.78 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.022 0.001 TYR B1067 PHE 0.039 0.001 PHE A 275 TRP 0.023 0.002 TRP B 436 HIS 0.002 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (24162) covalent geometry : angle 0.50503 / 0.27 (32862) SS BOND : bond 0.00217 / 0.15 ( 38) SS BOND : angle 0.76171 / 0.55 ( 76) hydrogen bonds : bond 0.05388 / 3.49 ( 874) hydrogen bonds : angle 5.93659 / 4.12 ( 2457) link_BETA1-4 : bond 0.00400 / 0.27 ( 1) link_BETA1-4 : angle 0.97680 / 0.75 ( 3) link_NAG-ASN : bond 0.00472 / 0.29 ( 21) link_NAG-ASN : angle 1.86353 / 1.37 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7832 (t70) cc_final: 0.7363 (t70) REVERT: A 144 TYR cc_start: 0.8944 (t80) cc_final: 0.8519 (t80) REVERT: A 153 MET cc_start: 0.7759 (mmp) cc_final: 0.7501 (mmm) REVERT: A 224 GLU cc_start: 0.8454 (mp0) cc_final: 0.8127 (mp0) REVERT: A 396 TYR cc_start: 0.8550 (m-10) cc_final: 0.8338 (m-10) REVERT: A 774 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8488 (mm-40) REVERT: B 265 TYR cc_start: 0.8098 (p90) cc_final: 0.7754 (p90) REVERT: B 342 PHE cc_start: 0.7680 (m-80) cc_final: 0.6867 (m-80) REVERT: B 418 ILE cc_start: 0.2421 (OUTLIER) cc_final: 0.2158 (mp) REVERT: B 436 TRP cc_start: 0.8318 (p-90) cc_final: 0.8023 (p-90) REVERT: B 740 MET cc_start: 0.8857 (tpp) cc_final: 0.8644 (tpt) REVERT: B 1141 LEU cc_start: 0.9123 (tp) cc_final: 0.8912 (tt) REVERT: C 237 ARG cc_start: 0.7262 (ttm110) cc_final: 0.7043 (ttm110) REVERT: C 421 TYR cc_start: 0.8496 (m-10) cc_final: 0.8003 (m-10) REVERT: C 979 ASP cc_start: 0.8847 (m-30) cc_final: 0.8594 (m-30) outliers start: 15 outliers final: 7 residues processed: 185 average time/residue: 0.1277 time to fit residues: 39.9922 Evaluate side-chains 169 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 145 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 218 optimal weight: 0.6980 chunk 226 optimal weight: 6.9990 chunk 280 optimal weight: 0.9990 chunk 38 optimal weight: 40.0000 chunk 16 optimal weight: 4.9990 chunk 287 optimal weight: 0.0870 chunk 223 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A 487 ASN A 655 HIS C 321 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.115653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.076527 restraints weight = 63266.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.079887 restraints weight = 32664.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.080423 restraints weight = 17912.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.080952 restraints weight = 14214.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.081064 restraints weight = 12868.481| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24222 Z= 0.152 Angle : 0.500 6.776 33004 Z= 0.263 Chirality : 0.043 0.275 3783 Planarity : 0.004 0.061 4226 Dihedral : 3.727 33.353 3185 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.92 % Allowed : 9.28 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.16), residues: 2917 helix: 2.67 (0.21), residues: 620 sheet: 0.43 (0.20), residues: 619 loop : -0.81 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1091 TYR 0.024 0.001 TYR C 904 PHE 0.018 0.001 PHE B 201 TRP 0.010 0.001 TRP C 886 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (24162) covalent geometry : angle 0.49397 / 0.26 (32862) SS BOND : bond 0.00209 / 0.14 ( 38) SS BOND : angle 0.84088 / 0.61 ( 76) hydrogen bonds : bond 0.04883 / 3.15 ( 874) hydrogen bonds : angle 5.38280 / 3.74 ( 2457) link_BETA1-4 : bond 0.00238 / 0.16 ( 1) link_BETA1-4 : angle 0.94722 / 0.74 ( 3) link_NAG-ASN : bond 0.00380 / 0.24 ( 21) link_NAG-ASN : angle 1.73801 / 1.30 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8947 (t80) cc_final: 0.8525 (t80) REVERT: A 374 PHE cc_start: 0.8454 (m-80) cc_final: 0.7785 (m-80) REVERT: A 380 TYR cc_start: 0.8865 (m-10) cc_final: 0.8658 (m-10) REVERT: A 661 GLU cc_start: 0.6972 (pp20) cc_final: 0.6611 (pp20) REVERT: A 774 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8564 (mm-40) REVERT: B 265 TYR cc_start: 0.8116 (p90) cc_final: 0.7702 (p90) REVERT: B 342 PHE cc_start: 0.7969 (m-80) cc_final: 0.7133 (m-80) REVERT: B 396 TYR cc_start: 0.8550 (m-80) cc_final: 0.7954 (m-80) REVERT: B 418 ILE cc_start: 0.2444 (OUTLIER) cc_final: 0.2200 (mp) REVERT: B 436 TRP cc_start: 0.8313 (p-90) cc_final: 0.8001 (p-90) REVERT: B 983 ARG cc_start: 0.8508 (ttp-170) cc_final: 0.7938 (ttp-170) REVERT: B 1141 LEU cc_start: 0.9146 (tp) cc_final: 0.8939 (tt) REVERT: C 237 ARG cc_start: 0.7235 (ttm110) cc_final: 0.7012 (ttm110) REVERT: C 238 PHE cc_start: 0.8407 (p90) cc_final: 0.7972 (p90) REVERT: C 417 ASN cc_start: 0.9164 (m-40) cc_final: 0.8807 (p0) REVERT: C 421 TYR cc_start: 0.8250 (m-10) cc_final: 0.7897 (m-10) REVERT: C 979 ASP cc_start: 0.8837 (m-30) cc_final: 0.8565 (m-30) outliers start: 24 outliers final: 14 residues processed: 184 average time/residue: 0.1269 time to fit residues: 39.5532 Evaluate side-chains 169 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 938 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 248 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 218 optimal weight: 0.4980 chunk 121 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 103 optimal weight: 0.0000 chunk 125 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 949 GLN B 49 HIS C 207 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.116941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.077783 restraints weight = 63407.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.081346 restraints weight = 32138.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.081746 restraints weight = 17016.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.082463 restraints weight = 14321.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.082760 restraints weight = 12617.421| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24222 Z= 0.099 Angle : 0.471 11.676 33004 Z= 0.242 Chirality : 0.042 0.249 3783 Planarity : 0.004 0.059 4226 Dihedral : 3.564 31.928 3184 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.15 % Allowed : 10.74 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.16), residues: 2917 helix: 2.86 (0.21), residues: 615 sheet: 0.55 (0.20), residues: 609 loop : -0.72 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.024 0.001 TYR A 365 PHE 0.030 0.001 PHE A 55 TRP 0.012 0.001 TRP A 436 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (24162) covalent geometry : angle 0.46589 / 0.24 (32862) SS BOND : bond 0.00239 / 0.17 ( 38) SS BOND : angle 0.70534 / 0.50 ( 76) hydrogen bonds : bond 0.04185 / 2.72 ( 874) hydrogen bonds : angle 5.04337 / 3.52 ( 2457) link_BETA1-4 : bond 0.00278 / 0.19 ( 1) link_BETA1-4 : angle 1.02324 / 0.78 ( 3) link_NAG-ASN : bond 0.00351 / 0.21 ( 21) link_NAG-ASN : angle 1.58448 / 1.20 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.9005 (t80) cc_final: 0.8583 (t80) REVERT: A 153 MET cc_start: 0.7934 (mmm) cc_final: 0.7531 (mmm) REVERT: A 374 PHE cc_start: 0.8579 (m-80) cc_final: 0.8138 (m-80) REVERT: A 380 TYR cc_start: 0.8866 (m-10) cc_final: 0.8587 (m-10) REVERT: A 661 GLU cc_start: 0.7007 (pp20) cc_final: 0.6624 (pp20) REVERT: A 774 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8522 (mm-40) REVERT: B 265 TYR cc_start: 0.7996 (p90) cc_final: 0.7523 (p90) REVERT: B 342 PHE cc_start: 0.7959 (m-80) cc_final: 0.7167 (m-80) REVERT: B 396 TYR cc_start: 0.8647 (m-80) cc_final: 0.8014 (m-80) REVERT: B 418 ILE cc_start: 0.2434 (OUTLIER) cc_final: 0.2187 (mp) REVERT: B 436 TRP cc_start: 0.8325 (p-90) cc_final: 0.8011 (p-90) REVERT: B 983 ARG cc_start: 0.8530 (ttp-170) cc_final: 0.7959 (ttp-170) REVERT: B 1141 LEU cc_start: 0.9194 (tp) cc_final: 0.8993 (tt) REVERT: C 237 ARG cc_start: 0.7180 (ttm110) cc_final: 0.6922 (ttm110) REVERT: C 238 PHE cc_start: 0.8343 (p90) cc_final: 0.8033 (p90) REVERT: C 417 ASN cc_start: 0.9174 (m-40) cc_final: 0.8829 (p0) REVERT: C 421 TYR cc_start: 0.8242 (m-10) cc_final: 0.7961 (m-10) REVERT: C 904 TYR cc_start: 0.7454 (t80) cc_final: 0.7240 (t80) REVERT: C 979 ASP cc_start: 0.8850 (m-30) cc_final: 0.8546 (m-30) REVERT: C 1029 MET cc_start: 0.8240 (ttm) cc_final: 0.8002 (ttt) REVERT: C 1031 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7238 (mp0) outliers start: 30 outliers final: 14 residues processed: 202 average time/residue: 0.1294 time to fit residues: 42.9183 Evaluate side-chains 181 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 278 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 189 optimal weight: 0.3980 chunk 190 optimal weight: 0.4980 chunk 131 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 291 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1071 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.115980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.077344 restraints weight = 62471.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.080576 restraints weight = 35134.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.080812 restraints weight = 19503.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.081550 restraints weight = 16167.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.081656 restraints weight = 13921.862| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24222 Z= 0.154 Angle : 0.503 10.480 33004 Z= 0.260 Chirality : 0.042 0.243 3783 Planarity : 0.004 0.057 4226 Dihedral : 3.693 31.871 3184 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.34 % Allowed : 12.19 % Favored : 86.46 % 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: 0.39 (0.16), residues: 2917 helix: 2.66 (0.21), residues: 621 sheet: 0.45 (0.20), residues: 597 loop : -0.76 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.022 0.001 TYR C1067 PHE 0.022 0.001 PHE B 823 TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (24162) covalent geometry : angle 0.49496 / 0.26 (32862) SS BOND : bond 0.00303 / 0.22 ( 38) SS BOND : angle 1.31225 / 0.67 ( 76) hydrogen bonds : bond 0.04561 / 2.96 ( 874) hydrogen bonds : angle 5.04235 / 3.51 ( 2457) link_BETA1-4 : bond 0.00242 / 0.16 ( 1) link_BETA1-4 : angle 1.04014 / 0.78 ( 3) link_NAG-ASN : bond 0.00336 / 0.22 ( 21) link_NAG-ASN : angle 1.62451 / 1.20 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8917 (t80) cc_final: 0.8449 (t80) REVERT: A 153 MET cc_start: 0.8005 (mmm) cc_final: 0.7631 (mmm) REVERT: A 374 PHE cc_start: 0.8379 (m-80) cc_final: 0.8085 (m-80) REVERT: A 380 TYR cc_start: 0.8873 (m-10) cc_final: 0.8661 (m-10) REVERT: A 661 GLU cc_start: 0.7132 (pp20) cc_final: 0.6687 (pp20) REVERT: A 774 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8555 (mm-40) REVERT: B 200 TYR cc_start: 0.7969 (m-80) cc_final: 0.7706 (m-80) REVERT: B 265 TYR cc_start: 0.8105 (p90) cc_final: 0.7612 (p90) REVERT: B 342 PHE cc_start: 0.7986 (m-80) cc_final: 0.7183 (m-80) REVERT: B 418 ILE cc_start: 0.2594 (OUTLIER) cc_final: 0.2330 (mp) REVERT: B 436 TRP cc_start: 0.8344 (p-90) cc_final: 0.8007 (p-90) REVERT: B 983 ARG cc_start: 0.8524 (ttp-170) cc_final: 0.7954 (ttp-170) REVERT: B 1141 LEU cc_start: 0.9137 (tp) cc_final: 0.8927 (tt) REVERT: C 237 ARG cc_start: 0.7301 (ttm110) cc_final: 0.7033 (ttm110) REVERT: C 238 PHE cc_start: 0.8425 (p90) cc_final: 0.8144 (p90) REVERT: C 417 ASN cc_start: 0.9068 (m-40) cc_final: 0.8775 (p0) REVERT: C 421 TYR cc_start: 0.8313 (m-10) cc_final: 0.8039 (m-10) REVERT: C 979 ASP cc_start: 0.8820 (m-30) cc_final: 0.8508 (m-30) outliers start: 35 outliers final: 24 residues processed: 186 average time/residue: 0.1267 time to fit residues: 39.8306 Evaluate side-chains 174 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 954 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 10 optimal weight: 8.9990 chunk 218 optimal weight: 0.6980 chunk 197 optimal weight: 0.3980 chunk 159 optimal weight: 0.6980 chunk 100 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 281 optimal weight: 0.1980 chunk 124 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 GLN C 774 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.117618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.078983 restraints weight = 63069.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.082219 restraints weight = 34570.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.082660 restraints weight = 19992.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.083331 restraints weight = 15861.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.083464 restraints weight = 13674.904| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24222 Z= 0.095 Angle : 0.474 8.745 33004 Z= 0.243 Chirality : 0.042 0.235 3783 Planarity : 0.004 0.083 4226 Dihedral : 3.553 31.461 3184 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.30 % Allowed : 13.23 % Favored : 85.47 % 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: 0.55 (0.16), residues: 2917 helix: 2.80 (0.21), residues: 620 sheet: 0.64 (0.20), residues: 608 loop : -0.70 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 357 TYR 0.018 0.001 TYR C 904 PHE 0.033 0.001 PHE A 275 TRP 0.010 0.001 TRP A 436 HIS 0.002 0.000 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (24162) covalent geometry : angle 0.46751 / 0.24 (32862) SS BOND : bond 0.00378 / 0.28 ( 38) SS BOND : angle 1.08364 / 0.56 ( 76) hydrogen bonds : bond 0.04010 / 2.60 ( 874) hydrogen bonds : angle 4.84701 / 3.38 ( 2457) link_BETA1-4 : bond 0.00262 / 0.17 ( 1) link_BETA1-4 : angle 1.02266 / 0.79 ( 3) link_NAG-ASN : bond 0.00329 / 0.20 ( 21) link_NAG-ASN : angle 1.49923 / 1.13 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8917 (t80) cc_final: 0.8497 (t80) REVERT: A 153 MET cc_start: 0.8019 (mmm) cc_final: 0.7602 (mmm) REVERT: A 374 PHE cc_start: 0.8150 (m-80) cc_final: 0.7853 (m-80) REVERT: A 380 TYR cc_start: 0.8941 (m-10) cc_final: 0.8729 (m-10) REVERT: A 661 GLU cc_start: 0.6996 (pp20) cc_final: 0.6564 (pp20) REVERT: A 774 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8453 (mm-40) REVERT: B 200 TYR cc_start: 0.7875 (m-80) cc_final: 0.7619 (m-80) REVERT: B 265 TYR cc_start: 0.8046 (p90) cc_final: 0.7621 (p90) REVERT: B 342 PHE cc_start: 0.7984 (m-80) cc_final: 0.7183 (m-80) REVERT: B 418 ILE cc_start: 0.2563 (OUTLIER) cc_final: 0.2306 (mp) REVERT: B 436 TRP cc_start: 0.8348 (p-90) cc_final: 0.8005 (p-90) REVERT: B 983 ARG cc_start: 0.8537 (ttp-170) cc_final: 0.7883 (ttp-110) REVERT: C 237 ARG cc_start: 0.7345 (ttm110) cc_final: 0.7142 (ttm110) REVERT: C 238 PHE cc_start: 0.8433 (p90) cc_final: 0.8101 (p90) REVERT: C 417 ASN cc_start: 0.9065 (m-40) cc_final: 0.8811 (p0) REVERT: C 421 TYR cc_start: 0.8264 (m-10) cc_final: 0.8000 (m-10) REVERT: C 979 ASP cc_start: 0.8787 (m-30) cc_final: 0.8504 (m-30) outliers start: 34 outliers final: 23 residues processed: 197 average time/residue: 0.1228 time to fit residues: 40.6843 Evaluate side-chains 183 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 954 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 182 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 83 optimal weight: 0.2980 chunk 281 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.116485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.077873 restraints weight = 63442.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.081078 restraints weight = 34501.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.081605 restraints weight = 18859.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082112 restraints weight = 16016.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.082223 restraints weight = 14182.032| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24222 Z= 0.129 Angle : 0.491 10.231 33004 Z= 0.251 Chirality : 0.042 0.232 3783 Planarity : 0.004 0.078 4226 Dihedral : 3.601 31.914 3184 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.42 % Allowed : 13.15 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.16), residues: 2917 helix: 2.73 (0.21), residues: 621 sheet: 0.65 (0.20), residues: 611 loop : -0.70 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1014 TYR 0.021 0.001 TYR C 904 PHE 0.023 0.001 PHE B 823 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (24162) covalent geometry : angle 0.48396 / 0.25 (32862) SS BOND : bond 0.00181 / 0.12 ( 38) SS BOND : angle 1.09842 / 0.59 ( 76) hydrogen bonds : bond 0.04212 / 2.73 ( 874) hydrogen bonds : angle 4.83866 / 3.37 ( 2457) link_BETA1-4 : bond 0.00289 / 0.19 ( 1) link_BETA1-4 : angle 1.05659 / 0.80 ( 3) link_NAG-ASN : bond 0.00310 / 0.20 ( 21) link_NAG-ASN : angle 1.54315 / 1.13 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8918 (t80) cc_final: 0.8455 (t80) REVERT: A 153 MET cc_start: 0.8001 (mmm) cc_final: 0.7528 (mmm) REVERT: A 374 PHE cc_start: 0.7965 (m-80) cc_final: 0.7761 (m-80) REVERT: A 508 TYR cc_start: 0.7738 (m-10) cc_final: 0.7476 (m-10) REVERT: A 661 GLU cc_start: 0.7100 (pp20) cc_final: 0.6613 (pp20) REVERT: A 774 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8526 (mm-40) REVERT: B 200 TYR cc_start: 0.7929 (m-80) cc_final: 0.7680 (m-80) REVERT: B 265 TYR cc_start: 0.8066 (p90) cc_final: 0.7615 (p90) REVERT: B 342 PHE cc_start: 0.8007 (m-80) cc_final: 0.7289 (m-80) REVERT: B 418 ILE cc_start: 0.2618 (OUTLIER) cc_final: 0.2171 (mp) REVERT: B 436 TRP cc_start: 0.8376 (p-90) cc_final: 0.8024 (p-90) REVERT: B 983 ARG cc_start: 0.8550 (ttp-170) cc_final: 0.7894 (ttp-110) REVERT: C 237 ARG cc_start: 0.7316 (ttm110) cc_final: 0.7110 (ttm110) REVERT: C 238 PHE cc_start: 0.8452 (p90) cc_final: 0.8163 (p90) REVERT: C 417 ASN cc_start: 0.9119 (m-40) cc_final: 0.8841 (p0) REVERT: C 421 TYR cc_start: 0.8298 (m-10) cc_final: 0.8032 (m-10) REVERT: C 767 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8292 (mm) REVERT: C 979 ASP cc_start: 0.8823 (m-30) cc_final: 0.8545 (m-30) outliers start: 37 outliers final: 25 residues processed: 188 average time/residue: 0.1266 time to fit residues: 40.6363 Evaluate side-chains 182 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 938 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 0 optimal weight: 7.9990 chunk 238 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 232 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.116399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.078895 restraints weight = 63737.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.080459 restraints weight = 35829.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.081928 restraints weight = 21572.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.082334 restraints weight = 16826.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.082268 restraints weight = 14579.841| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24222 Z= 0.129 Angle : 0.487 9.435 33004 Z= 0.252 Chirality : 0.042 0.235 3783 Planarity : 0.004 0.071 4226 Dihedral : 3.643 32.261 3184 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.46 % Allowed : 13.46 % Favored : 85.08 % 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: 0.51 (0.16), residues: 2917 helix: 2.69 (0.21), residues: 622 sheet: 0.61 (0.20), residues: 599 loop : -0.68 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1014 TYR 0.020 0.001 TYR C1067 PHE 0.024 0.001 PHE A 275 TRP 0.022 0.001 TRP C 886 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (24162) covalent geometry : angle 0.48057 / 0.25 (32862) SS BOND : bond 0.00199 / 0.13 ( 38) SS BOND : angle 1.04099 / 0.58 ( 76) hydrogen bonds : bond 0.04247 / 2.76 ( 874) hydrogen bonds : angle 4.81982 / 3.35 ( 2457) link_BETA1-4 : bond 0.00310 / 0.21 ( 1) link_BETA1-4 : angle 1.04466 / 0.79 ( 3) link_NAG-ASN : bond 0.00305 / 0.19 ( 21) link_NAG-ASN : angle 1.51783 / 1.11 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8961 (t80) cc_final: 0.8541 (t80) REVERT: A 153 MET cc_start: 0.8120 (mmm) cc_final: 0.7809 (mmm) REVERT: A 774 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8527 (mm-40) REVERT: B 200 TYR cc_start: 0.7936 (m-80) cc_final: 0.7695 (m-80) REVERT: B 265 TYR cc_start: 0.8062 (p90) cc_final: 0.7478 (p90) REVERT: B 342 PHE cc_start: 0.8045 (m-80) cc_final: 0.7312 (m-80) REVERT: B 418 ILE cc_start: 0.2390 (OUTLIER) cc_final: 0.2133 (mp) REVERT: B 436 TRP cc_start: 0.8407 (p-90) cc_final: 0.8072 (p-90) REVERT: B 977 LEU cc_start: 0.7492 (tt) cc_final: 0.7238 (tt) REVERT: B 983 ARG cc_start: 0.8571 (ttp-170) cc_final: 0.7905 (ttp-110) REVERT: C 84 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8190 (mm) REVERT: C 237 ARG cc_start: 0.7329 (ttm110) cc_final: 0.7108 (ttm110) REVERT: C 417 ASN cc_start: 0.9110 (m-40) cc_final: 0.8824 (p0) REVERT: C 421 TYR cc_start: 0.8232 (m-10) cc_final: 0.7958 (m-10) REVERT: C 767 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8300 (mm) REVERT: C 979 ASP cc_start: 0.8841 (m-30) cc_final: 0.8565 (m-30) outliers start: 38 outliers final: 29 residues processed: 180 average time/residue: 0.1275 time to fit residues: 39.1597 Evaluate side-chains 178 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 938 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 267 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 212 optimal weight: 5.9990 chunk 291 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 146 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.116449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.077722 restraints weight = 62460.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.080756 restraints weight = 34584.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.081348 restraints weight = 19015.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082043 restraints weight = 15769.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.082141 restraints weight = 13855.919| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24222 Z= 0.125 Angle : 0.487 9.796 33004 Z= 0.249 Chirality : 0.042 0.234 3783 Planarity : 0.004 0.067 4226 Dihedral : 3.630 32.343 3184 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.38 % Allowed : 13.73 % Favored : 84.89 % 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: 0.52 (0.16), residues: 2917 helix: 2.70 (0.21), residues: 621 sheet: 0.57 (0.20), residues: 605 loop : -0.67 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1014 TYR 0.020 0.001 TYR C1067 PHE 0.021 0.001 PHE A 275 TRP 0.019 0.001 TRP C 886 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (24162) covalent geometry : angle 0.48115 / 0.25 (32862) SS BOND : bond 0.00193 / 0.13 ( 38) SS BOND : angle 0.96292 / 0.55 ( 76) hydrogen bonds : bond 0.04209 / 2.73 ( 874) hydrogen bonds : angle 4.77088 / 3.33 ( 2457) link_BETA1-4 : bond 0.00216 / 0.14 ( 1) link_BETA1-4 : angle 1.03599 / 0.78 ( 3) link_NAG-ASN : bond 0.00302 / 0.19 ( 21) link_NAG-ASN : angle 1.50818 / 1.10 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8919 (t80) cc_final: 0.8503 (t80) REVERT: A 153 MET cc_start: 0.8027 (mmm) cc_final: 0.7716 (mmm) REVERT: A 508 TYR cc_start: 0.7728 (m-10) cc_final: 0.7475 (m-10) REVERT: A 774 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8521 (mm-40) REVERT: B 200 TYR cc_start: 0.7914 (m-80) cc_final: 0.7706 (m-10) REVERT: B 265 TYR cc_start: 0.8056 (p90) cc_final: 0.7580 (p90) REVERT: B 342 PHE cc_start: 0.8040 (m-80) cc_final: 0.7300 (m-80) REVERT: B 418 ILE cc_start: 0.2566 (OUTLIER) cc_final: 0.2308 (mp) REVERT: B 436 TRP cc_start: 0.8397 (p-90) cc_final: 0.8059 (p-90) REVERT: B 748 GLU cc_start: 0.8297 (pm20) cc_final: 0.7958 (pm20) REVERT: B 983 ARG cc_start: 0.8511 (ttp-170) cc_final: 0.7843 (ttp-110) REVERT: C 84 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8181 (mm) REVERT: C 237 ARG cc_start: 0.7375 (ttm110) cc_final: 0.7151 (ttm110) REVERT: C 417 ASN cc_start: 0.9050 (m-40) cc_final: 0.8798 (p0) REVERT: C 421 TYR cc_start: 0.8206 (m-10) cc_final: 0.7937 (m-10) REVERT: C 767 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8306 (mm) REVERT: C 979 ASP cc_start: 0.8832 (m-30) cc_final: 0.8554 (m-30) REVERT: C 1029 MET cc_start: 0.8196 (ttm) cc_final: 0.7936 (ttt) outliers start: 36 outliers final: 32 residues processed: 176 average time/residue: 0.1186 time to fit residues: 35.2145 Evaluate side-chains 181 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 80 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 227 optimal weight: 0.0970 chunk 180 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 283 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.115534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.080476 restraints weight = 63876.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.079100 restraints weight = 38962.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.080066 restraints weight = 27997.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.080693 restraints weight = 22680.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.080773 restraints weight = 19985.599| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24222 Z= 0.155 Angle : 0.506 9.724 33004 Z= 0.262 Chirality : 0.042 0.241 3783 Planarity : 0.004 0.068 4226 Dihedral : 3.743 32.604 3184 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.50 % Allowed : 13.84 % Favored : 84.66 % 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 (0.16), residues: 2917 helix: 2.62 (0.21), residues: 622 sheet: 0.51 (0.20), residues: 605 loop : -0.70 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1014 TYR 0.021 0.001 TYR C1067 PHE 0.029 0.001 PHE A 275 TRP 0.019 0.001 TRP C 886 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (24162) covalent geometry : angle 0.50020 / 0.26 (32862) SS BOND : bond 0.00218 / 0.15 ( 38) SS BOND : angle 1.01526 / 0.60 ( 76) hydrogen bonds : bond 0.04512 / 2.92 ( 874) hydrogen bonds : angle 4.83684 / 3.37 ( 2457) link_BETA1-4 : bond 0.00209 / 0.14 ( 1) link_BETA1-4 : angle 1.11444 / 0.82 ( 3) link_NAG-ASN : bond 0.00315 / 0.21 ( 21) link_NAG-ASN : angle 1.55959 / 1.12 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8817 (t80) cc_final: 0.8412 (t80) REVERT: A 153 MET cc_start: 0.7778 (mmm) cc_final: 0.7497 (mmm) REVERT: A 508 TYR cc_start: 0.7622 (m-10) cc_final: 0.7348 (m-10) REVERT: A 774 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8483 (mm-40) REVERT: A 902 MET cc_start: 0.8681 (tpp) cc_final: 0.8458 (tpp) REVERT: B 200 TYR cc_start: 0.7969 (m-80) cc_final: 0.7759 (m-10) REVERT: B 265 TYR cc_start: 0.8087 (p90) cc_final: 0.7523 (p90) REVERT: B 342 PHE cc_start: 0.8000 (m-80) cc_final: 0.7204 (m-80) REVERT: B 418 ILE cc_start: 0.2680 (OUTLIER) cc_final: 0.2395 (mp) REVERT: B 436 TRP cc_start: 0.8296 (p-90) cc_final: 0.8006 (p-90) REVERT: B 983 ARG cc_start: 0.8543 (ttp-170) cc_final: 0.7886 (ttp-110) REVERT: C 84 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8215 (mm) REVERT: C 237 ARG cc_start: 0.7365 (ttm110) cc_final: 0.7138 (ttm110) REVERT: C 421 TYR cc_start: 0.8230 (m-10) cc_final: 0.7959 (m-10) REVERT: C 767 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8372 (mm) REVERT: C 902 MET cc_start: 0.9462 (tpp) cc_final: 0.9239 (tpp) REVERT: C 979 ASP cc_start: 0.8842 (m-30) cc_final: 0.8567 (m-30) outliers start: 39 outliers final: 32 residues processed: 178 average time/residue: 0.1252 time to fit residues: 37.6794 Evaluate side-chains 178 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 938 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 66 optimal weight: 0.0170 chunk 59 optimal weight: 0.7980 chunk 275 optimal weight: 1.9990 chunk 192 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.116122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.077415 restraints weight = 63713.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.080520 restraints weight = 35427.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.081041 restraints weight = 19548.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.081686 restraints weight = 16590.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.081785 restraints weight = 14488.467| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24222 Z= 0.124 Angle : 0.498 11.752 33004 Z= 0.256 Chirality : 0.042 0.239 3783 Planarity : 0.004 0.065 4226 Dihedral : 3.697 32.478 3184 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.46 % Allowed : 14.07 % Favored : 84.47 % 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: 0.48 (0.16), residues: 2917 helix: 2.63 (0.21), residues: 627 sheet: 0.53 (0.20), residues: 606 loop : -0.69 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1014 TYR 0.019 0.001 TYR C1067 PHE 0.024 0.001 PHE A 275 TRP 0.018 0.001 TRP C 886 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (24162) covalent geometry : angle 0.49205 / 0.25 (32862) SS BOND : bond 0.00195 / 0.13 ( 38) SS BOND : angle 0.94523 / 0.56 ( 76) hydrogen bonds : bond 0.04303 / 2.79 ( 874) hydrogen bonds : angle 4.76365 / 3.32 ( 2457) link_BETA1-4 : bond 0.00224 / 0.15 ( 1) link_BETA1-4 : angle 1.03859 / 0.79 ( 3) link_NAG-ASN : bond 0.00304 / 0.19 ( 21) link_NAG-ASN : angle 1.50763 / 1.09 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3348.80 seconds wall clock time: 58 minutes 51.82 seconds (3531.82 seconds total)